title: Selective engagement of plasticity mechanisms for motor memory storage

status: Public on Oct 04 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Thirty-five adult (8-16 week old) C57BL/6 mice (which had undergone previous behavioral protocols) were anesthetized with isoflurane, and the brains were removed quickly, embedded in OCT, and frozen in a dry ice-ethanol mixture. The interval between decapitation and complete freezing was always less than 3 minutes. The brain was warmed up to -20oC, and cut into 10-14 m sections with a cryostat (Leica). Serial coronal sections were kept on slides in 100% ethanol until sectioning was complete. Tissue was then processed with hematoxylin and eosin (H&E) staining for cell layer visualization, followed by dehydration with increasing concentrations of ethanol and then xylene. We focused on two cell types, the Purkinje (Pk) and granule cells (gc) of the flocculus. We used an Arcturus PixCell II laser capture microdissection (LCM) scope to locate and capture cells from the appropriate areas, obtaining ten samples per cell type per mouse. We estimate that each Pk sample contained about 50-100 Purkinje cells, and each gc sample contained a few thousand granule cells. Granule cell samples (dorsal flocculus) were captured before Purkinje cell samples, to reduce contamination of the Purkinje cell samples by granule cell material. Samples were removed from the LCM caps with RNEasy lysis buffer (Qiagen) containing 1% -mercaptoethanol, then frozen at -80oC. For each mouse, all the samples of a given cell type were pooled together; samples from different mice were not pooled. Total RNA samples were isolated using RNEasy kits (Qiagen), then amplified in two rounds of in vitro transcription (IVT) using the Ambion MessageAmp aRNA kit. IVT-amplified samples were hybridized to microarrays if the end product after the second round of amplification was of concentration greater than or equal to 0.2 g/l, and at least 10 times the negative control signal (measured after two rounds of amplification of a blank sample). Due to the small starting sample sizes, samples often were rejected due to insufficient quantity for hybridization: thus, 18/35 granule cell samples and 23/35 Purkinje cell samples survived this quality control process, and were run on arrays (41 arrays total). Mus musculus spotted cDNA microarrays (MM arrays) containing ~42,000 spots were obtained from the Stanford Functional Genomics facility (complete information at http://www.microarray.org/), in order to analyze gene expression in each cell type. We used a type II experimental design, where all experimental samples were hybridized against a common reference sample for multi-way comparison. The reference sample comprised mRNA extracted from neonatal and adult brain and liver, and amplified twice by IVT. We used standard protocols for cDNA labeling, as well as array hybridization, washing, scanning, and data analysis (http://cmgm.stanford.edu/pbrown/protocols/index.html).
A cell type comparison design experiment design type compares cells of different type for example different cell lines.
Keywords: cell_type_comparison_design

overall_design: Using regression correlation


title: Stress-related gene expression of HK-2 cells exposed to GF/FAF HSA, GF HSA, or AngII

status: Public on Jun 28 2007

city: Liverpool

first: Rana

last: Rustom

address: Duncan Street

department: Metabolic and Cellular Medicine

country: United Kingdom

institute: University of Liverpool

summary:
Atlas Human Stress Arrays with 234 stress-related genes immobilised on nylon membranes (Clontech, UK) were used to identify the changes in mRNA expression in human proximal tubular HK-2 cells in response to HSA overload or AngII.
Keywords: Stress response

overall_design: Immortalised human proximal renal tubular epithelial HK-2 cells were growth arrested for 48 h in serum-free medium (SFM) without added growth factors. Prior to RNA isolation, cells were exposed for 24 h to 30 mg/ml of globulin-free fatty acid-free (GF/FAF) human serum albumin, globulin-free human serum albumin with attached fatty acids (GF) or 1 uM AngII in SFM. In order to minimize the number of false positives and negatives in mRNA expression equal amounts of total RNA from 3 separate experiments were pooled together.

