title: Circadian clock-mediated transcriptional  regulation in maize

status: Public on Aug 31 2011

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: The goal of the experiment was to perform a large scale study of circadian regulation of gene expression in maize. To identify maize genes with expression regulated by the circadian clock, transcript levels in the aerial tissues of young maize seedlings were determined by transcriptional profiling with the Affymetrix GeneChip Maize Genome Array. Maize inbred B73 seedlings were grown inside Conviron growth chamber. B73 seedlings were grown for 7 days under 12 h light:12 h dark (LD) photocycles, 26° C temperature and 70% humidity. At the 8th day, seedlings were transferred to continuous light (LL) and were allowed to entrain completely for 24 h prior to tissue harvest following which tissue was harvested every 4 hours under LL conditions for a period of 48h. Therefore, for the circadian LL time course 12 time points were collected as follows (also defined as factors in the treatment section):  ZT0 - 8:00 am/ subjective dawn/ Day1  ZT4 - 12:00 pm/ subjective mid-day/ Day1   ZT8 - 4:00 pm/ subjective late-day/ Day1  ZT12 - 8:00 pm/ subjective dusk/ Day1  ZT16 - 12:00 am/ subjective mid-night/ Day1  ZT20 - 4:00 am/ subjective pre-dawn/ Day1  ZT24- 8:00 am/ subjective dawn/ Day2  ZT28 - 12:00 pm/ subjective mid-day/ Day2  ZT32 - 4:00 pm/ subjective late-day/ Day2  ZT36 - 8:00 pm/ subjective dusk/ Day2  ZT40 - 12:00 am/ subjective mid-night/ Day2  ZT44 - 4:00 am/ subjective pre-dawn/ Day2    Tissue comprised of aerial portion of the seedlings (corresponding to tissue from the prop roots and up) for RNA isolation. Total RNA was isolated from the entire aerial portion of 7 day-old seedlings (corresponding to tissue from the prop roots and up) by Trizol extraction followed by Qiagen RNeasy columns and treatment with RNase-free DNase I (Qiagen; qiagen.com). RNA was isolated from 3 independent biological replicates was pooled. cRNA was generated from pooled total RNA from 3 biological replicates with the GeneChip One-Cycle Target Labeling kit according to the manufacturer’s recommendations (Affymetrix, affymetrix.com). The University of California, Berkeley Functional Genomics Laboratory hybridized samples to Affymetrix GeneChip Maize Genome Arrays and scanned the washed arrays as suggested by manufacturer. Probe sets called “Not Present” or “Marginal” on one or more microarrays were removed from the downstream analysis, as is common practice with circadian studies. Raw hybridization intensities were normalized across all twelve arrays using RMA express in Perfect Match mode.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Frank G. Harmon.  The equivalent experiment is ZM28 at PLEXdb.]

overall_design: Continuous Light: ZT0(1-replications);  Continuous Light: ZT4(1-replications);  Continuous Light: ZT8(1-replications);  Continuous Light: ZT12(1-replications);  Continuous Light: ZT16(1-replications);  Continuous Light: ZT20(1-replications);  Continuous Light: ZT24(1-replications);  Continuous Light: ZT28(1-replications);  Continuous Light: ZT32(1-replications);  Continuous Light: ZT36(1-replications);  Continuous Light: ZT40(1-replications);  Continuous Light: ZT44(1-replications)

last: Harmon


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

status: Public on Dec 31 2011

city: Seoul

first: Seung Min

last: Kim

address: 1 Gwanakro

country: South Korea

institute: Seoul National University

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

overall_design: For transcriptome analysis, the V. vulnificus whole genome TwinChip, manufactured by e-biogen (Seoul, South Korea), was used.

first: Seung

middle: M

first: Sang

middle: H

last: Choi


title: miRNAs in ovarian cancer: A systems approach (miRNA data)

status: Public on Jul 29 2011

city: Atlanta

first: Shubin

last: Shahab

state: GA

address: 310 Ferst Drive

department: Biology

country: USA

institute: Georgia Institute of Technology

summary: MicroRNAs (miRNAs) are short (~22 nucleotides) regulatory RNAs that can modulate gene expression and are aberrantly expressed in many diseases including cancer. We report the results of a systems analysis of miRNA regulation in ovarian cancer. We found that 33 miRNAs are up-regulated and 9 down-regulated in CEPI relative to OSE (p<0.01, ≥2 fold change). Of these, 12 were previously annotated miRNAs (Sanger miRBase) of which 9 are up-regulated and 3 are down-regulated in CEPI relative to OSE. Current models predict that changes in levels of miRNAs will be inversely correlated with changes in the levels of targeted mRNAs due to miRNA regulation. This predicted inverse correlation held for only ~9% of predicted target mRNAs. Computational analyses indicate the unexpected low inverse correlation may be at least partially explained by variation in the number of miRNA binding sites within the 3’ UTRs of targeted mRNAs and by miRNA-mediated changes in levels of transcription factors that can exert overriding trans-regulatory controls on target loci.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
synthetic construct

overall_design: miRNAs  were collected from three laser captured microdissected ovarian cancer epithelial (CEPI) samples. The miRNA expression pattern was compared with three healthy ovarian surface epithelia samples as controls using a custom-manufactured Affymetrix GeneChip® array.

first: Christopher

middle: G

last: Hill

first: Vinay

middle: K

last: Mittal

first: Roman

last: Mezencev

first: Lilya

last: Matyunina

first: Lila

middle: D

last: Walker

first: Nathan

middle: J

last: Bowen

first: Benedict

middle: B

last: Benigno

first: John

middle: F

last: Mcdonald


title: The role of dietary leucine and dairy protein on gastrocemius muscle gene expression

status: Public on Oct 22 2011

city: Calgary

first: Lindsay

last: Eller

state: AB

address: 2500 University Dr. NW

department: Faculty of Kinesiology

country: Canada

institute: University of Calgary

summary:
We used microarray to determine the differences in hepatic gene expression for diet-induced obese Sprague-Dawley rats consuming different dietary proteins.  Proteins of interest included skim milk powder (dairy), casein, and the branched-chain amino acid, leucine.
The primary aims of this study were: (i) to compare the effects of diets with protein derived from casein, casein supplemented with leucine, and complete dairy on body composition and insulin sensitivity; and (ii) to determine if there is a synergistic effect of dietary Ca and protein source on body composition and insulin sensitivity.  Secondarily, we used microarray analysis to examine the effect of casein, leucine, or complete dairy containing diets on the expression of gastrocnemius muscle genes related to lipid and glucose metabolism.

overall_design: Diet induced obese rats consumed ad libitum, a high fat, high sucrose diet for 8 weeks (n=4).  All diets had an energy density of 4.6 kcal/gram and provided 10% of total energy from protein [casein, complete dairy (skim milk powder), or leucine-supplemented casein (7.1% from casein plus 2.9% from leucine)]. The casein treatment was the control diet.

first: Raylene

middle: R

last: Reimer

first: Jane

last: Shearer

first: Dolan

last: Saha


title: Gene expression in TNF treated rat aortic rings cultured in collagen or fibrin gels.

status: Public on Jul 21 2011

city: Seattle

first: Alfred

middle: C

last: Aplin

state: WA

address: Box 357470 HSB-UW

department: Pathology

institute: University of Washington

summary:
Angiogenesis in cultures of rat aorta begins with neovessels sprouting from the aortic explant within the first three days of culture.
We used microarrys to examine the effects of TNF-alpha on gene expression in both fibrin and collagen gels during the first 48 hours or culture.

overall_design: Rat aortic rings were cultured in either collagen or fibrin maticies.  Half of the cultures from each matrix group were treated with 10ng/ml recombinant rat TNF-alpha, and half were left untreated. These cultures were used to prepare total RNA

first: Giovanni

last: Ligresti

first: Roberto

last: Nicosia


title: Gene expression during first day of collagen gel culture of rat aortic rings

summary:
Angiogenesis in collagen gel cultures of rat aorta begins with neovessels sprouting from the aortic explant within the first three days of culture.
We used microarrays to detail the pattern of gene expression underlying initial 24 hours of growth, prior to the sprouting of visible neovessles, and identified distinct classes of up-regulated genes during this process.

overall_design: Either freshly harvested aortic rings, representing day 0, or collagen gel cultures of rat aorta were grown in serum free medium and used to prepare total RNA.


title: C-peptide regulates early transcription in rat proximal tubular cells

status: Public on Jul 27 2011

city: Stockholm

first: Emma

last: Lindahl

address: Scheeles väg 2

country: Sweden

institute: Karolinska Institutet

summary: C-peptide exerts beneficial effects on glomerular hyperfiltration in type I diabetic patients. As C-peptide localizes to the nucleus, we investigated the transcriptional activities of C-peptide in proximal tubular cells isolated from diabetic rats.

