title: Ketamine suppresses hypoxia-induced inflammatory responses in the late-gestation ovine fetal kidney cortex

city: Gainesville

first: Eileen

middle: I.

last: Chang

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida College of Medicine

summary: Acute fetal hypoxia is a form of fetal stress that stimulates renal vasoconstriction and ischemia as a consequence of the physiological redistribution of combined ventricular output. We have demonstrated that hypoxia in late ovine gestation induces inflammation in the brain that is ameliorated by treatment with ketamine. We hypothesized that the fetal kidney would also respond to hypoxia with an increase in the expression of inflammatory genes, and that ketamine (an N-Methyl-D-aspartate receptor antagonist) would reduce or block this response. Enriched biological processes for the 427 upregulated genes were immune and inflammatory responses and for the 946 down-regulated genes were metabolic processes. Ketamine countered the effects of hypoxia on upregulated immune/inflammatory responses as well as the down-regulated metabolic responses. We conclude that our transcriptomics modeling predicts that hypoxia activates inflammatory pathways and reduces metabolism in the fetal kidney cortex, and ketamine blocks or ameliorates this response. The results suggest that ketamine may have therapeutic potential for protection from ischemic renal damage.

overall_design: At the time of surgery, fetuses were randomly assigned to one of the four groups (n=3-4/group): normoxic control, normoxia+ketamine, hypoxic control, and hypoxia+ketamine. Hypoxia was induced for 30 min in chronically catheterized fetal sheep (125±3 d; term=145-147d), with or without ketamine (3 mg/kg) administered intravenously to the fetus 10 min prior to hypoxia. Fetuses were euthanized 24 hours after the onset of hypoxia, and the kidney cortex were collected for RNA extraction and gene array studies.  Gene expression was analyzed using ovine Agilent 15.5 k array and validated with qPCR. Significant differences in gene expression between groups were determined with t-statistics using the limma package for R (P≤0.05).

middle: I

first: Maria

last: Rabaglino

first: Miguel

last: Zárate

first: Elaine

last: Richards

first: Charles

last: Wood


title: The transcriptomic profile of peripheral blood nuclear cells in dogs with atopy dermatitis

status: Public on Aug 31 2016

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

summary:
The aim of the study was to identify genes which are differentially expressed in the blood of dogs with canine atopic dermatitis (AD) in comparison to healthy control dogs.
Diagnosis of AD was based on compatible history and clinical signs determined using Willemse and Prélaud diagnostic criteria, completed by Favrot criteria as follows: pruritus sine material, indoor lifestyle  and  the exclusion of other causes of pruritus ongoing for at least one year. Clinical diagnosis of atopic dermatitis was confirmed by serological allergy testing (IDEXX allergic panel test) and intradermal skin testing (Artuvetrin test set, Netherlands). In order to avoid the role of food antigens as a cause of the skin condition elimination diets was used for 6–8 weeks. No anti-inflammatory drugs were given for at least 3 weeks prior examination with serological test,  intradermal test and blood collection. All dogs, which were classified to the investigated group had positive reactions in serological allergy testing and intradermal skin testing.

overall_design: Twenty eight two-color microarrays were performed,  one for each patient ( 8 from healthy dogs and 20 microarrays with samples from AD dogs ). RNA from healthy  dogs and dogs with  AD was hybridized to Agilent two color microarrays with a common reference. The common reference comprised a pool of equal amounts of RNA from 13 healthy dogs which did not take part in the experiment.

first: Kourou

last: Dembele

first: Małgorzata

last: Gajewska

first: Michał

last: Jank


title: Atr maintains chromosomal integrity during postnatal cerebellar neurogenesis [Affymetrix]

status: Public on Sep 01 2016

city: Chapel Hill

first: Timothy

last: Gershon

state: NC

address: 6109 Neuroscience Research Building

department: Pediatric Hematology Oncology

country: USA

institute: University of North Carolina at Chapel Hill

summary: Microcephaly and medulloblastoma result from mutations that compromise genomic stability. We report that Atr, which is mutated in the microcephalic disorder Seckel syndrome, is required to maintain chromosomal integrity during postnatal cerebellar neurogenesis. Atr deletion in cerebellar granule neuron progenitors (CGNPs) induced proliferation-associated DNA damage, p53 activation, apoptosis, and cerebellar hypoplasia. Co-deletions of either Bax and Bak or p53 prevented apoptosis in Atr-deleted CGNPs, but failed to fully rescue cerebellar growth. Atr-deficient CGNPs showed impaired cell cycle checkpoint function and continued to proliferate, accumulating chromosomal abnormalities. RNA-Seq demonstrated that the transcriptional response to Atr-deficient proliferation was p53-driven. Acute Atr inhibition in vivo by nanoparticle-formulated VE-822 reproduced the disruptions seen with Atr deletion. Our data show that p53-driven apoptosis and senescence, and non-apoptotic cell death redundantly limit growth in Atr-deficient progenitors. These overlapping mechanisms that suppress growth in Atr-disrupted CGNPs may be exploited for treatment of CGNP-derived medulloblastoma using Atr inhibition.