first: Francis

last: McArdle

first: Liliana

middle: D

last: Shalamanova


title: To study the genomic changes in senescent porcine coronary arterial endothelial cells by multiple passaging in vitro

status: Public on Sep 08 2007

city: Hong Kong

first: Mary

last: Lee

address: 21 Sassoon Road

department: Dept of Pharmacology

country: China

institute: The University of Hong Kong

summary:
Nitric oxide helps to prevent endothelial dysfunction and senescence. This study aimed to define genomic and proteomic changes in cultured porcine senescent endothelial cells and their resemblance with those observed in regenerated endothelial cells. Senescent endothelial cells were produced by passaging primary porcine coronary arterial endothelial cells until passage four. The protein presence of endothelial nitric oxide synthase, cyclic GMP levels [basal and during stimulation (bradykinin and A23187)], were reduced. The mRNA expression level was measured by microarray assays. Genes related to oxidative stress [superoxide dismutase (MnSOD), glutathione peroxidase 3, glutathione S-transferase M1] were downregulated, extracellular matrix components (type III collagen, thrombospondin 1 and 3, transforming growth factor beta) upregulated and nuclear factor kappa B (NFKB)-signaling pathway [IkappaB, TNF receptor-associated factor 1 and 5 (TRAF1 and 5)] activated in senescent cells. The differential gene expression of MnSOD and TRAF5 was confirmed at the protein level by Western blotting and biochemical assay (MnSOD). The basal and stimulated (by tumor necrosis factor-alpha) levels of NFKB were augmented as demonstrated by electrophoretic mobility shift assay. In summary, cultured senescent endothelial cells exhibit reduced nitric oxide production, and decreased antioxidative, proliferative capacities, augmented expression of extracellular matrix components and activation of NFKB. These molecular changes do not exactly mimick those occurring during endothelial regeneration in vivo.
Keywords: disease state comparison

overall_design: Totally 9 samples were analyzed with 3 replicates for each treatment group.

middle: Y


title: RNA affinity isolation with TAP-Pum and controls

status: Public on Feb 28 2006

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

summary:
Biochemical purification: Five grams of adult flies or 2.5 g of embryos were used in each affinity purification. Flies or embryos were suspended in 15 ml of buffer B (buffer A plus 1.5 mM dithiothreitol [DTT], 1 mM phenylmethylsulfonylfluoride [PMSF], 0.5 5g/ml leupeptin, 0.8 5g/ml pepstatin, 20 U/ml DNase I, 100 U/ml RNasin [Promega], and 0.2 mg/ml heparin) in a mortar filled with liquid nitrogen and ground with a pestle to a fine powder. The powder was transferred to a glass-dounce, thawed and dounced until the pestle reached the bottom. The suspension was centrifuged twice at 40C and 10,000 g for 10 min. The fat layer on top was aspirated off after each centrifugation. Cleared extract (12.5 ml) was incubated with 600 5l of a slurry (50% [v/v]) of IgG-agarose beads (Sigma) for 90 min at 4C. The beads were washed once with buffer B for 15 min at 4C, and three times for 15 min at 4C with buffer C (20 mM TrisHCl [pH 8.0], 150 mM NaCl, 1 mM EDTA [pH 8.0], 10% glycerol, 0.01% NP-40, 1 mM DTT, 10 U/ml RNasin). PumHD was released from beads by incubation with 150 Units of AcTEV protease (Invitrogen) for 2 hr at room temperature (RT). RNA was isolated from extracts and from the TEV eluates with TRIZOL reagent (Invitrogen) followed by RNeasy Mini-Kit (Qiagen) purification according to the manufacturer's instructions.
Microarray analysis: A pool of four control cDNAs (2 ng of each flp, gal4, lacZ and -Gal) was added to each RNA sample prior to labeling as controls for the labeling procedure. Total RNA (12 5g) derived from the extract and 300 ng or 30% of the affinity-isolated RNA were labeled with Cy3 and Cy5 fluorescent dyes, respectively, following cDNA synthesis with amino-allyl dUTP in addition to the four natural dNTPs using a 1:1 mixture of oligo(dT) and random nonamer primers. The Cy3- and Cy5-labeled cDNA samples were mixed and hybridized to Drosophila DNA microarrays.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: RNA IP


title: Expression data from non-infected and Salmonella Typhimurium infected mesenteric lymph nodes