overall_design: Two groups of proximal tubular cells isolated from type I diabetic rats: 1 treated with C-peptide, and 1 untreated. 2-3 replicates per group.

first: Lina

last: Nordquist

first: Patrick

last: Müller

first: Eli

last: El Agha

first: Malou

last: Friederich

first: Karin

last: Dahlman-Wright

first: Fredrik

last: Palm

first: Hans

last: Jörnvall


title: Muscle wasting and the temporal gene expresion pattern in a novel rat ICU model

status: Public on Jul 23 2011

city: Uppsala

first: Monica

last: Llano-Diez

address: Akademiska sjukhuset, Ing.85, 3tr

department: Neuroscience

institute: Uppsala university

summary: Acute quadriplegic myopathy (AQM) or critical illness myopathy (CIM) is frequently observed in intensive care unit (ICU) patients. In order to elucidate duration-dependent effects of the ICU intervention on molecular and functional networks that control the muscle wasting and weakness in AQM, gene expression profile was analyzed at time points varying from 6 hours to 14 days in a unique experimental rat model mimicking ICU conditions, i.e., post-synaptically paralyzed, mechanically ventilated and extensively monitored animals.

overall_design: A total of five sham operated controls and 23 experimental female Sprague-Dawley rats were included in this study. The experimental rats were anaesthetized, treated with the neuromuscular blocker (NMBA), α-cobrotoxin, mechanically ventilated and monitored for durations varying from 6h to 4 days (n=13), from 5 to 9 days (n=4), and from 9 to 14 days (n=6). Muscle biopsies were obtained from gastrocnemius muscle (proximal part) immediately after euthanasia and were quickly frozen in liquid propane cooled by liquid nitrogen, and stored at -80°C.RNA was extracted.

first: Ann-Marie

last: Gustafson

first: Carl

last: Olsson

first: Hanna

last: Goransson

first: Lars

last: Larsson


title: Analysis of FoxA2 occupancy in mouse liver with endoderm ChIP-chip array

status: Public on Jul 19 2011

city: Philadelphia

first: Kenneth

middle: S.

last: Zaret

state: PA

address: 9-132, SCTR, 3400 Civic Center Boulevard

department: Cell and Developmental Biology

institute: University of Pennsylvania School of Medicine

type: Genome binding/occupancy profiling by genome tiling array

summary: Understanding how silent genes can be competent for activation provides insight into development as well as cellular reprogramming and pathogenesis.  We performed genomic location analysis of the pioneer transcription factor FoxA in the adult liver and found that about one-third of the FoxA bound sites are near silent genes, including genes without detectable RNA polymerase II.  Virtually all of the FoxA-bound silent sites are within extended conserved sequences, suggesting possible function.  Such sequences are enriched in motifs for transcriptional repressors, including for Rfx1.  We found one such target site containing functional FoxA and Rfx1 sites is a cryptic enhancer 7 kb downstream of the Cdx2 gene, the latter being an effector of esophageal metaplasia.  Indeed, Rfx1 sites restrict transcriptional activation by FoxA at the +7 kb Cdx2 element.  Furthermore, Rfx1 expression in the esophageal epithelium becomes extinguished during its metaplastic progression to carcinoma.  We propose that motif analysis of other transcription factors bound to silent genes can reveal unanticipated regulatory networks that provide insights into reprogramming and oncogenic progression.

overall_design: We analyzed FOXA2 occupancy in a mouse liver sample. We ran three competitive hybridizations: (i) FOXA2 vs IgG, (ii) FOXA2 vs input, and (iii) IgG vs input.

first: Jason

middle: A

last: Watts

first: Chaolin

last: Zhang

first: Jay

last: Kormish

first: Jian

last: Fu

first: Andres

last: Klein-Szanto

first: Michael

middle: Q

middle: S


title: Farnesyl Diphosphate (FPP) Toxicity in E. coli, LB medium

status: Public on May 13 2011

city: Emeryville

first: Robert

last: Dahl

state: CA

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

summary: This experiment studied the effect of FPP accumulation on E. coli.  E. coli cells transformed with pMBIS (the S. cerevisiae mevalonate pathway enzymes converting mevalonate to FPP) and fed mevalonate produce large amounts of FPP, which causes toxicity when it accumulates.  When coupled with an active amorphadiene synthase (pADS) the cells produce amorphadiene, a non-toxic isoprenoid.  To accumulate FPP, but maintain similar protein burden, an amorphadiene synthase with 3 mutations to render it inactive was used (pADSmut) to accumulate FPP.  E. coli was transformed with pMBIS and pADS or pMBIS and pADSMut and grown in LB and fed 10 mM mevalonate and induced with 0.5 mM IPTG, then sampled at subsequent time points.

overall_design:
This comparison is between E. coli DH1 cells accumulating FPP via the heterologous mevalonate pathway (pMBIS/pADSmut) to cells producing amorphadiene via the same pathway (pMBIS/pADS).  Samples were collected 2.5, 5, 7, and 29.5 hr after addition of IPTG and mevalonate.
One biological replicate was used.  Total RNA was extracted, reverse transcribed, labeled, and hybridized to multiple slides for technical replicates.

last: Dahl II

last: Keasling


title: Gene Expression of Fathead Minnow Exposed to Primary and Secondary Treated Effluents

status: Public on May 18 2011

city: Gainesville

first: Reyna

middle: Cristina

last: Colli-Dula

state: Florida

address: Mowry Drive 471

department: CEHT

institute: University of Florida

summary: Contaminants of emerging concern (CECs) in treated municipal effluents have the potential to adversely impact exposed organisms prompting elevated public concern.  Using transcriptomic tools, we investigated changes in gene expression and cellular pathways in the liver of male fathead minnows (Pimephales promelas) exposed to 5% concentrations of full secondary-treated (HTP) or advanced primary-treated (PL) municipal wastewater effluents containing CECs.  Gene expression changes were associated with apical endpoints (plasma vitellogenin and changes in secondary sexual characteristics).  Of 32 effluent CECs analyzed, 28 were detected including pharmaceuticals, personal care products, hormones, and industrial compounds. Transcript patterns differed between effluents, however < 10% of these had agreement in the detected response (e.g. transcrips involved in xenobiotic detoxification, oxidative stress and apoptosis) in both effluents. Exposure to PL effluent caused changes in transcript levels of genes involved in metabolic pathways (e.g., lipid transport and steroid metabolism).  Exposure to HTP effluent affected transcripts involved in signaling pathways (e.g., focal adhesion assembly and extracellular matrix).  Exposure to both effluents produced significantly higher levels of plasma VTG and changes in secondary sexual characteristics (e.g., ovipositor development).  Taken together the results suggest, a potential association between some transcriptomic changes and higher biological responses following effluent exposure; and a potential adverse outcome pathway following exposure to complex chemical mixtures containing CECs -.  Furthermore, this study identified responses in key genes and pathways not previously implicated in exposure to CECS, , which could be consistent with effluent exposure (e.g., oxidative stress) in addition to other pathway responses specific to the effluent type. This may be useful for assessing the adverse health effects of fish by effluents exposure to CECs.

overall_design: To investigate gene expression responses resulting from exposure to POTW effluents, two laboratory experiments were conducted using effluent from San Diego (Point Loma; SD (PL)) and Los Angeles (Hyperion; LA (HTP)).  The LA effluent received secondary treatment and the SD effluent received advanced primary treatment.   Treatments used during exposures consisted of negative controls (moderately hard water), positive controls (E2), and 0.5% and 5% effluent concentrations.  The 0.5% concentration of effluent represented an environmentally realistic exposure level.  The 5% effluent concentration represented a higher level at which we expected biological responses.  The exposures lasted 14 days and had 3 replicates per treatment.

first: Doris

middle: E

last: Vidal-Dorsch

first: Nancy

last: Denslow


title: A unique iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis [ChIP_chip]

status: Public on Jul 13 2011

city: San Francisco

first: Changbin

last: Chen

state: California

address: HSE450, 513 Parnassus Avenue

department: Department of Microbiology & Immunology

institute: University of California, San Francisco

type: Genome binding/occupancy profiling by array

summary: The mammalian gastrointestinal tract and the bloodstream are highly disparate biological niches, and yet certain commensal-pathogenic microorganisms are able to thrive in both environments.  Here, we report the evolution of a unique transcription circuit in the yeast, Candida albicans, which determines its fitness in both host niches.  Our comprehensive analysis of the DNA-binding proteins that regulate iron uptake by this organism suggests the evolutionary intercalation of a transcriptional activator called Sef1 between two broadly conserved transcriptional repressors, Sfu1 and Hap43.  The Sef1 activator of iron uptake genes promotes virulence in a mouse model of bloodstream infection, whereas the Sfu1 repressor is dispensable for virulence but promotes gastrointestinal commensalism.  We propose that the ability to alternate between genetic programs conferring resistance to iron depletion in the bloodstream versus iron toxicity in the gut may be a fundamental attribute of gastrointestinal commensal-pathogens.