overall_design: Microarray on total RNA from P3 mouse cerebella of Math1-Cre;Atr-loxP/loxP;Bax-loxP/loxP;Bak--/- (n=3) vs. Math1-Cre;Bax-loxP/loxP;Bak--/- (n=3) and Math1-Cre;Atr-loxP/loxP;p53-loxP/loxP (n=3) vs. Math1-Cre;p53-loxP/loxP (n=3)

first: Patrick

middle: Y

last: Lang

first: Jeremy

middle: M

last: Simon

middle: R

first: Joel

middle: S

last: Parker


title: Effects of glucose and insulin resistance on gene expression profiling in the isolated working rat heart

status: Public on Aug 19 2016

city: Houston

first: Romain

last: Harmancey

state: Texas

address: 1881 East Rd.

department: Internal Medicine - Division of Cardiology

institute: The University of Texas Health Science Center at Houston

summary:
We investigated the isolated working rat heart as a model to study early transcriptional remodeling induced by cardiac surgery with cardiopulmonary bypass (CPB). Because the mechanisms linking stress hyperglycemia and insulin resistance to increased peri-operative morbidity and mortality in the setting of open-heart surgery are still unclear, we also used this model to determine the transcriptional effects of exogenous glucose supply in absence or in presence of a preexisting state of myocardial insulin resistance. Male Sprague Dawley rats (200-224g) were kept on chow diet for 8 to 10 weeks, or fed a high-sucrose diet to induce myocardial insulin resistance. Following the feeding period, hearts were recovered, arrested in ice-cold Krebs-Henseleit (KH) buffer and subjected to 60 minutes normothermic reperfusion in the working mode with KH buffer supplemented with non-carbohydrate substrates plus glucose (25 mM) or mannitol (25 mM; osmotic control). Compared to non-perfused hearts, perfused hearts from chow-fed rats displayed a more than twofold increased expression for 71 genes (mannitol group) and 103 genes (glucose group) connected to inflammation, cell proliferation, and apoptosis. The same biological pathways were activated in hearts from insulin resistant rats, with 109 genes (mannitol group) and 70 genes (glucose group) up-regulated more than twofold when compared to the non-perfused hearts from high-sucrose diet-fed rats.
The changes were highly similar to gene alterations occurring in the right atrium and left ventricle of open heart surgery patients, and included the up-regulation of the three master regulators of metabolic reprogramming MYC, NR4A1 and NR4A2. Targeted pathway analysis revealed an up-regulation of metabolic processes associated with the proliferation and activation of tissue-resident macrophages and fibroblasts. Although the remodeling occurred independently from glucose, glucose further increased the expression of a subset of genes associated with polarization of tissue reparative M2 macrophages. However, glucose failed to enhance the expression of M2-related markers in the isolated heart from rats rendered insulin resistant by high-sucrose feeding. These results expose the cellular components of the heart as a significant source of proinflammatory mediators released in response to stress associated with cardiac surgery with CPB, and suggest a major role for glucose as a signal in the determination of resident cardiac macrophage polarization.

overall_design: Changes in myocardial gene expression induced by cold arrest and 60 min normoxic and normothermic reperfusion in presence of 25 mmol/L glucose or mannitol (osmotic control) were determined for hearts from chow-fed (insulin sensitive) or high-sucrose diet-fed rats (insulin resistant) by comparing to non-perfused rat hearts from the same feeding groups. Each dietary group of rats (chow-fed or high-sucrose diet-fed) included 3 subgroups of hearts (non-perfused, perfused with glucose, perfused with mannitol), with 5 biological replicates per subgroup – Therefore, the experiment included 30 biological samples total.

first: Ahmed

last: Bux

first: Merry

middle: L

last: Lindsey

first: Hernan

last: Vasquez

first: Heinrich

last: Taegtmeyer


title: Tumor hypoxia causes DNA hypermethylation by reducing TET activity (BeadChip)