status: Public on Jun 01 2007

city: Ames

first: Christopher

middle: K

last: Tuggle

state: IA

address: 2255 Kildee Hall

department: Animal Science

country: USA

institute: Iowa State University

summary:
A first generation Affymetrix GeneChip® Porcine genome array was used to profile the gene expression in porcine mesenteric lymph nodes over a time course of infection with S. Typhimurium, including the acute (8 hours post inoculation (hpi), 24 hpi, 48 hpi) and chronic (21 days post-inoculation (dpi)) stages of infection. Our objectives were to 1) identify and examine the stereotypical gene expression response within host MLN to S. Typhimurium infection, 2) characterize global host responses by revealing the specific features of the host’s innate immunity pathways, and 3) explore if and how S. Typhimurium may escape the host immune response and develop into a carrier state.
Our study has attempted to investigate the features of host gene expression profiling during S. Typhimurium infection at the acute and chronic infection stages and to explore the mechanism by which S. Typhimurium can escape from the host immune response and develop a carrier state in the host. In conclusion, by using the Affymetrix porcine GeneChip, 848 differentially expressed genes were identified in porcine MLN during infection and several specific features of host response were revealed by gene cluster and pathway analysis. Our data are the first report to investigate global host responses to S. Typhimurium in porcine MLN, and this new study provides data applicable for studying enteric salmonellosis of pigs, as well as humans.
Keywords: time course

overall_design: Fifteen piglets from Salmonella spp.-free sows were weaned at 10 days (d) of age, shipped to the National Animal Disease Center, Ames, IA and raised in isolation facilities. To confirm that all piglets were free of Salmonella spp. prior to challenge, bacteriological cultures were performed on rectal swabs twice. Seven week old pigs were randomly divided into 2 groups, 3 non-infected pigs and 12 infected pigs. Three non-infected control pigs were necropsied 2 days prior to experimental infection. On day 0, pigs in the infected groups were intranasally challenged with 1 billion CFU of Salmonella enterica serovar Typhimurium. Three infected pigs were necropsied at 8 hours post-inoculation (hpi), 24 hpi, 48 hpi and 21 days post-inoculation (dpi). Tissue samples from the mesenteric lymph nodes (MLN) were collected and immediately frozen in liquid nitrogen for RNA isolation.

first: Yanfang

last: Wang

first: Long

last: Qu

first: Jolita

middle: J

last: Uthe

first: Shawn

middle: M

last: Bearson

first: Daniel

last: Kuhar

first: Joan

last: Lunney

first: Oliver

middle: P

last: Couture

first: Dan

last: Nettleton

first: Jack

middle: C

last: Dekkers


title: Antiangiogenic Antithrombin

status: Public on Dec 31 2005

state: CA

summary:
Confluent passage-2 HUVECs in Falcon T12.5 flasks grown in the presence or absence of VEGF-165 (10ng/mL) (R&D systems) were treated with human native, cleaved or latent antithrombins (20 5g/mL) for 24 hours in 3 mL M-199 with 2% heat-inactivated FBS and antibiotics. Following this treatment, total RNA was extracted from the cells by the Trizol method (Invitrogen). The total RNA was subjected to one cycle of linear RNA amplification using the MessageAmp aRNA kit according to the manufacturers instructions (Ambion, Austin, TX). The quality of the antisense RNA was verified on a denaturing agarose gel. Only samples showing a distribution of sizes from 250-5500 nt with a peak centered at 1000-1500 nt were used to generate the test cDNA samples for the subsequent array experiments. DNA labeling and hybridizations were performed essentially as described (Pollack et al., 1999, Nat. Genet.), with slight modifications. Briefly, the test endothelial cell antisense RNA samples together with Universal Human Reference RNA (Stratagene, Cedar Creek, TX) were used to generate Cy3/Cy5 (Amersham Biosciences) labeled cDNA for array hybridization on the Stanford 43K human cDNA microarray (www.microarray.org/sfgf). The Stanford microarray used in this study consists of 18,416 named genes with UniGene symbol, 4,145 ESTs with known function, 19,365 ESTs with unknown function and ~1,000 repeated spots as internal controls. Hybridized arrays were scanned on a GenePix 4000B scanner (Axon Instruments), and fluorescence ratios (test/reference) calculated using the Stanford Microarray Database software (available at http://genomewww5.
A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment
Keywords: Computed