overall_design: ChIP analyses to profile genome-wide of distribution of Sef1, Sfu1 and Hap43 in response to various iron availability. 12 independent ChIP experiments were performed on 6 biological replicates of the untagged control and 2 biological replicates each of Sef1-Myc, Sfu1-Myc, and Hap43-Myc.

first: Kalyan

last: Pande

first: Sarah

last: French

first: Brian

last: Tuch

first: Suzanne

last: Noble


title: A unique iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression data from monoiodoacetate-induced arthritis in a rat model

status: Public on Apr 30 2011

city: Columbus

first: Jin

last: Nam

state: OH

address: 305 W. 12th Ave., 4010 Postle Hall

institute: The Ohio State University

summary:
The progression of arthritis involves sequential regulation of catabolic and anabolic genes that degenerate cartilages.
We used microarrays to determine temporal regulation of genes during the progression of monoiodoacetate-induced arthritis in the knees of rats.

overall_design: Experimental arthritis was induced by intra-articular injection of monoiodoacetate (2 mg/ 50 ul) in the knees of rats. Cartilages from distal end of femur were collected on day 5, 9 and 21 post-injection. Saline injection was used as a sham control.

first: Priyangi

last: Perera

first: Jie

last: Liu

first: Bjoern

last: Rath

first: James

last: Deschner

last: Gassner

first: Timothy

last: Butterfield

first: Sudha

last: Agarwal


title: Regulation of neuronal gene and miRNA expression by the complement protein C1q associated with neuroprotection

status: Public on Mar 07 2011

city: Irvine

first: Marie

middle: Emeline

last: Benoit

address: 2419 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: UC Irvine

summary:
Identification of transcriptional profiles stimulated by the complement protein C1q in rat immature neurons associated with the C1q-dependent neuroprotection observed in vitro.
Use of the unbiased whole genome microarray approach to identify genes regulated by C1q.

overall_design: Immature neurons grown in vitro for 3 days were stimulated with 10 nM C1q for 3h.

first: Andrea

last: Tenner


title: Biofilm matrix regulation by Candida albicans Zap1

status: Public on Jun 09 2011

city: Merced

first: Clarissa

middle: Jane

last: Nobile

address: 5200 North Lake Rd

department: Molecular and Cell Biology

institute: University of California - Merced

summary:
The Zap1 ChIP-chips were performed in a/alpha cell types using C-terminally Myc-tagged proteins and Myc antibodies.
ChIPs were performed on 48 hour biofilm cells grown in Spider medium.  Two biological replicates were performed, and normalized data is reported in matrix.

overall_design: Myc tagged strains were compared to untagged control strains.


title: Basic helix-loop-helix transcription factor Tcf21 is downstream target of male sex-determining gene SRY

status: Public on Apr 25 2011

city: Pullman

first: Michael

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

summary: The cascade of molecular events involved in mammalian sex determination has been shown to involve the SRY gene, but specific downstream events have eluded researchers for decades.  The current study identifies one of the first direct downstream targets of the male sex-determining factor SRY as the basic-helix-loop-helix (bHLH) transcription factor TCF21.  SRY was found to directly associate with the Tcf21 promoter SRY/SOX9 response element both in vitro and in vivo during male sex determination.  TCF21 was found to promote an in vitro sex reversal of embryonic ovarian cells to promote precursor Sertoli cell differentiation.  Therefore, SRY acts directly on the Tcf21 promoter to, in part, initiate a cascade of events associated with Sertoli cell differentiation and embryonic testis development.

overall_design: We used microarrays to determine genes whose expression was stimulated in rat E13 ovarian cell sub-cultures in the presence of a pCMV-myc-expression plasmid over-expressing the Sry, Tsf21, and/or Tcf12 (Reb-alfa) genes. RNA samples from the control group (untreated E13 rat ovarian cells) are compared to RNA from 4 groups of treated E13 rat ovarian cells: 1) Sry overexpressing, 2) Tcf21 overexpressing, 3) Tcf12 (Reb alfa) overexpressing, and 4) Tcf21 + Tcf12 (Reb-alfa) overexpressing. Untreated E13 testis cell sub-cultures were also analyzed. 3 biological replicates each group.

first: Ramji

last: Bhandari

first: Ingrid

last: Sadler-Riggleman

first: Tracy

middle: M

last: Clement

first: Marina

middle: I

last: Savenkova


title: Changes of mRNA expressin in rat kidney inner medulla in response to dDAVP stimulation/ withdrawal

status: Public on Feb 23 2011

city: Taegu

first: Tae-Hwan

last: Kwon

address: Dongin-dong 101

department: Department of Biochemistry and Cell Biology

institute: School of Medicine, Kyungpook National University

summary: The E3 ubiquitin -protein ligases (E3s) plays a role as regulators of protein trafficking and degradation. We aimed to identify E3s in rat kidney which are associated with dDAVP-induced urine concentration.

overall_design: Kidney inner medulla collected from vehicle treated control (n=2), dDAVP infusion for 5 d (D5d, n=2) and  3 h-withdrawal of dDAVP after 5 d-infusion (D5d-3h, n=2) groups were subjected to a transcriptome analysis.

first: Yu-Jung

last: Lee


title: Inhibitory Actions of Anti-Müllerian Hormone (AMH) on Ovarian Primordial Follicle Assembly

status: Public on Mar 04 2011

middle: K

summary:
The current study was designed to investigate the actions of Anti-Müllerian Hormone (AMH) on primordial follicle assembly.  Ovarian primordial follicles develop from the breakdown of oocyte nests during fetal development for the human and immediately after birth in rodents.  AMH was found to inhibit primordial follicle assembly, decrease the initial primordial follicle pool size and promote the persistence of small oocyte nests in a rat ovarian organ culture.  The AMH expression was found to be primarily in the stromal tissue of the ovaries at this period of development, suggesting a stromal-epithelial cell interaction for primordial follicle assembly.  AMH was found to promote alterations in the ovarian transcriptome during primordial follicle assembly with over 200 genes with altered expression.  A gene network was identified suggesting a potential central role for the Fgf2/Nudt6 antisense transcript in the follicle assembly process.  A number of signal transduction pathways are regulated by AMH actions on the ovarian transcriptome, in particular the transforming growth factor – beta (TGFß) signaling process.  AMH is the first hormone/protein shown to have an inhibitory action on primordial follicle assembly.  Due to the critical role of the primordial follicle pool size for female reproduction, elucidation of the factors, such as AMH, that regulate the assembly process will provide insights into potential therapeutics to manipulate the pool size and female reproduction.
We used microarrays to determine genes expressed differentially between control and AMH (Anti-Müllerian Hormone) treated P0 ovary

overall_design: RNA samples from 3 control groups are compared to 3 AMH treated ovary groups

first: Eric

last: Nilsson

first: Ryan

last: Schindler


title: In vitro and in vivo analysis of hypoxic gene expression in rat gliomas

status: Public on Jan 13 2011

first: Constantinos

last: Koumenis

address: 3620 Hamilton Walk

department: Radiation Oncology

institute: University of Pennsylvania

summary:
In vivo profiling of hypoxic gene expression in gliomas using the hypoxia marker EF5 and laser-capture microdissection
We have employed the hypoxia marker EF5 coupled with laser capture microdissection to isolate RNA from viable hypoxic and normoxic regions of 9L experimental gliomas.

overall_design: We report the identification of the hypoxic gene expression profile in a solid tumor using a prototypical hypoxia marker EF5, Laser Capture Microdissection (LCM) and Microarray Gene Expression Profiling (EF5-LCM-MGEP). We have utilized LCM to isolate total RNA from normoxic and hypoxic regions in the rat 9L glioma tumor model grown in its isogenic host (Fischer rat). Microarray analysis of the isolated RNA generated an in vivo hypoxia expression profile. For comparison, we also analyzed RNA samples isolated from rat 9L glioma cells in culture exposed to hypoxia or normoxia.

first: Amit

last: Maity

first: Cameron

last: Koch


title: Neonat cardiomyocytes_hypertrophy_HDAC4

status: Public on Jan 01 2011

city: cincinnati

first: izhak

last: kehat

address: 3333 burnet ave

institute: CCHMC

summary: In order to identify targets for HDAC4, NRVM were infected with adenoviral vectors encoding beta-Galactosidase or Flag- HDAC4, and incubated in serum free or 10% fetal calf serum containing growth medium for 48 hrs.