city: Heverlee

first: Bernard

last: thienpont

address: Herestraat 49

department: Vesalius Research Center

country: Belgium

institute: VIB

summary:
Genome wide DNA methylation profiling of normoxic and hypoxic non-small-cell lung cancer samples for 5mC and 5hmC. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation and hydroxymethylation profiles across 485,512 CpGs from DNA extracted from fresh-frozen tumor samples. Samples included 12 hypoxic and 12 normoxic tumor samples, with hypoxia determined according to the hypoxia metagene score (Buffa et al, Br J Cancer 2010). To profile hydroxymethylation, 5hmC was glycosylated and 5mC was oxidised as described by Yu and colleagues (Nat Protoc 2012), and hydroxymethylation and methylation were differentially profiled according to the Nazor and colleagues (Genomics 2014).
Hypermethylation of tumor suppressor gene (TSG) promoters confers growth advantages to cancer cells, but how these changes arise is poorly understood. Here, we report that tumor hypoxia reduces the activity of oxygen-dependent TET enzymes, which catalyze DNA de-methylation through 5-methylcytosine oxidation. This occurs independently of hypoxia-associated alterations in TET gene expression, basal metabolism, HIF activity or nuclear reactive oxygen species, but directly depends on oxygen shortage. Hypoxia-induced loss of TET activity increases hypermethylation at gene promoters in vitro, while also in patients, gene promoters are markedly more methylated in hypoxic than normoxic tumors. Affected genes are frequently involved in DNA repair, cell cycle regulation, angiogenesis and metastasis, indicating cellular selection of hypermethylation events. Overall, up to 50% of the tumor-associated hypermethylation is ascribable to hypoxia across various cancer types. Accordingly, spontaneous murine breast tumors become hypermethylated when rendered hypoxic through vessel pruning, whereas vessel normalisation rescues this effect. Tumor hypoxia thus acts as a novel regulator underlying DNA methylation.

overall_design: 12 normoxic and 12 hypoxic non-small-cell lung cancer samples were compared for their 5hmC and 5mC distribution


title: Evaluating the gene expression of frozen tissue-derived prognostic signatures in FFPE colorectal cancer samples

city: Nashville

first: Jing

last: Zhu

state: TN

institute: Vanderbilt University

summary: Defining molecular features that can predict the recurrence of colorectal cancer (CRC) for stage II-III patients remains challenging in cancer research. Most available clinical samples are Formalin-Fixed and Paraffin-Embedded (FFPE). NanoString nCounter® and Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA) are the two platforms marketed for high-throughput gene expression profiling for FFPE tissue samples. In this study, to identify an optimal platform for the gene expression profiling of FFPE CRC samples, we evaluated the expression of 516 genes from published frozen tissue-derived prognostic signatures in 42 CRC patient samples measured by these two platforms. Based on HTA platform-derived data, we identified both gene (99 individual genes, FDR < 0.05) and gene set (four of the six reported multi-gene signatures with sufficient information for evaluation, P < 0.05) expression differences associated with survival outcomes. Using nCounter platform-derived data, only one of the six multi-gene signatures (P < 0.05) but no individual gene was associated with survival outcomes. Therefore, the HTA appears to provide a more robust gene expression dataset using genes from published gene signatures. Our study indicated that sufficiently high quality RNA could be obtained from FFPE tumor tissues to detect frozen tissue-derived prognostic gene expression signatures for CRC patients.

overall_design: In this study, we evaluated the expression of 516 genes from published frozen tissue-derived prognostic signatures in 42 Stage II & III CRC patients samples measured by NanoString nCounter and Affymetrix GeneChip Human Transcriptome Array 2.0 platforms.             ***This represents the NanoString component only.***

first: Natasha

middle: G

last: Deane

first: Keeli

middle: B

last: Lewis

first: Chandrasekhar

last: Padmanabhan

first: M

middle: K

last: Washington

first: Kristen

last: Ciombor

first: Cynthia

last: Timmers

first: Richard

last: Goldberg

first: R

middle: D

last: Beauchamp

first: Xi

last: Chen


title: Serum miRNA profiles for gastric cancer diagnosis

city: Nanjing

first: Zebo

last: Huang

state: Jiangsu

address: 300 Guangzhou Road

country: China

summary: Circulating microRNAs (miRNAs) in serum may serve as promising diagnostic biomarkers for patients with gastric cancer (GC). Using quantitative reverse transcription polymerase chain reaction (qRT-PCR) based Exiqon panel, we identified 58 differentially expressed miRNAs from 3 GC pool samples and 1 normal control (NC) pool in the initial screening phase. Identified miRNAs were further validated in the training (49 GC VS. 47 NCs) and validation phases (154 GC VS. 120 NCs) using qRT-PCR. Consequently, six serum miRNAs (miR-10b-5p, miR-132-3p, miR-185-5p, miR-195-5p, miR-20a-3p and miR-296-5p) were significantly overexpressed in GC compared with NCs. The areas under the receiver operating characteristic (ROC) curve of the six-miRNA panel were 0.764 and 0.702 for the training and validation phases, respectively. In conclusion, we identified a six-miRNA panel in serum for the detection of GC.

overall_design: All blood samples were collected from First Affiliated Hospital of Nanjing Medical University. The serum sample was stored at -80°C for further processing. In the initial screening phase, serum samples were collected from 30 GC patients and 10 NCs and pooled as 3 GC pool samples (GC pool 1, GC pool 2 and GC pool 3) and 1 NC pool sample (10 serum samples were pooled as 1 pool sample).

