title: Global gene expression patterns in Clostridium thermocellum from microarray analysis of chemostat culture on cellulose or cellobiose

status: Public on Dec 15 2010

first: Brian

last: Fox

address: 141b Biochemistry

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: Earlier studies pointed to the ability of C. thermocellum to exquisitely control gene expression in response to growth rate and the presence of insoluble cellulose or soluble compounds such as cellobiose.  This microarray study was carried out in order to examine expression responses of the entire genome. The use of the chemostat technique allowed the effects of different growth rates to be analyzed separately from the effects of different substrates.

overall_design: An 11-chip study of 11 separate C. thermocellum chemostat cultures grown on cellulose or cellobiose at different dilution rates.

first: Allison

last: Riederer

first: Taichi

last: Takasuka

first: Shin-Ichi

last: Makino

first: David

middle: M

last: Stevenson

first: Yury

middle: V

last: Bukhman

first: Nathaniel

last: Elsen


title: Stem Cells Secrete Factors That Induce Proliferation In Differentiated Cardiomyocytes

status: Public on Jun 01 2010

city: Pittsburgh

first: John

middle: Michael

last: Krill-Burger

state: PA

address: Rm. WG21.3 Shadyside Hospital

country: USA

institute: University of Pittsburgh Medical Center

summary: Media conditioned by undifferentiated human embryonic stem cells enhanced karyokinesis, cytokinesis and cell proliferation in cultures of differentiated, beating primary rat cardiomyocytes without altering their final contractile phenotype. Transcriptome analysis of proliferating cardiomyocytes revealed comprehensive activation of the ROCK 1 and 2 G-protein coupled receptor (GPCR) pathway associated with cytokinesis, and the RAS/RAF/MEK/ERK receptor tyrosine kinase pathways (RTK) and JAK/STAT-cytokine pathway involved in cell cycle progression. Correlative multi-analyte profiling (85 proteins) of conditioned media identified 33 proteins at significantly elevated levels compared to unconditioned media including ligands specific to the GPCR signal transduction pathways (serum amyloid A, monocyte chemoattractant protein-1, macrophage inhibitory protein, IL-8, macrophage inflammatory protein 1-alpha, eotaxin), RTK activation (IGFbp-1, IGFbp-2, HGF) and JAK-STAT stimulation pathways (IL-6, IFNa) activated in the treated cardiomyocytes. These data indicated that ES cells secreted a unique admixture of factors associated with induction of mitotic replication, cytokinesis and proliferation in cardiomyocytes.

overall_design: Rat neonatal cardiomyocytes were harvested from day 1 ventricles (n=24). Cardiomyocytes were purified via serial Percoll gradients and plated at 2.5x10^5 cells per 100 mm sq dish. Cardiomyocytes were given 24 hours in cardiac media before extracting 6 dishes as time zero controls. Of the remaining 12 dishes, 6 were diluted 50% with unconditioned hesc media and 6 were diluted 50% with stem cell conditioned hesc media. The FBS and HS percentages were held constant at 5% and 10% respectively. Three conditioned and three unconditioned samples were extracted at 24 hours and the same was repeated at 48 hours.

first: William

middle: A

last: LaFramboise

first: Patti

last: Petrosko

first: Dane

middle: R

last: Morris

first: Andrew

last: McCoy

first: Debra

last: Scalise

middle: E

last: Malehorn

first: Robert

middle: D

last: Guthrie

first: Michael

middle: J

last: Becich


title: Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation: ChIP-chip data

status: Public on Oct 18 2010

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

type: Genome binding/occupancy profiling by genome tiling array

summary: Metazoan transcription is controlled through either coordinated recruitment of transcription machinery to the gene promoter, or subsequently, through regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a key difference between genes that use these distinct regulatory strategies lies in the chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly-regulated genes whose sequences inherently disfavor nucleosome formation within the gene, but favor nucleosomal occlusion of the promoter. Pausing of polymerase maintains these genes in an active state by inhibiting the formation of repressive promoter chromatin. In contrast, promoters of housekeeping genes that lack paused Pol II are deprived of nucleosomes regardless of polymerase binding, but show higher nucleosome occupancy downstream. Our results suggest that the “default” chromatin state of a gene instructs its regulation, and that highly-regulated promoters have evolved to encourage competition between nucleosomes and paused Pol II for promoter occupancy.