overall_design: NRVM were infected with adenoviral vectors encoding beta-Galactosidase (control) or Flag- HDAC4 (experiment), and incubated in serum free or 10% fetal calf serum containing growth medium for 48 hrs. 2 biological samples of each condition were analyzed.

first: Izhak

last: Kehat

first: Bruce

last: Aronow

first: Jeffery

middle: D

last: Molkentin


title: Seeds of Pisum sativum L. cv Alaska Early: non-aged controls vs. Aged

status: Public on Oct 22 2010

city: Villamayor

first: Daniel

last: Osuna

state: Salamanca

address: Río Duero, 12

department: Fisiología Vegetal, Universidad de Salamanca.

country: Spain

institute: Centro Hispano-Luso de Investigaciones Agrarias.

summary:
Seeds of Pisum sativum L. cv Alaska Early (purchased from the ‘Abundant Life Seed Foundation’, Port Townsend, USA) were equilibrated for approximately 5 weeks in tightly sealed boxes over 300 g-1 non-saturated LiCl (Hay et al. 2008), producing 60% relative humidity, in a temperature-controlled room (20 ± 1 ºC) until their water potential was stable at 12 % MC. Relative humidity was recorded with a Rotronic AWVC-D10 Hygropalm. These equilibrated seeds are referred to as 0 day ‘non-aged controls’. Following equilibration, accelerated ageing was carried out by placing seeds in sealed bottles at 50 °C until viability loss, thereafter referred to as ‘ageing’. Samples were taken at intervals after 8, 12, and 15 days of ageing. At each interval, germination tests were performed on 1 % water agar at 25 °C under warm white fluorescent light (15 micromol m-2 s-1) at a day / night cycle (8/16h). Germination was defined as radical emergence by at least 2 mm.
To summarize, we have performed a transcriptional profiling of Pisum sativum seeds comparing 0 day ‘non-aged controls’ with 8, 12 and 15 days of artificially aged seeds.

overall_design: Four-condition experiment, 0 days, 8 days, 12 days and 15 days. Biological replicates: 3 for each comparison. Each biological replicate was independently grown and harvested.

first: Hongying

last: Chen

first: Oscar

last: Lorenzo

first: Ilse

last: Kranner


title: Multinucleated Tartrate Resistant Acid Phosphatase Positive Cells with Macrophage and Osteoclast Phenotypes in Bone

status: Public on Dec 31 2010

first: Erik

last: Karlström

address: Division of Pathology

department: Department of Laboratory Medicine

summary: Prothrombin (PT) and osteopontin (OPN) promotes adhesion of different TRAP-positive multinucleated cells isolated from rat long bone (Hu et al. Exp Cell Res. 2008; 314: 638-50).  The PT-adhering cell could represent either an immature precursor to the OPN-adherent osteoclast or constitute a distinct multinucleated cell population with a unique role in bone.  Herein, phenotypic differences between PT- and OPN- cells were investigated with microarray- expression analysis. Characteristic for PT-cells was expression of innate immune response genes and scavenger receptors whereas OPN-cells expressed typical osteoclast proteins such as collagenases implicated in bone degradation.

overall_design: Bone cells were extracted from neonatal Sprague Dawley rat long bones. The extracted cells were attached to PT or OPN, and thereby two cell populations were isolated. mRNA was extracted from these cells and their expression was compared with the Affymetrix GeneChip Rat Gene 1.0 ST Array.

first: Barbro

last: Ek-Rylander

first: Mikael

last: Wendel

first: Göran

last: Andersson


title: Tonicity iduced changes in gene expression in IMCD cells and the effect of Cyclosporin A

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

country: Germany

institute: University Hospital Halle (Saale)

summary: Cyclosporin A induces expression of proapoptotic factors when cells are challenged by increased tonicity

overall_design: 18 Samples were analyzed. We performed the following pairwise comparison using BRB Array Tools: 300 vs. 600_24; 300 vs. 600_24_CSA; 600 vs. 900_24; 600 vs. 900_24_CSA


title: Induction of Ovarian Primordial Follicle Assembly by Connective Tissue Growth Factor CTGF

status: Public on Sep 16 2010

first: Michael

last: Skinner

summary:
Primordial follicle assembly is a process that occurs in the embryonic or early post natal ovary in which oocyte nests break down to form individual primordial follicles.  The size of this initial pool of primordial follicles in part determines the reproductive lifespan of the female.  Connective tissue growth factor (CTGF) was identified as a potential regulatory candidate for this process in a previous microarray analysis of follicle development.  The current study examines the effects of CTGF and associated transforming growth factor beta 1 (TGFbeta-1) on follicle assembly.  Ovaries were removed from newborn rat pups and placed in an organ culture system for two days to measure the effect of these factors on follicle assembly.  In addition, ovaries were cultured and treated for ten days to determine the potential of CTGF and TGFbeta-1 to manipulate the primordial follicle pool size over a longer developmental time period.  The ovaries treated with CTGF for two days were found to have an increased proportion of assembled follicles.  TGFbeta-1 had no effect on primordial follicle assembly and in combination with CTGF decreased oocyte number in the ovary after two days of culture.  Over ten days of treatment only the combined treatment of CTGF and TGFbeta-1 was found to cause an increase in the proportion of assembled follicles.  Interestingly, treatment with TGFbeta-1 alone resulted in fewer total oocytes in the ovary and decreased the primordial follicle pool size after ten days of culture.  Observations indicate that CTGF alone or in combination with TGFbeta-1 stimulates primordial follicle assembly and TGFbeta-1 can decrease the primordial follicle pool size.  CTGF was found to regulate the ovarian transcriptome during primordial follicle assembly and an integrative network of genes was identified.  CTGF is one of the first growth factors shown to promote primordial follicle assembly, while TGFbeta-1 is one of the first factors shown to decrease the primordial follicle pool size.  These observations suggest the possibility of manipulating primordial follicle pool size and influencing female reproductive lifespan.
We used microarrays to determine genes expressed differentially between control and CTGF (connective tissue growth factor) treated P0 ovary

overall_design: RNA samples from 3 control groups are compared to 3 CTGF treated ovary groups

first: Eric

last: Nilsson

first: Marina

last: Savenkova

first: Ryan

last: Schindler


title: miRNA expression data from A549 exposed to formaldehyde

status: Public on Oct 01 2010

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
We are investigating the miRNA expression profiles of human lung cells to gaseous formaldehyde
We used microarrays to detail the global programme of miRNA expression upon response to formaldehyde

overall_design: A549 cells were grown to confluency and exposed to formaldehyde or mock-treated. RNA was collected 9 hrs after exposure.

first: Julia

last: Rager

first: Lise

last: Smeester

first: Ilona

last: Jaspers

first: Kenneth

middle: G

last: Sexton


title: Dose-dependent gene expression analysis of cardiomyocytes treated with DEHP (1-50 ug/mL)

status: Public on Sep 01 2010

city: Washington

first: Nikki

middle: Gillum

last: Posnack

state: Please select a region, state or province.

address: 111 Michigan Ave, NW

institute: Childrens National Hospital

summary: We used microarrays to expression profile cardiomyocytes from neonatal Sprague-Dawley rats treated with 1 to 50 ug/mL DEHP and control (0.1% DMSO) to identify changes in gene expression related to connexin-43 expression, calcium handling, arrhythmogenesis and mechanical motion.

overall_design: Rat neonatal cardiomyocytes were treated with 1 ug/ml, 10 ug/ml, or 50 ug/ml DEHP (diluted in 0.1% DMSO) for 3 days, control samples were treated with 0.1% DMSO. Cardiomyocytes used in the experiments were from the same litter. Samples within a treatment group (control, DEHP) are biological replicates.

first: Norman

last: Lee

first: Narine

last: Sarvazyan


title: Genome-wide gene expression analysis of Di-(2-ethyl hexyl) phthalate-treated cardiomyocytes


title: Gene expression analysis of cardiomyocytes treated with a clinically relevant concentration of DEHP (50 ug/mL)

summary: We used microarrays to expression profile cardiomyocytes from neonatal Sprague-Dawley rats treated with 50 ug/mL DEHP and control (0.1% DMSO) to identify changes in gene expression related to connexin-43 expression, calcium handling, arrhythmogenesis and mechanical motion.

overall_design: Rat neonatal cardiomyocytes were treated with DEHP (diluted in 0.1% DMSO) for 3 days, control samples were treated with 0.1% DMSO. Cardiomyocytes used in the experiments were from the same litter. Samples within a treatment group (control, DEHP) are biological replicates.


title: Comparison of thymic epithelial cells and hair follicle stem cells

status: Public on Aug 23 2010

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary:
Thymic epithelial cells (TECs) are essential for thymopoiesis and form a complex three-dimensional network, the organization of which is strikingly different from other epithelia. Interestingly, TECs express simple epithelia keratins in the cortex, stratified epithelia keratins in the medulla and epidermal differentiation markers in Hassall's bodies. Here we investigate the relationship between thymic epithelium and epidermal differentiation and show that the thymus of the rat contains a population of clonogenic TECs that can be extensively cultured and cloned using conditions developed for epidermal cell therapy in human. Clonogenic TECs conserve a thymic identity and the capacity to integrate in a thymic epithelial network, but they acquire new functionalities when exposed to an inductive skin microenvironment, permanently adopting the fate of hair follicle multipotent stem cells. This change in fate, maintained over time in serial transplantation, correlates with a down-regulation of transcription factors important for thymic identity, and an up-regulation of epidermal markers. Consequently, the TECs’ capacity to integrate in a thymic epithelial network is altered or even lost. Our results demonstrate that the thymus contains a population of holoclone-like epithelial cells that can function as bona fide multipotent keratinocyte stem cells, and that microenvironmental cues are sufficient to re-direct epithelial-cell fate, allowing crossing of primitive germ layer boundaries from endoderm to ectoderm.