first: Wei

first: Yongqian

last: Shu

first: Ping

last: Liu


title: Comparison of gene expression profiles of wildtype and two lines of Nrf2 knockout rat livers with or without CDDO-Im treatment

status: Public on Aug 10 2016

city: Sendai

first: Keiko

last: Taguchi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba

department: Tohoku Medical Megabank Organization

country: Japan

institute: Tohoku University

summary: Whole livers were collected from rats treated with or without CDDO-Im.  Total RNA was purified using Sepazol-RNA I Super G.

overall_design: Gene expression was measured in livers.

first: Misaki

last: Takaku


title: Equine dendritic cells generated with horse serum have enhanced functionality in comparison to dendritic cells generated with fetal bovine serum

status: Public on Jul 06 2016

city: Guildford

first: Falko

last: Steinbach

address: Daphne Jackson Road

country: United Kingdom

institute: Univ of Surrey

summary:
EqMoDC generated with horse serum-supplemented medium showed improved morphological characteristics, higher cell viability and exhibited a more robust performance in the functional T cell assays.
The study is further described in A. Ziegler, H. Everett, E. Hamza et al., BMC Vet Research, 2016

overall_design: A two chip study, comparing monocytes, iMoDC and mMoDC derived in vitro from three horses using total RNA extract

first: A

last: Ziegler

first: H

last: Everett

first: E

last: Marti

first: F


title: Depletion of undecaprenyl pyrophosphate phosphatases (UPP-Pases) disrupts cell envelope biogenesis in Bacillus subtilis

status: Public on Aug 12 2016

city: Ithaca

first: John

middle: Daniel

last: Helmann

state: NY

address: 372 Wing Hall, Cornell University

department: Microbiology

institute: Cornell University

summary: The integrity of the bacterial cell envelope is essential to sustain life by countering the high turgor pressure of the cell and providing a barrier against chemical insults. In Bacillus subtilis, synthesis of both peptidoglycan and wall teichoic acids requires a common C55 lipid carrier, undecaprenyl-pyrophosphate (UPP), to ferry precursors across the cytoplasmic membrane. The synthesis and recycling of UPP requires a phosphatase to generate the monophosphate form Und-P, which is the substrate for peptidoglycan and wall teichoic acid synthases. Using an optimized CRISPR-dCas9 based transcriptional repression system (CRISPRi), we demonstrate that B. subtilis requires either of two UPP phosphatases, UppP or BcrC, for viability. We show that a third predicted lipid phosphatase (YodM), with homology to diacylglycerol pyrophosphatases, can also support growth when overexpressed. Depletion of UPP phosphatase activity leads to morphological defects consistent with a failure of cell envelope synthesis and strongly activates the M-dependent cell envelope stress response, including bcrC which encodes one of the two UPP phosphatases. These results highlight the utility of an optimized CRISPRi system for investigation of synthetic lethal gene pairs, clarify the nature of the B. subtilis UPP-Pase enzymes, and provide further evidence linking the M regulon to cell envelope homeostasis pathways.

overall_design: Two-condition experiment (with or without xylose induction of dCas9),WT vs. Depletion strain. Two biological replicates for dye swap, independently grown and harvested.

first: Heng

last: Zhao


title: Gene Expression Profiles in Engineered Cardiac Tissues Respond to Mechanical Loading and Inhibition of Tyrosine Kinase

status: Public on Jun 25 2016

city: Louisville

first: Bradley

middle: B.

last: Keller

state: United States

address: 302 E Muhammad Ali Blvd

department: Cardiovascular Innovation Institute

institute: University of Louisville

summary:
Engineered cardiac tissues (ECTs) are platforms to investigate cardiomyocyte maturation and functional integration, to evaluate the feasibility of generating implantable tissues for cardiac repair and regeneration, and may be useful models for pharmacology and toxicology bioassays.  These ECTs rapidly mature in vitro to acquire the features of functional cardiac muscle and respond to mechanical load with increased proliferation and maturation.  ECTs can be generated from various immature cardiac cell sources and little is known regarding the broad changes in regulatory transcript expression that occur in these in vitro tissues during normal maturation and in response to mechanical or pharmacologic interventions.
We tested the hypothesis that global ECT gene expression patterns are sensitive to mechanical loading conditions and tyrosine kinase inhibitors, similar to the maturing myocardium.  We generated 3D ECTs from day 14.5 rat embryo ventricular cells, as previously published, and then treated constructs after 5 days in culture for 48 hours with mechanical stretch (5%, 0.5 Hz) and/or the p38MAPK (p38 mitogen-activated protein kinase) selective inhibitor BIRB796.  RNA was isolated from 3 sets of experiments and assayed using a standard Agilent rat 4x44k V3 microarray and Pathway Analysis software for transcript expression fold changes and changes in regulatory molecules and networks.   At the threshold of a 1.5 fold change in expression, mechanical stretch altered 1,559 transcripts, versus 1,411 for BIRB796, and 1,846 for stretch plus BIRB796.  As anticipated, top pathways altered in response to these stimuli include Cellular Development, Cellular Growth and Proliferation; Tissue Development; Cell Death, Cell Signaling, and Small Molecule Biochemistry as well as numerous other pathways.  Changes in transcript expression were confirmed by quantitative-PCR for selected regulatory molecules.  Thus, ECTs display a broad spectrum of altered gene expression in response to mechanical load and/or tyrosine kinase inhibition, reflecting the complex regulation of proliferation, differentiation, and architectural alignment that occurs during ECT maturation and adaptation.  This approach can now be used to test the role of individual molecules and pathways on the regulation of ECT maturation and remodeling.