overall_design: All experiments were done using two channels per chip, comparing DNA immunoprecipitated by the indicated antibody to matching input chromatin used for affinity purification. Where appropriate, replicate data sets were averaged.

first: Daniel

last: Gilchrist

first: Gilberto

last: Dos Santos

middle: C

last: Fargo

first: Bin

last: Xie

first: Yuan

last: Gao

first: Leping

last: Li


title: Gene expression changes in the medial prefrontal cortex and nucleus accumbens following abstinence from cocaine self-administration

status: Public on Mar 16 2010

city: Hershey

first: Penn State

last: COM

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

summary:
Many studies of cocaine-responsive gene expression have focused on changes occurring during cocaine exposure, but few studies have examined the persistence of these changes with cocaine abstinence. Persistent changes in gene expression, as well as alterations induced during abstinence may underlie long-lasting drug craving and relapse liability.

Results: Whole-genome expression analysis was conducted on a rat cocaine binge-abstinence model that has previously been demonstrated to engender increased drug seeking and taking with abstinence. Gene expression changes in two mesolimbic terminal fields (mPFC and NAc) were identified in a comparison of cocaine-naïve rats with rats after 10 days of cocaine selfadministration followed by 1, 10, or 100 days of enforced abstinence (n=6-11 per group). A total of 1,461 genes in the mPFC and 414 genes in the NAc were altered between at least two time points (ANOVA, p<0.05; ±1.4 fold-change). These genes can be subdivided into: 1) changes with cocaine self-administration that do not persist into periods of abstinence, 2) changes with cocaine self-administration that persist with abstinence, 3) and those not changed with cocaine self-administration, but changed during enforced abstinence. qPCR analysis was conducted to confirm gene expression changes observed in the microarray analysis.

overall_design: Gene expression changes in two mesolimbic terminal fields (mPFC and Nac) were identified in a comparison of cocaine-naϊve rats with rats after 10 days of cocaine self-administration followed by 1, 10 or 100 days of enforced abstinence. 5-6 replicates per condition.

first: Willard

last: Freeman

first: Melinda

last: Lull

first: Kruti

last: Patel

last: Brucklacher

first: Drake

last: Morgan

first: David

last: Roberts

first: Kent

last: Vrana


title: Whole transcriptome analysis of the hippocampus: toward a molecular portrait of epileptogenesis

status: Public on Feb 09 2010

city: Sao Paulo

first: Oswaldo

middle: Keith

last: Okamoto

state: SP

address: R. Botucatu, 862.

department: Neurology

country: Brazil

institute: UNIFESP

summary:
Purpose: to evaluate changes in the transcriptome of hippocampal cells during the course of epileptogenesis, from the early events post status epilepticus (SE) to the onset of recurrent spontaneous seizures.
Experimental Design: Gene expression profiling was analyzed in hippocampi of rats subjected to the pilocarpine model of epilepsy at different times during the course of epileptogenesis: 3 days post-SE (3D), 7 days post-SE (7D), and immediately (up to 12h) after the first spontaneous seizure (Chronic). All three pilocarpine subgroups had a corresponding age-matched control group (saline-treated rats), from which normal hippocampi samples were obtained at the same experimental time points. Independent microarray hybridizations were carried out for each sample (n = 5, per experimental group) with oligonucleotide microarrays covering 34,000 transcripts representing most of the known and predictive genes of the rat genome (CodeLink™ Rat Whole Genome Bioarrays, GE Healthcare), following the manufacturer’s protocol.
Results: differential expression of almost 1,400 genes was detected during the course of epileptogenesis, from the early events post status epilepticus (SE) to the onset of recurrent spontaneous seizures. Most of these genes are novel and displayed an up-regulation after SE. Noteworthy, a group of 128 genes functioning in neurogenesis, apoptosis, immune response, and intracellular signal transduction was found consistently hyper-expressed throughout epileptogenesis, indicating stable molecular alterations within the hippocampus. Those include modulation of the MAPK, Jak-STAT, PI3K, TGF-beta, and mTOR signaling pathways. Differential expression of genes from the p38 MAPK pathway, mediating inflammation and neurogenesis, was also confirmed by real-time PCR. These findings reveal dynamic molecular changes occurring in the hippocampus that may serve as a starting point for the generation of new hypothesis regarding the underlying mechanisms of epilepsy and for the designing of alternative therapeutic strategies.
Keywords: gene expression changes during epileptogenesis.