Keywords: Cell type comparison

overall_design: Expression profile difference between hair follicle clones and TECs before and after transplatation

first: Paola

last: Bonfanti

first: Stephanie

last: Claudinot

first: Alessandro

last: Amici

first: Alison

last: Farley

first: Clare

last: Blackburn

first: Yann

last: Barrandon

first: Otto

last: Hagenbüchle


title: The role of dietary leucine and dairy protein on hepatic gene expression

status: Public on Aug 12 2010

city: Calgary

first: Lindsay

last: Eller

address: 2500 University Dr. NW

institute: University of Calgary

summary:
We used microarray to determine the differences in hepatic gene expression for diet-induced obese Sprague-Dawley rats consuming different dietary proteins.  Proteins of interest included skim milk powder (dairy), casein, and the branched-chain amino acid, leucine.
The primary aims of this study were: (i) to compare the effects of diets with protein derived from casein, casein supplemented with leucine, and complete dairy on body composition and insulin sensitivity; and (ii) to determine if there is a synergistic effect of dietary Ca and protein source on body composition and insulin sensitivity.  Secondarily, we used microarray analysis to examine the effect of casein, leucine, or complete dairy containing diets on the expression of hepatic genes related to lipid and glucose metabolism.

overall_design: Diet induced obese rats consumed ad libitum, a high fat, high sucrose diet for 8 weeks (n=4).  All diets had an energy density of 4.6 kcal/gram and provided 10% of total energy from protein [casein, complete dairy (skim milk powder), or leucine-supplemented casein (7.1% from casein plus 2.9% from leucine)]. The casein treatment was the control diet.

first: Raylene

middle: R

last: Reimer

first: Jane

last: Shearer


title: Rhodospirillum rubrum S1H in simulated microgravity

status: Public on Jun 05 2010

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

country: Belgium

summary: In the frame of the European MELiSSA project, which aims to develop a closed biological life support system for forthcoming long term space exploration missions, the study of the alpha-proteobacterium Rhodospirillum rubrum S1H cultivated in space related environmental conditions has started. In the present work, the bacterium was grown using two different microgravity simulators, namely the Rotating Wall Vessel (RWV) and the Random Positioning Machine (RPM) and its response was evaluated at both the transcriptomic and proteomic levels using respectively a dedicated whole-genome microarray and high-througput proteomics. At the transcriptomic level, 13 genes were found significantly induced in the RWV samples and all 13 were included in the more pronounced response of 235 induced genes of R. rubrum S1H to the RPM cultivation. On the other hand, at the proteomic level, a few common proteins were found to be differentially expressed in RWV and RPM while the RWV appeared to induce a higher number of significantly regulated proteins. However, the transcriptomic and the proteomic approaches appeared to be complementary pointing out the likely interrelation between quorum sensing, cell pigmentation and cell aggregation in R. rubrum S1H. Future studies will aim to characterize this unknown quorum sensing regulon.

overall_design:
At least, three independent cultures of R. rubrum S1H grown to stationary phase in Sistrom-succinate medium A containing 2 g/L Na-succinate (Sistrom, 1960) in dark aerobic conditions were resuspended in 0.85 % NaCl  to a final OD680 of ca. 0.600 to constitute stock cultures.
All cultures were allowed to grow for 10 days at 21 °C which are typical time frame and growth temperature of a Soyuz space flight mission (Mastroleo et al., 2009). The RWV bioreactors (Cellon, Bereldange, Luxembourg) were filled completely with ca. 58 ml of culture medium containing 1 % inoculum from the stock culture. Air bubbles were carefully removed through the sampling ports, using syringes (without needle), in order to avoid undesired shear stress. The vessels were mounted on separate RWV devices and were placed in a culture chamber, one in vertical position creating the low-shear modeled microgravity (LSMMG) environment while the control was placed in horizontal position.
Gas exchange in the RWV bioreactors during growth was ensured by the gas-permeable silicone membrane present at the back of each RWV culture vessel. Bacterial growth in RWV conditions was allowed at a rotational speed of 25 rpm. After cultivation, oxygen concentration was measured by inserting the oxygen probe directly into the vessel without homogenization. After homogenization, optical density was measured at 600 nm and cells were harvested for pigment quantification as previously described (Favier-Teodorescu, 2004) and for transcriptomic and proteomic analysis.
The same RWV vessels were used to cultivate R. rubrum in liquid aerobic condition using the RPM. The horizontal RWV incubation described above was also used as control for the RPM cultivation. The RPM was operated as a random walk  three-dimensional clinostat (basic
mode) with an angular velocity of rotation of 60 deg s-1 as previously described (Mastroleo et al., 2009).
RPM - 4 technical replicates, RWV - 3 technical replicates

first: Felice

last: Mastroleo

first: Rob

last: Van Houdt

first: Max

last: Mergeay

first: Larissa

last: Hendrickx

first: Ruddy

last: Wattiez


title: Gene Bionetwork Analysis of Ovarian Primordial Follicle Development

status: Public on Jun 13 2010

first: Michael

last: Skinner

summary:
Ovarian primordial follicles are critical for female reproduction and comprise a finite pool of gametes arrested in development. A systems biology approach was used to identify regulatory gene networks essential for primordial follicle development. Transcriptional responses to eight different growth factors known to influence primordial follicles were used to construct a bionetwork of regulatory genes involved in primordial follicle development. Over 1500 genes were found to be regulated by the various growth factors and a network analysis identified critical gene modules involved in a number of signaling pathways and cellular processes. A set of 55 genes was identified as potential critical regulators of these gene modules, and a subnetwork associated with development was determined. Within the network two previously identified regulatory genes were confirmed (i.e. Pdgfa and Fgfr2) and a new factor was identified, connective tissue growth factor (CTGF). CTGF was tested in ovarian organ cultures and found to stimulate primordial follicle development. Therefore, the relevant gene network associated with primordial follicle development was validated and the critical genes and pathways involved in this process were identified. This is one of the first applications of network analysis to a normal developmental process. These observations provide insights into potential therapeutic targets for preventing ovarian disease and promoting female reproduction.
For GSM509254-9: We used microarrays to determine genes expressed differentially between control and CTGF (connective tissue growth factor) treated P4 ovary.
For GSM510028-65: We used microarrays to determine genes expressed differentially between control and growth factors treated P4 ovary and co-expressed in the same manner for P4 ovaries treated with 8 growth factors AMH, BMP4, GDNF, FGF2, FGF7, KITLG, LIF, PDGFab.

overall_design:
For GSM509254-9: RNA samples from 3 control groups are compared to 3 CTGF treated ovary groups.
For GSM510028-65: RNA samples from 14 control samples are compared to 3 growth factor treated ovary samples for each AMH, BMP4, GDNF, FGF2, FGF7, KITLG, LIF, PDGFab treatment.

first: Eric

last: Nilsson

first: Marina

last: Savenkova

first: Ryan

last: Schindler

first: Bin

last: Zhang

last: Schadt


title: Effect of phenylalanine-rich peptide on growth and survival of Mycobacterium tuberculosis H37Rv (Mtb)

status: Public on Nov 11 2009

city: New Delhi

first: krishan

last: kumar

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: ICGEB

summary: During our efforts to isolate potantial binding partners of Esat6, we isolated few peptides rich in phenylalanine residues that strongly interacted with Esat6. All peptides were less than fifty amino acids in length, One of them, Hcl1, when expressed in mycobacteria showed significant retardation in growth and survival within macrophages. Microarray analysis showed that Hcl1 affects a host of genes and cellular pathways.

overall_design: RNA was isolated from exponentially growing mycobacteria containing either plasmid vector pVV16 encoding peptide or vector pVV16 alone. Comparisons were made between Experimental (Mtb/Hcl1) and control (Mtb/pVV16) samples by extracting raw intensity values from multiple arrays.

first: Krishan

last: Kumar

first: Jameel

last: Khan

first: Anand

last: Ranganathan


status: Public on Jul 28 2010

city: Seattle

first: Ashley

last: Sherrid

address: 307 Westlake Ave N

institute: Seattle Biomedical Research Institute

summary:
Reaeration timecourse from a defined hypoxia model in Mycobacterium tuberculosis.