overall_design: 7 and 4 biological replicates with four groups (control, mechanical stretch, BIRB and mechanical stretch with BIRB)

first: Fei

last: Ye

first: Fangping

last: Yuan

first: Xiaohong

last: Li

first: Nigel

last: Cooper

first: Joseph

middle: P

last: Tinney


title: Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: a Randomized Double-blind Placebo-controlled Trial

status: Public on Jul 15 2016

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: The gut microbiota has been implicated in obesity and cardiometabolic diseases, although evidence in humans is scarce. We investigated how gut microbiota manipulation by antibiotics (7-day administration of amoxicillin, vancomycin, or placebo) affects host metabolism in 57 obese, prediabetic men. Vancomycin, but not amoxicillin, decreased bacterial diversity and reduced Firmicutes involved in short-chain fatty acid and bile acid metabolism, concomitant with altered plasma and/or fecal metabolite concentrations. Adipose tissue gene expression of oxidative pathways was upregulated by antibiotics, whereas immune-related pathways were downregulated by vancomycin. Antibiotics did not affect tissue-specific insulin sensitivity, energy/substrate metabolism, postprandial hormones and metabolites, systemic inflammation, gut permeability, and adipocyte size. Importantly, energy harvest, adipocyte size, and whole-body insulin sensitivity were not altered at 8-week follow-up, despite a still considerably altered microbial composition, indicating that interference with adult microbiota by 7-day antibiotic treatment has no clinically relevant impact on metabolic health in obese humans.

overall_design: This randomized, placebo-controlled, double-blind study had a 3-armed parallel design. Overweight/obese participants were randomized to oral intake of amoxicillin, vancomycin or placebo for 7 consecutive days. After an overnight fast, subcutaneous adipose tissue biopsies were taken that were subjected to gene expression profiling by array. http://clinicaltrials.gov/show/NCT02241421

first: D

last: Reijnders

first: G

middle: H

last: Goossens

last: Neis

first: C

last: van der Beek

first: J

last: Most

middle: J

last: Holst

first: K

last: Lenaerts

first: R

last: Kootte

first: M

last: Nieuwdorp

last: Groen

middle: V

last: Boekschoten

last: Hermes

last: Smidt

last: Zoetendal

last: Dejong

middle: E

last: Blaak


title: Studies of canine breed development on the island of Sardinia recapitulate genomic features of human population isolates [MEDI]

status: Public on Jun 10 2016

city: Bethesda

first: Dayna

last: Dreger

state: MD

address: 50 South Drive

department: NHGRI

institute: National Institutes of Health

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

summary: The Italian island of Sardinia is well known in studies of human population isolates. It is also home to the Fonni's Dog, a breed of canine whose development was reliant on the functionality of the dog. Using genome-wide variant and sequence analyses, we have characterized the Fonni's Dog relative to 27 other dog breeds from the Mediterranean region. We determine introgression events relevant to Mediterranean breed development and describe how the Fonni's dog presents an intriguing model demonstrating the characteristics of traditional human population isolates and, in particular, exhibiting the unique demographic composition of the people of Sardinia.

overall_design: 82 canine samples representing 9 dog breeds

first: Brian

middle: W

last: Davis

first: Raffaella

last: Cocco

first: Sara

last: Sechi

first: Alessandro

last: DiCerbo

first: Heidi

last: Parker

first: Michele

last: Polli

first: Stefano

last: Marelli

first: Paola

last: Crepaldi

first: Elaine

middle: A

last: Ostrander


title: Studies of canine breed development on the island of Sardinia recapitulate genomic features of human population isolates [COO]

overall_design: 51 canine samples representing 12 dog breeds


title: Protective role of Apolipoprotein E in experimental acute renal allogaft rejection