overall_design:
We performed a genome wide analysis of genes differentially expressed during epileptogenesis. Virtually, all possible changes in the rat transcriptome were monitored at distinct time points corresponding to the latent to chronic phase transition of the pilocarpine model of epilepsy, which is probably the most extensively studied chemically inductive model of TLE. Genes identified as being differentially expressed were classified based on their respective biological functions to envisage processes and pathways likely implicated in epileptogenesis, as well as their possible value as targets for therapy.
Results were expressed as fold variation, and genes displaying greater than 2-fold changes in transcript abundance and p<0.01 were selected.

middle: K

first: Luciana

last: Janjoppi

first: Felipe

last: Bonone

first: Aline

middle: P

last: Pansani

first: Alexandre

last: Silva

first: Fulvio

last: Scorza

first: Esper

last: Cavalheiro


title: An Integrated Analysis of Molecular Acclimation to High Light in the Marine Diatom Phaeodactylum tricornutum

status: Public on Nov 06 2009

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to adapt their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate the mechanisms of high light acclimation in Phaeodactylum tricornutum using an integrated approach involving global transcriptional profiling, metabolite profiling and variable fluorescence technique. Algae cultures were acclimated to low light (LL), after which the cultures were transferred to high light (HL). Molecular, metabolic and physiological responses were studied at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to HL conditions. The integrated results indicate that the acclimation mechanisms in diatoms can be divided into an initial response phase (0.5 h), an intermediate acclimation phase (3-12 h) and a late acclimation phase (12-48 h). The initial phase is recognized by strong and rapid regulation of genes encoding proteins involved in photosynthesis, pigment metabolism and reactive oxygen species (ROS) scavenging systems. A significant increase in light protecting metabolites occur together with the induction of transcriptional processes involved in protection of cellular structures at this early phase. During the following phases, the metabolite profiling display a pronounced decrease in light harvesting pigments, whereas the variable fluorescence measurements show that the photosynthetic capacity increases strongly during the late acclimation phase. We show that P. tricornutum is capable of swift and efficient execution of photoprotective mechanisms, followed by changes in the composition of the photosynthetic machinery that enable the diatoms to utilize the excess energy available in HL. Central molecular players in light protection and acclimation to high irradiances have been identified.

overall_design: The experiment was designed as a time series, with diatom cultures were harvested at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to high light conditions. The reference samples were kept at low light and harvested in parallel with the treated samples. Three biological replicates were harvested for all samples.

first: Marianne

last: Nymark

first: Kristin

last: Valle

first: Tore

last: Brembu

first: Kasper

last: Hancke

first: Kjersti

last: Andresen

first: Geir

last: Johnsen

first: Atle

last: Bones


title: Analysis of SDC-2, DPY-26, MIX-1, DPY-27 and RNA Polymerase II ChIP-chip and RNA abundance in C. elegans

status: Public on Nov 16 2009

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: 408 Fordham Hall, CB# 3280

department: Biology

institute: University of North Carolina at Chapel Hill

summary:
In C. elegans, a condensin-like protein complex associates specifically with both X chromosomes of XX animals to execute dosage compensation. Dosage Compensation Complex (DCC) reduces the level of transcripts arising from each of the two X chromosomes. Recruitment to X is specified in part by discrete DNA sequence motifs, but following recruitment, the DCC is targeted to the promoters of individual active genes by an unknown mechanism. Here, we investigated three outstanding questions regarding the molecular mechanism of DCC recruitment and spreading along X. By examining the genome-wide binding patterns of several DCC subunits in different stages of C. elegans development, and in strains harboring X:Autosome chromosomal fusions, we provide evidence that: (1) DCC binding is dynamically specified according to gene activity during development (2) The condensin-like subunits of the DCC spread from recruitment sites to active promoters more readily than the non-conserved SDC subunits, which are involved in initial X-targeting and (3) the mechanism of DCC spreading is independent of X-chromosome DNA sequence, and will proceed onto any active promoter near a recruitment site. Our results contribute to understanding how chromatin complexes can be targeted to achieve domain-scale transcriptional regulation during development.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: ChIP-chip analysis of SDC-2, DPY-26 and MIX-1 were done in C elegans N2 embryos. DPY-27 and RNA Polymerase II ChIP-chip were performed in N2 L4s. DPY-27 ChIP-chip in X-autosome fusions were done, X chromosome fused to either V (YPT47), II (YPT41) or I (11dh). RNA abundance analysis in N2, YPT41 and YPT47 embryos are included.