The mechanism by which mycobacteria return to a replicating state upon re-exposure to favorable conditions is not well understood. In this study, we utilized reaeration from a defined hypoxia model to characterize the adaptive response of Mycobacterium tuberculosis (MTB) following a return to favorable growth conditions. Global transcriptional analysis identified the ~100 gene Reaeration Response, induced relative to both log-phase and hypoxic MTB. This response includes chaperones and proteases, as well as the transcription factor Rv2745c, a Clp protease gene regulator (ClgR) orthologue.  During reaeration, genes repressed during hypoxia are also upregulated in a wave of transcription that includes genes crucial to transcription, translation and oxidative phosphorylation.

overall_design: Each reaerating culture compared at multiple timepoints to a sample from the same culture at seven days of hypoxia. Three or more replicates at each timepoint.

first: Tige

last: Rustad

first: Gerard

last: Cangelosi

first: David

last: Sherman


title: Maltose-1-Phosphate Stress Stimulon in Mycobacterium tuberculosis

status: Public on Feb 24 2010

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

summary:
New chemotherapeutics are urgently required to control the tuberculosis pandemic fueled by the emergence of multidrug- and extensively-drug-resistant Mycobacterium tuberculosis strains and the bacterium`s catastrophic alliance with HIV. Here we describe a novel trehalose-to-α-glucan pathway in M. tuberculosis comprising four enzymatic steps mediated by TreS, Pep2, GlgB, and GlgE, identified as an essential maltosyltransferase capable of utilizing maltose 1-phosphate. Using traditional and chemical reverse genetics, we show that GlgE inactivation causes rapid death of M. tuberculosis in vitro and in mice, through self-poisoning by maltose 1-phosphate accumulation driven by a self-amplifying feedback loop promoting pleiotropic phosphosugar-induced stress responses. Moreover, this α-glucan pathway exhibited a synthetic lethal interaction with the glucosyltransferase Rv3032 involved in biosynthesis of specialized α-glucan derivatives. The unique combination of gene essentiality within a synthetic lethal pathway validates GlgE as a new class of drug targets, revealing novel synergistic mechanisms to induce death in M. tuberculosis.  Transcriptional profiling was performed to characterize the lethality induced by maltose 1-phosphate accumulation. Triplicate 10 mL cultures of the conditional lethal Mtb mutant strain H37Rv Delta treS Delta glgE (pMV361::treS) and of the vector control strain H37Rv Delta treS Delta glgE (pMV361) were grown in liquid culture to log-phase in the presence of 5 mM validamycin A (VA) to suppress M1P formation. Subsequently, cells were washed to remove the inhibitor; after 48 h of starvation for VA cultures were harvested.

Keywords: tuberculosis, trehalose, compound treatment design, genetic modification design, and stimulus or stress design

overall_design: Three biological replicates with one dye-flip

first: Rainer

last: Kalscheuer


title: Study of Gastric Cancer

status: Public on Mar 23 2010

city: new delhi

first: Thoudam

middle: Regina

last: Devi

state: delhi

address: Safdarjung hospital campus

department: Safdarjung Hospital Campus

institute: Institute of Pathology

summary: The objective of my study was to identify the genes differentially expressed in gastric adenocarcinoma associated with prevalent risk factor such as tobacco use (Meiziol, Tuibur etc) in high-risk Indian population. The Tumor tissue and matched normal tissue distant to the tumor were collected during endoscopy in RNA later, Snap-frozen in liquid nitrogen and stored at -70°C until processed. Data of clinicopathologic parameters were obtained from patients’ clinical report, operative notes and pathologic report. Institutional Human ethics committee approved the study.

overall_design:
Total RNA was isolated from tumor and matched normal of five patients. We pooled total RNA of normal tissue from three patients in one slide and the other two in another slide. Individual slide were used for each tumor samples.

Isolation Kit: RNeasy mini Kit (Qiagen)
Scanner Used: AFFYMETRIX,428 Array

first: Sunita

last: Saxena

first: Sujala

last: Kapoor

last: Zomawia

last: Regina Devi


title: Gene expression microarray analysis of early oxygen-induced retinopathy (OIR)

status: Public on Nov 13 2009

city: Adelaide

first: Melinda

middle: N

last: Tea

state: South Australia

address: Flinders Medical Centre, Carpark Building

department: Ophthalmology

country: Australia

institute: Flinders University

summary: Different inbred strains of rats differ in their susceptibility to OIR, an animal model of human retinopathy of prematurity. We examined gene expression profiles in Fischer 344 (F344, resistant to OIR) and Sprague Dawley (SD, susceptible to OIR) rats at the early time point of day 3 to identifying gene pathways related to the underlying genetic cause of phenotypic differences between strains.

overall_design: To examine gene expression changes in rats strains which are resistant and susceptible to OIR, four different experimental conditions were analysed: F344 cyclic hyperoxia (O2) exposed, F344 room air (RA) exposed, SD O2 exposed and SD RA exposed. A minimum of two samples of pooled RNA, comprising of 3 individual rats from 2 separate litters, was used for each experimental condition. Pooled RNA from different rats were used as biological replicates. An additional sample for F344 O2 and SD RA rats was included on the basis of the principal components analysis from the initial 8 samples. Pooled RNA from age-matched room air-exposed rats were used as controls.

first: Rhys

last: Fogarty

first: Helen

last: Brereton

first: Michael

middle: Z

last: Michael

first: Mark

middle: B

last: Van der Hoek

first: Anna

last: Tsykin

first: Douglas

middle: J

last: Coster

first: Keryn

last: Williams


title: Nicotinamide Starvation of Mycobacteria Defective for de novo NAD Biosynthesis

summary: Mycobacteria can synthesize NAD+ using either the de novo biosynthesis pathway or the salvage pathway.  The deletion of the three genes involved specifically in the NAD+ de novo biosynthesis pathway in the human pathogen Mycobacterium tuberculosis had no effect on the growth of the strain in vivo.  In contrast, the same deletion in the bovine pathogen Mycobacterium bovis resulted in a strain that could not grow in vivo and could only grow in vitro with substantial nicotinamide supplmentation.  This striking difference was attributed to the known defect in the nicotinamidase PncA of M. bovis, since introducing the M. tuberculosis pncA gene into the M. bovis strain defective for de novo NAD+ biosynthesis restored growth in vitro and in vivo.  This study demonstrates that NAD+ starvation is a cidal event in mycobacteria and confirms that enzymes common to the de novo and salvage pathways may be good drug targets.  We also propose that simultaneously targeting both the salvage and the de novo NAD+ biosynthesis pathways represents a potentially effective way to treat infection with tubercle bacilli. To characterize the lethality induced by nicotinamide starvation transcriptional profiling of the auxotrophs was performed. Triplicate 50 mL cultures of M. tuberculosis and M. bovis Delta nadABC mutants were grown in 7H9 OADC glycerol 0.05% tween broth in 500 mL roller bottles to an OD600nm= 0.1 in a roller incubator at 37°C.  The cells were washed 1x in PBS and resuspended in 50 mL 7H9 OADC glycerol 0.05% tween broth with or without 20mg/L nicotinamide and returned to the incubator.  After 7 days, cultures were harvested.