status: Public on Jun 01 2016

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary:
Objective: Apolipoprotein E (Apo E) is a multifunctional protein, originally described in the context of lipoprotein metabolism and cardiovascular disease. More recently, anti-inflammatory functions of ApoE have been documented. ApoE was studied in the context of several inflammatory disorders, but its role in the pathogenesis of acute organ rejection is unknown. In this study, we test the hypothesis that ApoE attenuates acute renal allograft rejection.
Materials and methods: The Dark Agouti (DA) to Lewis (Lew) and the Brown Norway (BN) to Lew rat strain combinations were used to investigate fatal acute rejection. In addition, Fischer 344 (F344) kidneys were transplanted to Lew rats to study reversible acute rejection. Isograft recipients and untreated Lew rats were used as controls. ApoE mRNA expression was quantified in intravascular leukocytes accumulating in the blood vessels of renal grafts and in graft tissue. Apo E protein levels were assessed in blood plasma. To test the protective potential of ApoE, recipients of BN kidneys were treated with ApoE-mimetic peptide.
Results: Intravascular graft leukocytes and renal tissue obtained from animals undergoing reversible acute rejection expressed increased levels of ApoE mRNA, whereas during fatal rejection, ApoE expression remained unchanged in the BN to Lew rat strain combination or was significantly reduced when DA rats were used as donors of the kidney. On the protein level, no changes in ApoE were seen in plasma. However, we do not know if local leukocytic ApoE expression results in increased ApoE concentrations inside graft blood vessels. Peptide treatment of allograft recipients reversed fatal rejection and significantly improved animal survival.
Conclusions: ApoE plays a protective role in acute organ rejection. Further studies are needed to understand the exact mechanism how ApoE reverses acute rejection.

overall_design: dual-color balanced dye-swap design with 4 biological replicates, hybridized on 4 arrays

first: Anna

last: Zakrzewicz


title: Gene expression from the New Zealand White rabbit calvarial defects treated with human particulated dentin

status: Public on Jun 21 2016

city: Taipei

first: YU-CHIH

last: HUANG

address: No.250, WuXing St,

department: College of Oral Medicine

country: Taiwan

institute: Taipei Medical University

summary: In this study, human particulated dentin (HPD) was developed. The characteristic of HPD was examinated by XRD, EDX and cytotoxicity test. HPD was used to implant in the calvarial defects of New Zealand White rabbits. bone tissue and blood samples were taken at 3, 5 and 7 days post-implantation for microarray experiment. The gene expression profiles and signaling pathways were monitored using GeneSpring software and Ingenuity Pathways Analysis (IPA), respectively. We used microarray and IPA to elucidate the global programme of gene expression and identified distinct classes of up- and down- regulated genes during HPD treated healing process.

overall_design: In this study, 24 New Zealand White rabbits, weighing 3.0–3.5 kg, were anesthetized with intramuscular Zoletil 50 at a dose of 0.5 mL. Four circular defects (5 mm inner diameter) were made in the parietal bone using a trephine on a slow-speed electric handpiece. The two right defects were grafted with 0.2 g of prepared HPD and the other two were unfilled control. After 3, 5, and 7 days, The bone tissue and blood samples were taken for RNA extration and microarray experiment. The samples at 3 time points were defined as below: Control_3d, HPD_3d, Control_5d, HPD_5d, Control_7d, HPD_7d.

first: Yu-Chih

last: Huang

first: Wei-Zhen

last: Lew

first: Haw-Ming


title: Quantitative transcriptomic analysis metabolic mutant of Clostrdidium acetobutylicum ATCC824 under different physiological conditions

status: Public on May 11 2016

city: Toulouse

first: Philippe

last: Soucaille

address: 135 avenue de Rangueil

country: France

institute: INSA Toulouse

summary:
Transcriptomic analysis was applied to acidogenic, solventogenic and alcohologenic steady-state C. acetobutylicum cells for understanding the regulation of the metabolism of this organism.
Used microarray is Clostridium acetobutylicum ATCC824 transcriptional 44k v4, correspondance to GPL10908

overall_design: Phosphate-limited continuous cultures of C. acetobutylicum were performed under acidogenesis (pH 6.3, 995 mM of carbon from glucose), solventogenesis (pH 4.4, 995 mM of carbon from glucose) and alcohologenesis (pH 6.3, 498 mM of carbon from glucose and 498 mM of carbon from glycerol). Samples were collected for three biological replicates from one control strain and three metabolic mutants, respectively.  Total RNA of 36 samples was extracted using an RNeasy Midi kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions with the supplementation of DNase treatment using RNase-Free DNase Set (Qiagen). Agilent microarray for Clostridium acetobutylicum ATCC 824 (4x44K AMADID 024247) was used. The RNAs were labeled with a Low Input Quick Amp Labeling kit and hybridized following a one-color microarray-based gene expression analysis protocol.