first: Sevinc

last: Ercan

first: Lindsay

middle: L

last: Dick


title: Transcriptional profile analysis of Candida dubliniensis chlamydospores compared to yeast cells

status: Public on Sep 01 2010

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

summary: In order to investigate the biology of chlamydospores, we compared global gene expression in C. dubliniensis yeast cells and chlamydospores.  This revealed that 11% of the genes greater than 2-fold upregulated in chlamydospores were genes regulated by the transcriptional repressor Nrg1. These mainly included genes involved in glucose metabolism and glucose transport. Other upregulated genes included genes involved in stress response, cell cycle control, chromatin regulation, chromosome rearrangements, DNA repair-recombination and pheromone response. Genes related to mitochondrial respiratory functions and biogenesis were found to be downregulated in chlamydospores. Our data confirm that chlamydospores represent a specialised growth form of C. albicans and C. dubliniensis.

overall_design: 2 experimental parameters were analysed (chlamydospores, yeast cells). Three biological replicates each, one technical replicate.

first: Francesco

last: Citiulo

first: Derek

last: Sullivan


title: Whole genome microarray of the retina reveals a progressive response with increasing duration of diabetes.

status: Public on Jun 11 2008

first: Penn State

last: COM

summary:
Using the streptozotocin-induced rat model of diabetes, levels of retinal
permeability, caspase activity, and gene expression were examined after 1 and 3 months of diabetes.
Gene expression changes were identified by whole genome microarray and confirmed by qPCR in the same set of animals as used in the microarray analyses and subsequently validated in independent sets of animals.  Significantly more and larger magnitude gene expression changes were observed after 3 months than after 1 month of diabetes.

overall_design:
Time course study using the streptozotocin-induced rat model of diabetes.
Selected time-points were 1M and 3M post-STZ injection with corresponding age-related controls, total 4 groups.  All groups contain n = 6 biological replicates.

first: Robert

last: Brucklacher

first: Kruti

last: Patel

first: Heather

last: VanGuilder

first: Georgina

last: Bixler

first: Alistair

last: Barber

first: David

last: Antonetti

first: Cheng-Mao

last: Lin

first: Kathryn

middle: F

last: LaNoue

first: Thomas

middle: W

last: Gardner

first: Sarah

last: Bronson

first: Willard

last: Freeman


title: Effer/Affer Interaction in Vestibular Caliceal vs. Dimorphic and Bouton Primary Afferent Neurons

status: Public on Apr 01 2006

city: Milwaukee

first: Ashley

last: Wackym

state: WI

address: 9200 W. Wisconsin Ave

department: Otolaryngology

institute: Medical College of Wisconsin

summary:
The functional diversity of neuropeptides and/or their receptors may provide a complex means to modulate vestibular primary afferent neuronal function.  The precise role of these neuropeptides in the physiology of the vestibular neuroepithelium is poorly understood.  The vestibular caliceal afferent neurons when compared to the dimorphic and bouton afferent neurons have different functional properties.  Immunofluorescent laser capture microdissection utilizing calretinin (calbindin 2, Calb2) antibodies allowed selective acquisition of these two primary afferent neuronal populations from the rat (Rattus norvegicus).  After capturing the caliceal afferent neurons, as well as the dimorphic and bouton afferent neurons, microarray expression profiling was completed.  Analysis of the resulting data revealed that there were 732 genes involved in synaptic/signaling, calcium binding/solute transport, and other.  Of those genes, 52 were related to afferent modulation, including 21 genes representing neuropeptides or their receptors.  The observed expression of 52 genes related to afferent modulation identified using microarray were confirmed using PCR from the Wackym-Soares normalized rat vestibular periphery cDNA library or by RT-PCR from fresh ganglia tissue.  The majority of the neuropeptides and/or receptors were found to be expressed in both groups, although there were neuropeptides and/or receptors that were unique to the dimorphic and bouton afferent neuron pool.  The expression of selected neuropeptides or their receptors was confirmed using immunohistochemistry in the crista ampullares.  Our results suggest that the unexpected neuropeptide diversity and their differences in expression pattern could serve unique roles in the physiology of the vestibular neuroepithelium.
Keywords: expression profiling, neuropeptides, vestibular neuroepithelium, calretinin

overall_design: Pooled Immunoflourescent guided laser capture microdisection of calyceal vestibular primary afferent neurons (calretinin positive) and dimorphic-bouton vestibular primary afferent neurons (calretinin negative)were used for microarray expression profiling.  Transcription analysis of each of these biological diverse pools was completed.