title: Transcriptional profiling of the protein phosphatase 2C family in yeast

status: Public on Jan 24 2007

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

summary:
Type 2C protein phosphatases are encoded in Saccharomyces cerevisiae by several related genes (PTC1-5 and PTC7). To gain insight into the functions attributable to specific members of this gene family, we have investigated the transcriptional profiles of ptc1-5 mutants. Two main patterns were obtained as follows: the one generated by the ptc1 mutation and the one resulting from the lack of Ptc2-5. ptc4 and ptc5 profiles were quite similar, whereas that of ptc2 was less related to this group. Mutation of PTC1 resulted in increased expression of numerous genes that are also induced by cell wall damage, such as YKL161c, SED1, or CRH1, as well as in higher amounts of active Slt2 mitogen-activated protein kinase, indicating that lack of the phosphatase activates the cell wall integrity pathway. ptc1 cells were even more sensitive than slt2 mutants to a number of cell wall-damaging agents, and both mutations had additive effects. The sensitivity of ptc1 cells was not dependent on Hog1. Besides these phenotypes, we observed that calcineurin was hyperactivated in ptc1 cells, which were also highly sensitive to calcium ions, heavy metals, and alkaline pH, and exhibited a random haploid budding pattern. Remarkably, many of these traits are found in certain mutants with impaired vacuolar function. As ptc1 cells also display fragmented vacuoles, we hypothesized that lack of Ptc1 would primarily cause vacuolar malfunction, from which other phenotypes would derive. In agreement with this scenario, overexpression of VPS73, a gene of unknown function involved in vacuolar protein sorting, largely rescues not only vacuolar fragmentation but also sensitivity to cell wall damage, high calcium, alkaline pH, as well as other ptc1-specific phenotypes.
Keywords: yeast, type 2C protein phosphatases, mutant strains, transcriptional profiles

overall_design:
6 samples were analyzed: wt, ptc1, ptc2, ptc3 ptc4 and ptc5 mutant strains.
We compared the expression profile of each ptc mutant with that of the wt: ptc1 vs wt; ptc2 vs wt; ptc3 vs wt; ptc4 vs wt and ptc5 vs wt.
A Dye-swap was carried out for each RNA sample.
Total number of chips analyzed: 10

first: Asier

last: Gonzales

first: Amparo

last: Ruiz

first: Raquel

last: Serrano

first: Joaquin

last: Arino


title: Simultaneous activation of heat shock and oxidative stress pathways by celastrol

status: Public on Aug 26 2006

city: Houston

first: Kevin

middle: A

last: Morano

state: TX

address: 6431 Fannin St, MSB 1.300

department: Microbiology and Molecular Genetics

institute: UT Medical School at Houston

summary:
Stress response pathways allow cells to rapidly sense and respond to deleterious environmental changes, including those caused by pathophysiological disease states. A previous screen for small molecules capable of activating the human heat shock response identified the triterpenoid celastrol as a potent activator of the heat shock transcription factor HSF1. We show here that celastrol likewise activates the homologous Hsf1 of Saccharomyces cerevisiae. Celastrol induced Hsf1 hyperphosphorylation and concurrently activated a synthetic transcriptional reporter as well as endogenous inducible Hsp70 proteins at the same effective concentration seen in mammalian cells. Moreover, celastrol treatment conferred significant resistance to subsequent lethal heat shock. Transcriptional profiling experiments revealed that in addition to Hsf1, celastrol treatment induced the Yap1-dependent oxidant defense regulon. Oxidative stress-responsive genes were likewise induced in mammalian cells, demonstrating that celastrol simultaneously activates two major cellular stress-mediating pathways.  As the induction of cellular stress pathways has implications in the treatment of a variety of human diseases including neurodegenerative diosorders, cardiovascular disease and cancer, celastrol thus represents an attractive therapeutic compound.
Keywords: single-dose, single time-point gene induction by natural small molecule celastrol compared to heat shock in wild type (BY4741) Saccahromyces cerevisiae

overall_design: Two heat shock experiments and two drug treatment experiments were conducted and analyzed independently.  Heat shock arrays are 39 vs. 30 degrees for 30 min, and drug (celastrol) arrays are 10 µM celastrol in DMSO over DMSO alone, same volumes.  Expression numbers are duplicated and averaged on each chip, normalized to the median signal of all hybridizations on the chip.