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design: Three biological replicates of each of two species with one dye-flip each

first: Catherine

last: Vilcheze


title: Comparison of Saffron and Photobiomodulation on the light damaged rat retina.

status: Public on Jul 16 2010

city: Acton

first: Riccardo

last: Natoli

state: ACT

address: Sullivans Creek Road

department: CMBE

institute: ANU

summary:
Aim: To identify the genes and non-coding RNAs (ncRNAs) involved in the neuroprotective actions of a dietary anti-oxidant (saffron) and of photobiomodulation.
Methods: We used a previously published assay of photoreceptor damage, in which albino Sprague Dawley rats raised in dim cyclic illumination (12h 5 lux, 12h darkness) are challenged by 24h exposure to bright (1,000 lux) light. Experimental groups were protected against light damage by pretreatment with dietary saffron (1mg/kg/day for 21d) or photobiomodulation (10 J/cm2 at the eye, daily for 5d). RNA from 1 eye of each of 4 animals in each of the 6 experimental groups (control, light damage (LD), saffron, photobiomodulation (PBM), saffronLD, and PBMLD) was hybridized to Affymetrix rat genome ST arrays. Quantitative real-time PCR analysis of 14 selected genes was used to validate microarray results.
Results: LD caused the regulation of 175 entities (genes and ncRNAs) beyond criterion levels (P < 0.05 in comparisons with controls, fold-change >2). PBM pretreatment reduced the expression of 126 of these 175 LD-regulated entities below criterion; saffron pretreatment reduced the expression of 53 entities (50 in common with PBM). In addition, PBM pretreatment regulated the expression of 67 entities not regulated by LD, while saffron pretreatment regulated 122 entities not regulated by LD (48 in common with PBM). PBM and saffron, given without LD, regulated genes and ncRNAs beyond criterion levels, but in lesser numbers than during their protective action. A high proportion of the entities regulated by LD (>90%) were known genes; by contrast, ncRNAs where prominent among the entities regulated by PBM and saffron in their neuroprotective roles (73% and 62% respectively).
Conclusions: Given alone, saffron and (more prominently) PBM both regulated significant numbers of genes and ncRNAs. Given prior to retinal exposure to damaging light, thus while exerting their neuroprotective action, they regulated much larger numbers of entities, among which ncRNAs were prominent. Further, the downregulation of known genes and of ncRNAs was prominent in the protective actions of both neuroprotectants. These comparisons provide an overview of gene expression induced by two neuroprotectants and provide a basis for more focused study of their mechanisms.

overall_design: The were 3 biological repliactes of each of the following groups: Control, Saffron pretreated, Photobiomodulation pretreated, Light Damage, Saffron Light Damage and Photobiomodulation Light Damage. 18 chips in total were performed.

first: Yuan

last: Zhu

first: Krisztina

last: Valter

first: Silvia

last: Bisti

first: Janis

last: Eells

first: Jonathan

last: Stone


title: Intrinsic response of thoracic propriospinal neurons to axotomy

status: Public on Mar 17 2010

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: Analysis of expression changes in prelabeled laser-microdissected thoracic propriospinal neurons at different times after low-thoracic spinal cord transection in adult rats.

overall_design: Propriospinal neurons projecting to the lumbar enlargement were captured at various time points following no lesion or low thoracic spinal cord transection.

first: Justin

last: Siebert

first: Dennis

last: Stelzner


title: Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori

status: Public on Aug 28 2009

city: BeiBei

first: Qingyou

last: Xia

state: Chongqing

address: No.2 Tiansheng Road

country: China

institute: Southwest University

summary: We designed and constructed a genome-wide microarray with 22,987 70-mer oligonucleotides covering the presently known and predicted genes in the silkworm genome, and surveyed the gene expression in multiple silkworm tissues on day 3 of the fifth instar. Clusters of tissue-prevalent and tissue-specific genes and genes that are differentially expressed in different tissues were identified, and they reflect well major tissue-specific functions on the molecular level. The data presented in this study provide a new resource for annotating the silkworm genome.

overall_design: In the present study, we surveyed gene expression in the A/MSG, the PSG, testis, ovary, fat body, midgut, integument, hemocyte, malpighian tubule, and head from silkworm individuals on day 3 of the fifth instar. In order to establish gene expression differences between sexes, we prepared male and female samples of the same tissue. In addition, we also selectively performed the biological replicates at least twice for five tissues including testis, ovary, A/MSG, PSG and malpighian tubule, to evaluate biological reproducibility. In all, we prepared 30 two-channel hybridizations across the selected tissues for study. We extracted the single channel intensity instead of the ratio value from each two-channel hybridization for further analysis, a strategy that has been reported as being more flexible and valid previously.

first: Daojun

last: Cheng

first: Jun

last: Duan

first: Genhong

last: Wang

first: Tingcai

first: Xingfu

last: Zha

first: Chun

last: Liu

first: Ping

last: Zhao

first: Fangyin

last: Dai

first: Ze

last: Zhang

first: Ningjia

last: He

first: Liang

first: Zhonghuai

last: Xiang


title: CREB ChIP-chip and HaloCHIP-chip experiments

status: Public on Oct 01 2009

city: Madison

first: Danette

last: Hartzell

state: WI

address: 2800 Woods Hollow Road

institute: Promega

summary: Regulation of gene expression is essential for normal development and cellular growth.  Transcriptional events are tightly controlled both spatially and temporally by specific DNA-protein interactions. In this study we finely map the genome-wide targets of the CREB protein across all known and predicted human promoters, and characterize the functional consequences of a subset of these binding events using high-throughput reporter assays.  To measure CREB binding, we used HaloCHIP, an antibody-free alternative to the ChIP method that utilizes the HaloTag fusion protein, and also high-throughput promoter-luciferase reporter assays, which provide rapid and quantitative screening of promoters for transcriptional activation or repression in living cells.

overall_design: CREB ChIP-chip two biologcal replicates. HaloCHIP-chip three biological replicates with and without Forskolin

first: Nathan

last: Trinklein

first: Jacqui

last: Mendez

first: Nancy

last: Murphy

first: Shelley

middle: F

last: Aldred

first: Keith

last: Wood

first: Marjeta

last: Urh


title: M. tuberculosis transcriptional profile of delta pepD strain vs wild-type strain

status: Public on Oct 30 2009

city: Milwaukee

first: Tom

last: Zahrt

address: 8701 Watertown Plank Rd

department: Microbiology and Molecular Genetics

institute: Medical College of Wisconsin

summary: pepD is regulated by a 2CS, MprAB, and impacts upon the regulation of sigE, an important M.tb sigma factor.  Here we examine the global impact of gene regulation in a delta pepD mutant strain.

overall_design: Analysis compares total RNA from early log growth cultures of both wild-type and a delta pepD strain.

first: Mark

last: White

middle: C


title: Defined hypoxic model timecourse of H37Rv and H37Rv:deltadosR

status: Public on Feb 20 2008

first: Tige

last: Rustad

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

summary:
Background:
A significant body of evidence accumulated over the last century suggests a link between hypoxic microenvironments within the infected host and the latent phase of tuberculosis.  Studies to test this correlation have identified the M. tuberculosis initial hypoxic response, controlled by the two-component response regulator DosR.  The initial hypoxic response is completely blocked in a dosR deletion mutant.
Methodology/Principal Findings:
We show here that a dosR deletion mutant enters bacteriostasis in response to in vitro hypoxia with only a relatively mild decrease in viability.  In the murine infection model, the phenotype of the mutant was indistinguishable from that of the parent strain.  These results suggested that additional genes may be essential for entry into and maintenance of bacteriostasis.  Detailed microarray analysis of oxygen starved cultures revealed that DosR regulon induction is transient, with induction of nearly half the genes returning to baseline within 24 hours.  In addition, a larger, sustained wave of gene expression follows the DosR-mediated initial hypoxic response.  This Enduring Hypoxic Response (EHR) consists of 230 genes significantly induced at four and seven days of hypoxia but not at initial time points.  These genes include a surprising number of transcriptional regulators that could control the program of bacteriostasis.  We found that the EHR is independent of the DosR-mediated initial hypoxic response, as EHR expression is virtually unaltered in the dosR mutant.
Conclusions/Significance:
Our results suggest a reassessment of the role of DosR and the initial hypoxic response in MTB physiology.  Instead of a primary role in survival of hypoxia induced bacteriostasis, DosR may regulate a response that is largely optional in vitro and in mouse infections.  Analysis of the EHR should help elucidate the key regulatory factors and enzymatic machinery exploited by M. tuberculosis for long-term bacteriostasis in the face of oxygen deprivation.
Keywords: time-course

overall_design: Each hypoxic timecourse compared to the matching log phase sample.  Each time point/strain represented by a minimum of three replicates.

first: David

last: Sherman


title: MNNG treated Excherichia coli reveal new up or down regulated genes belonging to the Ada regulon

status: Public on Aug 18 2009

city: Oslo

first: Gard

last: Thomassen

state: Oslo

address: Rikshospitalet University Hospital

department: Molecular microbiology

country: Norway

institute: Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology

type: Expression profiling by genome tiling array

summary:
An oligonucleotide tiling array technology is utilized to measure the entire Escherichia coli transcriptome and its transcriptional changes after induction of the adaptive response by the alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG).