first: P

first: Paul

last: Popper

first: Ricardo

last: Cristobal

first: Joseph

last: Cioffi

first: Anne

last: Kwitek

first: Christy

last: Erbe

first: Tina

last: Samuels

first: Wolfgang

last: Siebeneich


title: Analysis of non-coding RNAs in drn1∆ deletion strains

status: Public on Dec 31 2009

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: The turnover of introns spliced from pre-mRNA occurs first by debranching the lariat intron followed by destruction of the linear intron by other nucleases.  We have identified a novel component of intron turnover, DRN1 (YGR093W).  In order to identify RNAs affected by Drn1 turnover, we used a microarray containing probes specific to ~400 yeast non-coding RNAs to analyze a strain deleted for Drn1.  These data implicated Drn1 in the turnover of a number of introns spliced from ribosomal-protein genes.

overall_design: Two-color experiment with biological replicate and dye swap.

first: Stanley

last: Fields


title: Silicon metabolism in diatoms

status: Public on Sep 29 2009

city: Paris

first: Laurent

last: Jourdren

address: 46 rue d'Ulm

department: Biologie

country: France

institute: École Normale Supérieure

summary:
We investigated the effects of extracellular silicic acid on the whole Phaeodactylum triconutum transcriptome. In this work, global transcription analyses were combined with comparative studies of other elements, and detailed analyses of the silicon transporters. Our results provide insight on Si-sensing genes and further extend current models for Si uptake.

Keywords: Comparative transcriptome analyses from Phaeodactylum triconutum fusiform cells acclimated in a Si-free or silicic acid medium.

overall_design: Three biological samples in dye swap

first: Guillaume

last: Sapriel

first: Michelle

last: Quinet

first: Marc

last: Heijde

first: Véronique

last: Tanty

first: Stéphane

last: Le Crom

first: Pascal

last: Lopez


title: Comparison of gene expression differences between Caenorhabditis elegans grown in liquid culture versus on plates

status: Public on May 04 2010

first: Christina

middle: M

last: Whittle

address: 406 Fordham Hall, CB#3280

institute: University of North Carolina-Chapel Hill

summary:
The two major methods for growing C. elegans are liquid and plate culture. Differences in oxygenation and other environmental variables could affect many experimentally relevant biological processes, such as metabolism, cellular structure, and gene regulation. Worms on solid support move with deliberate sinusoidal movements, while worms in liquid thrash rapidly and almost constantly, often appearing elongated. We investigated differential gene expression under these two commonly used growth conditions.

Embryos were isolated from adults grown on plates. After hatching, animals were placed either on plates or in liquid under standard conditions, and grown until young adulthood, approximately 48 hours later.  RNA was isolated independently from each growth, differentially labeled with a fluorescent dye, and mixed directly for comparative hybridization to NimbleGen DNA microarrays, which contained probes designed to measure expression from all predicted C. elegans coding genes. The experiment was performed in triplicate. Analysis of the expression data yielded surprisingly few genes with differential expression, about 1%.  Overall, 176 genes were downregulated significantly (p<0.01; Student's t) in liquid culture relative to plates, but of these only 102 genes were down two-fold or more. A total of 121 genes were upregulated (p<0.01. Student's t) in liquid; of these, RNA corresponding to 50 increased by at least two-fold.

Surprisingly few genes directly associated with a stress response were differentially regulated in this experiment.  However, the single gene most strongly upregulated in liquid is nnt-1, which encodes a mitochondrial NADP transhydrogenase, which protects against oxidative stress (Arkbladt et al., 2005 PMID: 15890626).  Other molecules associated with reducing oxidation are also upregulated in liquid culture, including thioredoxin, and two glutathione-S-transferases. As a class, however, the group of genes most differentially regulated encode collagens. A total of 12 collagen genes were downregulated in liquid culture relative to plates, while none are upregulated. Other genes affected include those encoding proteins involved in ubiquitin-mediated proteolysis, Ras signaling, transcriptional regulation, ribosome function, and multiple membrane-associated proteins.