first: Amy

last: Trott

first: Lada

last: Klaic

first: James

last: West

first: Sandy

last: Westerheide

first: Richard

middle: B

last: Silverman

middle: I

last: Morimoto


title: Genomic Analysis of the Xenopus Organizer

status: Public on Jun 30 2006

first: Andrew

middle: Lee

last: Hufton

address: 300 Pasteur Dr., Alway Bldg, Rm M313

department: Genetics

institute: Stanford

summary:
Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation.  Here, we use this wealth of knowledge as leverage in the design and analysis of a genomic visualization of organizer-related gene transcription.  Using ectopic expression of the two major activities of the organizer, BMP and Wnt inhibition, as well as endogenous tissues, we generate a focused set of samples that represent different aspects of organizer signaling.  The genomic expression values of each sample are then measured with oligonucleotide arrays.  From this data, genes regulated by organizer signaling are selected and then clustered by their patterns of regulation.  A new GO biological process annotation of the Xenopus genome allows us to rapidly identify clusters that are highly enriched for known gastrula patterning genes.  Within these clusters, we can predict the expression patterns of unknown genes with remarkable accuracy, leading to the discovery of new organizer-related gastrula stage expression patterns for 19 genes.  Moreover, the patterns of gene response observed within these clusters allow us to parse apart the contributions of BMP and Wnt inhibition in organizer function.  We find that the majority of gastrula patterning genes respond transcriptionally to these activities according to only a few stereotyped patterns, allowing us to describe suites of genes that are likely to share similar regulatory mechanisms.  These suites of genes demonstrate a mechanism where BMP inhibition initiates the organizer program before gastrulation, and Wnt inhibition maintains and drives the organizer program during gastrulation.
Keywords: development, organizer, noggin, dkk-1, xenopus, gastrulation

overall_design: In order to describe and separate the genomic expression changes induced by the two main organizing activities, BMP inhibition and Wnt inhibition, we created a panel of gastrula stage ventral tissues that ectopically overexpressed one or both of these activities, and compared these samples to endogenous dorsal and ventral gastrula stage tissue.  Two well-studied organizer secreted factors, Noggin and Dickkopf-1 (Dkk-1), were used to ectopically inhibit BMP and Wnt signaling, respectively.  Four different overexpression mixtures were injected ventrally into 4-cell embryos: noggin and eGFP (anti-BMP); noggin, dkk-1, and eGFP (anti-BMP and anti-Wnt); dkk-1 and eGFP (anti-Wnt); and eGFP alone.  eGFP mRNA was used to trace targeting.  Plasmid DNA was used for noggin and dkk-1 overexpression, instead of mRNA, in order to limit ectopic expression of these genes to post-MBT stages, more closely mimicking the endogenous regulation of these genes.  The ventrally injected embryos were grown to early stage 10, sorted for appropriately targeted eGFP florescence, and then bisected between the dorsal and ventral halves at either stage 10 (early gastrula) or stage 11.5 (late gastrula).  For the noggin and/or dkk-1 injected embryos, only the ventral halves of the embryos were saved, eliminating endogenous organizer tissues.  For the embryos injected with only eGFP, both the ventral and dorsal halves were saved, creating separate ventral and dorsal control conditions.  These five conditions were each generated twice at both stage 10 and 11.5, with each set of five samples coming from a single clutch of embryos, creating twenty total tissue samples from 4 different clutches.  For each batch of injections some sorted embryos were allowed to develop through tailbud stages in order to validate the phenotypes induced by our constructs.  Total RNA was then isolated from the twenty tissue samples and applied to Affymetrix oligonucleotide arrays.

middle: L

first: Arunachalam

last: Vinayagam

first: SÃndor

last: Suhai

first: Julie

last: Baker


title: Transcriptome architecture across tissues in the pig

status: Public on Apr 16 2008

city: Bellaterra

first: Miguel

last: Perez-Enciso

address: Veterinary School

institute: Universitat Autonoma Barcelona

summary:
Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask what are the relative contributions of breed or sex when assessed across tissues.
Are all tissues equally affected by breed or sex? How relevant is tissue in terms of total transcriptome variability?
Keywords: breeds, sex and tissues comparison

overall_design: In order to gain insight on these issues, we have microarrayed 16 different tissues hybridization on Affymetrix microarrays from four animals of the extreme pig breeds Large White and Iberian, two males and two females

first: Andre

last: Ferraz

first: Ana

last: Ojeda

first: Manel

last: López-Béjar

first: Lana

middle: T

last: Fernandes

first: Anna

last: Castelló

first: Josep

last: Folch

last: Pérez-Enciso


title: Paneth cell granule dissolution and bacterial colonization in the intestine of CF mice