Keywords: Gene expression during the adaptive response in Escherichia coli

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
Escherichia coli K-12 MG1655 single colony in five parallells was grown to mid-log phase and exposed to the ada-response inducer MNNG. Total RNA was extracted from induced and uninduced cells and cDNA was prepared, fragmented and labelled prior to hybridizing to arrays.
The Escherichia coli genome was split in two; sequences encoding proteins, tRNAs or rRNAs with a known function on either strand, and sequences without such annotation. A selective tiling approach was used to ensure sufficient coverage of unnanotated genomic regions due to the limited number of array probes.

middle: O

first: Ragnhild

last: Weel-Sneve

first: Alexander

last: Rowe

first: James

last: Booth

first: Karin

last: Lagesen

first: Knut

last: Kristiansen

first: Magnar

last: Bjørås

first: Torbjørn

last: Rognes

first: Jessica

last: Lindvall


title: knock-out Slr1738 mutant strain analysis exposed to cadmium (50 microM).

status: Public on Dec 07 2005

city: Gif sur yvette CEDEX

first: Franck

last: Chauvat

department: DSV/DBJC

country: France

institute: CEA Saclay

summary:
The transcriptome approach was used to characterize the global change in slr1738 null-mutant gene expression in response to cadmium (50 microM, 180 min), compared to wild type strain gene expression in response to cadmium (50 microM, 180 min). Total RNA were isolated from null-mutant and wild type stressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays.
Keywords: stress responses

overall_design: Our analysis (slr1738 null-mutant strain Cd VS wild type strain Cd) is composed of 2 arrays (dye swap).

first: Laetitia

last: Houot

first: Martin

last: Floutier

first: Benoit

last: Marteyn

first: Pierre

last: Legrain

first: Corinne

last: Cassier-Chauvat


title: Synechocystis PCC6803 time course responses to cadmium (CdSO4, 50 microM, 300 min.

summary:
The transcriptome approach was used to characterize the of the global change in Synechocystis gene expression in response to continuous exposure to cadmium (50 microM). Total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays.
Keywords: stress responses

overall_design: We analysed cadmium responses on the new version of Takara cyanochip (version 2.0, GPL3214). This analysis is composed of 2 arrays (dye swap).


title: Synechocystis PCC6803 time course responses to zinc (ZnSO4, 776 microM.

summary:
The transcriptome approach was used to characterize the of the global change (2 time points) in Synechocystis gene expression in response to continuous exposure to zinc excess (776 microM), compared to standard medium (776 nM). For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays.
Keywords: stress responses

overall_design: We made 2 time points of exposure to zinc (776 microM). For each time point, we analyzed 2 arrays (dye swap).


title: Role of Chlamydia pneumoniae in coronary artery disease patients

status: Public on Jan 06 2010

first: Hem

middle: Chandra

last: Jha

address: Lab no-204, IOP-ICMR, Safdarjung Hospital Campus,

department: Tissue Culture/Microbiology

institute: Institute of Pathology- Indian Council of Medical Research

summary: To date there is no clear explanation as to how Chlamydia pneumoniae heat shock protein 60 (cHSP60) gets activated either through TLR-2/4, MAPKinase (p38/JNK/ERK), apoptotic/antiapoptotic, chemokines and inflammatory cytokines pathways leading to coronary artery disease (CAD). Hence to better understanding towards cHSP60 signaling in CAD patients, we performed experiments at RNA levels in cHSP60 positive and negative groups of CAD patients. For the determination of positivity for C. pneumoniae, Helicobacter pylori, Cytomegalovirus and Herpes Simplex Virus in atheromatous plaque multiplex Real Time PCR was performed. Monoplex Real Time PCR was also performed with 16S rRNA and HSP60 gene Chlamydia pneumoniae. Further study was performed only on cHSP60 positive (negative for H. pylori, CMV & HSV-1) and cHSP60 negative (also negative for H. pylori, CMV & HSV-1) CAD patients.

overall_design:
1. Patients
Forty patients (28 males, 12 females) in age group (51±13 year) attending Department of Cardio Thoracic & Vascular Surgery, Safdarjung Hospital, New Delhi from September 2007 to April 2008 were enrolled in the study. These patients had manifestations of CAD and were undergoing open by-pass heart surgery. Prior written consent was obtained from each patient. The study received clearance from Ethical committee, Safdarjung hospital. Patients who had a recent acute coronary syndrome or transient ischemic attack were not included in our study.

2. Atheroma collection and handling
Atheromatous tissue were collected in aseptic conditions and placed in 30 ml transport medium immediately upon resection. Three types of transport medium were used for tissue: viz. Dulbecco?s phosphate-buffered saline (PBS; Gibco Life Technologies, Paisley, Scotland) for DNA, RNA later (Ambion Inc., Woodward st. Austin, Texas, USA) for RNA and optimum cutting temperature compound (Sigma, St. Louis, MO, USA) for protein.

3. Atheroma DNA & RNA isolation and testing
Total DNA was isolated for checking the positivity for C. pneumoniae from atheromatous plaques as described earlier [1]. Total RNA from the atheroma samples were isolated using RNeasy fibrous tissue mini kit (Qiagen Sciences, Maryland, USA) and the concentration was determined by a RNA dye-binding assay (Pico-Green, Molecular Probes, Eugene, OR). For cDNA synthesis, RETRO script (Ambion Inc., Woodward st. Austin, Texas, USA) was used as per manufacturer instructions. For detecting positivity for C. pneumoniae, Helicobacter pylori, Cytomegalovirus and Herpes Simplex Virus in atheromatous plaques, multiplex RT-PCR was performed [as describe in reference 1]. Monoplex RT PCR amplification primers and probes were custom designed by Applied Biosystems (Foster City, CA, USA). Briefly, sequences for the 16S rRNA and HSP60 gene of the organisms of interest were aligned and inspected for regions of conserved and variable sequences.

4. Microarray experiment
Further study was performed only on cHSP60 positive (negative for H. pylori, CMV & HSV-1) and cHSP60 negative (also negative for H. pylori, CMV & HSV-1) CAD patients. cHSP60 positive samples represented the test samples and cHSP60 negative samples represented the control samples. 3 samples were analysed: samples 17 and 23 were biological replicates of test samples and also performed in duplicate as technical replicates, and sample 26 was a control sample and was also performed in duplicate as a technical replicate.

Reference
1. Hem C Jha, Pragya Srivastava, Aabha Divya , Jagdish Prasad, Aruna Mittal. Prevalence of Chlamydophila pneumoniae is higher in aorta and coronary artery than in carotid artery of coronary artery disease patients. APMIS, 2009: 117 (12): 905-911.

last: Chandhra Jha

first: Jagdish

last: Prasad

first: Aruna

last: Mittal


title: Synechocystis PCC6803 dose responses to iron starvation (96h).

summary:
The transcriptome approach was used to characterize the global change (2 Fe concentrations) in Synechocystis gene expression in response to continuous iron starvation, compared to standard medium (17 microM). For iron depletion, exponentially growing cells were washed in Fe-free medium, and grown for 48 hrs under standard conditions in liquid medium cotaining either 1 mM or 2 mM of ferric ammonium citrate. Then, cells were washed, and resuspended in Fe-free medium (Fe contaminations 0.5 microM) and grown for another 48 hrs period. For each concentration point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each concentration point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays.
Keywords: stress responses

overall_design: We made 2 concentration points of iron starvation (2 to 0.5 microM, or 1 to 0.5 microM). For each concentration point, we analyzed 2 arrays (dye swap).


title: Synechocystis PCC6803 time course responses to iron (ferric ammonium citrate, 17 mM.

summary:
The transcriptome approach was used to characterize of the global change (2 time points) in Synechocystis gene expression in response to continuous exposure to iron excess (17 mM), compared to standard medium (17 microM). For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays.
Keywords: stress responses

overall_design: We made 2 time points of exposure to iron (17 mM). For each time point, we analyzed 2 arrays (dye swap).


title: Synechocystis PCC6803 Stress Response

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Synechocystis PCC6803 time course responses to H2O2 3mM.

summary:
The transcriptome approach was used to characterize the kinetics (5 time points) of the global change in Synechocystis gene expression in response to continuous exposure to H2O2 (3 mM). For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : IntelliGeneTM CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays.
Keywords: time course, stress responses

overall_design: We made a kinetic (5 time points) of exposure to H2O2 (3 mM). For each time point, we analyzed 2 arrays (dye swap).


title: Synechocystis PCC6803 time course responses to 50 µM cadmium

status: Public on Dec 01 2005

summary:
The transcriptome approach was used to characterize the kinetics (9 time points) of the global change in Synechocystis gene expression in response to continuous exposure to Cd (CdSO4, 50 _M). For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point), covering 2,845 of the 3,168 ORFs of Synechocystis (Custom-commercial array : IntelliGeneTM CyanoCHIP version 1.2, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays.
Keywords: time course, stress responses

overall_design: We made a kinetic (9 time points) of exposure to cadmium (CdSO4, 50 _M). For each time point, we analyzed 2 arrays (dye swap).