The limited changes in relative RNA levels under different culture conditions provide increased confidence in comparisons made between worms grown in liquid and solid culture, and more generally between datasets obtained in different labs under slightly different culture conditions. Knowing which genes are most responsive to different culture conditions inform us about how environment affects the animal, and should be of interest for comparison to other stress and longevity global datasets.

overall_design: Total RNA was extracted from young adult hermaphrodite C. elegans grown either in s-basal liquid cultures or nematode growth medium plates under standard conditions.

first: Valerie

last: Reinke

first: Frederick

middle: G

last: Mann

first: Jason

last: Lieb


title: Trophic Factor Gene Expression in Supporting Cells of the Crista Ampullaris:Implications for Hair Cell Regeneration

status: Public on Nov 27 2007

first: Ashley

last: Wackym

summary:
Current global gene expression techniques allow the evaluation and comparison of the expression of thousands of genes in a single experiment, providing a tremendous amount of information. However, the data generated by these techniques are context-dependent, and minor differences in the individual biological samples, methodologies for RNA acquisition, amplification, hybridization protocol and gene chip preparation, as well as hardware and analysis software, lead to poor correlation between the results. In the inner ear the acquisition of RNA from individual cell populations remains a challenge due to the high density of the different cell types and the paucity of tissue. Consequently laser capture microdissection was used to selectively collect individual cells and regions of cells from cristae ampullares followed by extraction of total RNA and amplification to amounts sufficient for high throughput analysis. To demonstrate hair cell specific gene expression, myosin VIIA, calmodulin, and alpha9 nicotinic acetylcholine receptor subunit mRNAs were amplified using RT-PCR. To demonstrate supporting cell specific gene expression, cyclin-dependent kinase inhibitor p2kip1 mRNA was amplified using RT-PCR.  Subsequent experiments with alpha9 RT-PCR demonstrated phenotypic differences between type I and type II hair cells, with expression only in type II hair cells. Using the laser capture microdissection technique, microarray expression profiling demonstrated 408 genes with more than a five-fold difference in expression between the hair cells and supporting cells, of these 15 were well annotated. There were 9 annotated genes with greater than a five-fold expression difference in the hair cells relative to the supporting cells, and 8 annotated genes with greater than a five-fold expression difference in the supporting cells relative to the hair cells.
Keywords: hair cell specific gene expression, laser capture microdissection

overall_design: Using laser capture microdisection, the more superficial layer of the cristae ampullaris sensory epithelium encompassing types I and II hair cells, and the supporting cell cytoplasm interspersed between them was captured in the first pass, and the underlying supporting cell bodies resting on the basal lamina were captured in a second pass.  Individual hair cells were identified under light microscopy at 200X magnification by their stereociliary tuft and the calyceal nerve ending surrounding them and the presence of their nucleus in the outermost portion of the epithelia.

first: Ricardo

last: Cristobal

first: PA

first: Joseph

last: Cioffi

first: Paul

last: Popper


title: Distinctive gene expression patterns in gastrointestinal stromal tumors identified with cDNA arrays

status: Public on Apr 10 2003

city: Heidelberg

first: Wolfgang

last: Huber

address: Im Neuenheimer Feld 280

department: Molecular Genome Analysis

country: Germany

institute: German Cancer Research Center

summary:
Gastrointestinal stromal tumors (GIST) are phenotypically and clinically heterogeneous mesenchymal tumors. Using the cDNA array technique, we analyzed the gene expression profiles of 22 GIST and 7 non-neoplastic gastrointestinal smooth muscle specimens, in order to detect molecular differences between GIST and non-neoplastic tissue, and to detect differences between GIST of various phenotypic and clinical subgroups. As a result, we found 796 differentially expressed genes and ESTs between GIST and smooth muscle tissue, including promising new candidate genes for the pathogenesis of GIST. Furthermore, we identified differences in gene expression between GIST of different site, size, and immunohistochemical expression of CD34 and SMA. Our data show that alterations in gene expression are associated with morphologically and clinically detectable features of GIST and provide new aspects for the understanding of these tumors.
Keywords = Gastrointestinal Stromal Tumor (GIST)
Keywords: other

first: F

last: Bergmann

first: A

last: von Heydebreck

first: W

last: Buness

first: J

last: Höer

first: C

last: Langer

first: B

last: Gunawan

first: L

last: Füzesi

last: Poustka

first: H

last: Sültmann


title: Thiamine supplementation prevents obesity and obesity-associated metabolic disorders in OLETF rats.