first: Ngoc-Phuong

middle: T

last: Nguyen


title: Transcriptomic response in colon of rat with increased dietary protein content

status: Public on Apr 05 2016

first: Weiyun

last: Zhu

address: No.1, Weigang, Xuanwu District

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

summary: Increase of fecal hazardous compounds and decrease of butyrate-producing bacteria has been implicated to be detrimental to colonic health during weight loss by high-protein diet in human. The question remains that whether the change of luminal microenvironment were paralleled with the alteration of colonic function in vivo.To reveal the change of gene expression involved in metabolic or immmunological process, we have employed the whole genome microarray profiling to identify differentially expressed genes in rat dietary normal protein (20% protein) or high protein (45% protein) diet. Colonic epithelium were sampled in adult male wistar rats (weighing 180-200g) fed each diet for six weeks.Each group contained six replicates.A total of 181 transcripts were significantly changed: 88 genes were up-regulated and 93 genes were down-regulated in high protein compared with normal protein rats. Transcriptome analysis identified the upregulation of chemotaxis, TNF-α signal process, antigen presentation, apoptosis, glutathione S-transferase activity and downregulation of innate immune, O-linked glycosylation of mucin, oxidative phosphorylation.Expression of ten genes, including calmodulin1,acetyl-CoA acyltransferase 2,isovaleryl-CoA dehydrogenase and occludin,  were quantified in the same RNA samples by real-time PCR, validating the microarray analysis.

overall_design: Colonic gene expression was measured in male wistar rat (weighing 180-200g) after dietary normal protein or high protein diet for six weeks. Six replicates in each group were analyzed.

first: Chunlong

last: Mu


title: A bacterial hemolytic lipid toxin subverts neutrophils and neutrophil extracellular traps to promote gbs invasion, fetal injury and preterm labor in nonhuman primates

status: Public on Apr 26 2016

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Preterm birth is a leading cause of neonatal morbidity and mortality. Microbial infection and inflammation of the amniotic cavity are associated with the majority of early preterm births and thought to arise from ascension of bacteria from the lower genital tract. Group B Streptococci (GBS) are beta-hemolytic, gram-positive bacteria, which commonly colonize the vagina and have been recovered from the amniotic fluid in cases of preterm birth. Host immune defenses that are critical for prevention of microbial invasion of the amniotic cavity (MIAC) and preterm labor are not completely understood. We recently showed that increased expression of the hemolytic pigment promotes GBS penetration of human placenta ex vivo and hyperhemolytic/hyperpigmented GBS strains with mutations in the hemolysin repressor (CovR/CovS) can be isolated from women in preterm labor. To understand placental/ choriodecidual immune responses that are necessary to prevent MIAC and preterm labor, we utilized a unique chronically catheterized nonhuman primate model that closely emulates human pregnancy. We observed that preterm labor, MIAC, and fetal injury occurred significantly more frequently in pregnant nonhuman primates infected with hyperpigmented GBS (ΔcovR) despite the strong induction of proinflammatory responses in the chorioamnion. Placental histopathology revealed a systematic progression in development of chorioamnionitis in GBSΔcovR animals beginning with chorionic vasculitis and subsequently progressing to neutrophilic infiltration in the chorioamnion.

overall_design: In this study, eleven chronically catheterized pregnant NHP (Macaca nemestrina) containing catheters surgically implanted via laparotomy into the maternal femoral vein, amniotic cavity, and choriodecidual interface in the lower uterine segment (between uterine muscle and fetal membranes, external to amniotic fluid) received one of two experimental treatments: i.e. choriodecidual inoculation of either GBS COH1ΔcovR (n=6; hyperpigmented strain) or GBS COH1ΔcovRΔcylE (n=6; isogenic, nonpigmented strain). Results obtained from these animals were compared to saline controls (n=5; choriodecidual and amniotic fluid saline inoculations) that were performed previously.

first: Erica

last: Boldenow

first: Craig

last: Bierle

first: Clair

last: Gendrin

first: Lisa

last: Ngo

first: Jay

last: Vornhagen

first: Sean

last: Merillat

first: Blair

last: Armistead

first: Christopher

last: Whidbey

first: Varchita

last: Alishetti

first: Jason

last: Ogle

first: Michael

last: Gough

first: Sengkeo

last: Srinouanprachanh

first: Theodor

last: Bammler

first: Asthaa

last: Bansal

first: H

last: Liggitt

first: Lakshmi

last: Rajagopal

first: Kristina

middle: M

last: Adams Waldorf


title: Rat Primary Cultured Hepatocytes:  Control vs SQ1 or Pravastatin treatment.

status: Public on May 20 2016

city: Detroit

first: Thomas

last: Kocarek

state: MI

address: 6135 Woodward Ave

department: Institute of Environmental Health Sciences

institute: Wayne State University

summary: Transcriptional profiling of rat primary cultured hepatocytes comparing control (untreated), SQ1, and Pravastatin treated hepatocytes.