status: Public on Jul 18 2005

city: Cincinnati

first: Lara

last: Gawenis

state: OH

institute: University of Cincinnati College of Medicine

summary:
Paneth cells of intestinal crypts contribute to host defense by producing antimicrobial peptides that are packaged as granules for secretion into the crypt lumen. Here, we provide evidence using light and electron microscopy that postsecretory Paneth cell granules undergo limited dissolution and accumulate within the intestinal crypts of cystic fibrosis (CF) mice. On the basis of this finding, we evaluated bacterial colonization and expression of two major constituents of Paneth cells, i.e., {alpha}-defensins (cryptdins) and lysozyme, in CF murine intestine. Paneth cell granules accumulated in intestinal crypt lumens in both untreated CF mice with impending intestinal obstruction and in CF mice treated with an osmotic laxative that prevented overt clinical symptoms and mucus accretion. Ultrastructure studies indicated little change in granule morphology within mucus casts, whereas granules in laxative-treated mice appear to undergo limited dissolution. Protein extracts from CF intestine had increased levels of processed cryptdins compared with those from wild-type (WT) littermates. Nonetheless, colonization with aerobic bacteria species was not diminished in the CF intestine and oral challenge with a cryptdin-sensitive enteric pathogen, Salmonella typhimurium, resulted in greater colonization of CF compared with WT intestine. Modest downregulation of cryptdin and lysozyme mRNA in CF intestine was shown by microarray analysis, real-time quantitative PCR, and Northern blot analysis. Based on these findings, we conclude that antimicrobial peptide activity in CF mouse intestine is compromised by inadequate dissolution of Paneth cell granules within the crypt lumens.
Keywords: other

overall_design: Total RNA was extracted from pooled small intestines of three WT and three CF mice using Tri-Reagent (Molecular Research Center, Cincinnati, OH), and poly(A) RNA was purified by using the MicroPoly(A) mRNA purification kit (Ambion, Austin, TX). The WT and CF poly(A) RNA samples were sent to IncyteGenomics (St. Louis, MO) where they were labeled with cyanine 3 (Cy3) and Cy5, respectively, and hybridized with the UniGEM1.31 array representing 9,570 known genes and expressed sequence tags.


title: Trans-acting regulatory variation in Saccharomyces cerevisiae

status: Public on Sep 03 2003

city: Seattle

first: Gael

last: Yvert

state: WA

institute: Fred Hutchinson Cancer Research Center

summary:
Natural genetic variation can cause significant differences in gene expression, but little is known about the polymorphisms that affect gene regulation. We analyzed regulatory variation in a cross between laboratory and wild strains of Saccharomyces cerevisiae. Clustering and linkage analysis defined groups of coregulated genes and the loci involved in their regulation. Most expression differences mapped to trans-acting loci. Positional cloning and functional assays showed that polymorphisms in GPA1 and AMN1 affect expression of genes involved in pheromone response and daughter cell separation, respectively. We also asked whether particular classes of genes were more likely to contain trans-regulatory polymorphisms. Notably, transcription factors showed no enrichment, and trans-regulatory variation seems to be broadly dispersed across classes of genes with different molecular functions
Keywords: other

first: G

first: R

last: Brem

first: J

last: Whittle

last: Akey

first: E

last: Foss

middle: N

last: Smith

last: Mackelprang

first: L

last: Kruglyak


title: Transcriptional profiling of stress-response in cultured porcine islets

status: Public on May 05 2006

city: Minneapolis

first: Bhupinder

last: Juneja

state: MN

address: 1988 Fitch Avenue S

institute: University Of Minnesota

summary:
An increasing demand for cell-based diabetes therapy could be met through xenotransplantation of adult porcine islets. Use of islet xenotranplantation on a large scale would require rigorous safety and quality control measures to maximize transplant success. Development of molecular tools to monitor porcine islet cellular responses to ischemic, osmotic, mechanical and oxidative stresses during islet cell processing and post-isolation culturing would aid the rational design of cytoprotective strategies aimed at improving transplant outcomes. In addition, gene expression signatures informative for islet quality could serve as an adjunct to physiological testing to establish the suitability of islet products for transplantation.
Keywords: stress response

overall_design: Nine adult Landrace sows (2-3.5 y old, 249±27 kg) were sacrificed, the pancreases were dissected, and islet cells isolated as previously described [8]. Islet preparation purity was assessed by light microscopy after staining with diphenylthiocarbazone and ranged between 90-95% for the preparations used. Islet yield, based on islet equivalents (IEQ, number of islets standardized to 150 µm diameter), was estimated at 1930±520 per gram of pancreas tissue.Profiles of islet cells cultured under standard conditions were compared to islet cells cultured under stress conditions with elevated glucose (16.7 mM) or addition of inflammatory cytokines (IL-1beta, TNF-alpha, and IFN-gamma), or both, for 48 hours.

last: Dvorak

first: M.

last: Hårdstedt

first: H.

last: Xie

last: Wang

last: Papas

last: Murtaugh

last: Fahrenkrug