status: Public on Dec 07 2009

city: Takatsuki

first: Takao

last: Tanaka

state: Osaka

address: 4-20-1 Nasahara

country: Japan

institute: Osaka University of Pharmaceutical Sciences

summary: Thiamine prevents diabetic complications, and its deficiency, resulting from mutation of thiamine transporter gene SLC19A2 has been linked to diabetes mellitus. We previously found that thiamine mitigates metabolic disorders in spontaneous hypertensive rats, harboring defects in glucose and fatty acid metabolism. The current study extends our hypothesis that that thiamine intervention may impact metabolic abnormalities in polyphagia-induced Otsuka Long-Evans Tokushima Fatty (OLETF) rats that lack functional cholecystokinin A receptors. Male OLETF rats exhibit progressive obesity and metabolic disorders similar to human metabolic syndrome. Male OLETF rats (4-week-old) were given free access to water containing either 0.2 % or 0 % of thiamine for 51 weeks. At the end of treatment, blood parameters and cardiac functions were analyzed. After sacrifice, the organs were removed and weights of organs and histological findings were evaluated. In addition, differential gene expression in the liver was analyzed. Thiamine intervention averted obesity, mainly resulting from reduction of visceral adiposity, and prevented metabolic disorders in OLETF rats. Histological evaluation revealed that thiamine alleviated adipocyte hypertrophy, steatosis in the liver, heart, and skeletal muscle, interstitial fibrosis in the heart and kidney, fatty degeneration in the pancreas, thickening of the basement membrane of vasculature, and glomerulopathy and mononuclear cell infiltration in the kidney. Cardiac and renal functions were preserved in thiamine treatment. Seventy-six genes showed at least two-fold difference in hepatic expression with thiamine treatment. Several of them participated in carbohydrate metabolism (Hk1, Pygb, Slc2a8, Rtn4, Rhbdl1, and Tspan8), lipid metabolism (Pla2g15, Por, and Lmf1), vascular physiology (S1pr1, Epha8, Rtn4, Slc7a13, Cdh15, Itga9, Cd151, Cd40lg, Nid1 and Lamb1), and carcinogenesis (Lmo7, Fgfr3, and Dmbt1). Modification of transcript expression well accorded with the findings of blood parameters and organ morphologies. Thiamine prevented polyphagia-induced obesity and metabolic and functional disorders in OLETF rats.

overall_design: The control and treated rats were sacrificed at 55 weeks of age (thiamine treatments for 51 weeks; n = 8 per group). After 16 h of fasting, a rat was anesthetized with pentobarbital (50 mg/Kg), and an indwelling catheter was inserted in the right carotid artery. From exsanguinated animals, samples of liver were removed, and rinsed in ice-cold saline. Parts of liver were placed in RNAlater® (Ambion, Austin, TX) and stored at -80 deg C, until further analysis. Individual samples were run on separate microarrays (n = 2, for each thiamine-treated and control groups); no samples were pooled.

first: Tatsuji

last: Kono

first: Fumio

last: Terasaki


title: Mutator transposon activity alters the transcriptome and proteome of developing maize anthers

status: Public on May 01 2009

city: Stanford

first: John

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
MuDR/Mu are a highly active transposon family moving by either cut only (or cut-and-paste) in strictly somatic tissues or net replicative transposition (absence of excision alleles) in reproductive tissues. Aside from the
MuDR-encoded MURA and MURB proteins, other factors required for Mu transposition, particularly those contributing to the developmentally specific behavior, have yet to be identified. To address this question and assess
the impact of a highly active transposon on the transcriptome, RNA was extracted from anthers at three developmental stages in Mu-active and -inactive stocks and compared on a 44,000 element oligonucleotide array.
We found that approximately 30,000 unique genes are expressed at each stage. Of the ~10% (ca. 3000) differentially regulated transcripts per stage, there was approximately equal representation by the active or inactive individuals.

Keywords: anther development, maize, Mu, transposon

overall_design: Dye swap design with 4 replicates comparing Mu-active to -inactive lines at 3 anther stages.  Spike-in controls were included.

first: David

middle: S

last: Skibbe

first: Virginia

last: Walbot