overall_design: Control (untreated) versus SQ1 or Pravastatin treated primary hepatocytes. Biological replicates: 8 control replicates, 8 treated replicates. 4 each using dye swap design.

first: Kocarek

last: TA


title: Gene expression signature of Lewis rats with experimental NMO and controls

status: Public on Mar 22 2016

city: Vienna

first: Monika

last: Bradl

address: Spitalgasse 4

department: Neuroimmunology

country: Austria

institute: MedUni Vienna, Center for Brain Research

summary: study was performed to reveal the extent to which NMO-IgG contributes to tissue damage in experimental NMO

overall_design: Gene expression was studied in Lewis rats after transfer of myelin basic protein-specific T cells on day 0 and NMO-IgG on day 4. The animals were sacrificed 24 hours later. Controls did either not receive T cells (0), did receive control IgG or PBS instead of NMO-IgG, or were left completely untreated.


title: Induced of RBM24 expression effect on nasopharyngeal carcinoma cells

status: Public on Mar 13 2016

city: Guangzhou

first: Mei-Yin

last: Zhang

state: Guangdong

address: 651 Dongfeng East Road

department: State Key Laboratory of Oncology in South China

institute: Sun Yat-sen University Cancer Center

summary: RNA-binding proteins (RBPs) are key components in the determination of miRNA function, as they control different stages of miRNA biogenesis and their localization, degradation and activity. To further investigate the underlying mechanisms of RBM24 in nasopharyngeal carcinoma (NPC) carcinogenesis, we compared the miRNA expression profiles in RBM24 induced and control cells by using human miRNA microarray. Microarray analysis identified 11 commonly upregulated and 12 commonly downregulated miRNAs in RBM24 induced cells. Among the 23 miRNAs, miR-25 ranked highest of all the commonly upregulated genes sorted in ascending order according to fold change values. RBM24 expression was controlled by tetracycline-off system in NPC cells.

overall_design: microRNA profiling of RBM24 expression induced cells vs. repressed cells: The expression of RBM24 in HONE-1, 5-8F, and CNE-2 cells was induced by removing doxycycline or repressed by adding doxycycline.

first: Wen-Feng

last: Hua

first: Mu-Sheng

last: Zeng


title: The expression profiles of extracellular matrix-related genes in the presence or absence of IL-12, IL-23 or IL-27 as measured with PCR array

status: Public on Mar 03 2016

city: Kumamoto

first: Wakana

last: Nakayama

address: 1-1-1 Honjo

department: Department of Dermatology & Plastic Surgery

institute: Faculty of Life Sciences, Kumamoto University

summary:
We performed a PCR array of 84 ECM-related genes using RNA obtained from dermal fibroblasts stimulated presence or absence of IL-12, IL-23 or IL-27.
The effects of IL-12, -23 or -27 on COL1A2 mRNA expression were less than 2-fold, as compared with untreated cells.

overall_design: In this study, we examined the involvement of the IL-12, IL-23 or IL-27 in the expression of the extracellular matrix.


title: Azoxymethane-induced colorectal tumorigenesis in hypertensive rat models

status: Public on Apr 04 2016

city: Toledo

first: Bina

last: Joe

state: Ohio

address: Block Health Science Bldg, 3000 Arlington Ave

department: Department of Physiology and Pharmacology

institute: University of Toledo, College of Medicine and Life Sciences

summary: To compare the tumor susceptibility between the hypertensive Dahl salt-sensitive rats (S) rat and S.LEW(10)x12x2x3x5 (S.LEW) congenic strain, one of the S.LEW congenic strains our laboratory previously constructed on rat chromosome 10 [Hypertension. 2007 Nov;50(5):891-8], Azoxymethane (AOM)-induced colon tumorigenesis in rats was assessed. At six weeks of age, both S and S.LEW congenic rats received intraperitoneal (IP) injection of AOM in sterial saline at a dose of 15mg/kg body weight once a week for two consecutive weeks. At 30 weeks of age, all the rats were euthanized through carbon dioxide inhalation. The colon tissue was harvested, dissected longitudinally, and washed with saline. The number and size of the colon tumors were recorded. We found that the total number of colon tumors was significantly higher in the S.LEW congenic strain compared with the S rat. To further study the genetic and molecular mechanisms causing the higher tumor susceptibility in the S.LEW congenic strain, we have employed the whole genome microarray expression profiling to identify genes and signaling pathways that are differential between the S and S.LEW congenic strain.

overall_design: At six weeks of age, both S and S.LEW congenic rats received intraperitoneal (IP) injection of AOM in serial saline at a dose of 15mg/kg body weight once a week for two consecutive weeks. At 30 weeks of age, all the rats were euthanized through carbon dioxide inhalation. The colon tissue was harvested, dissected longitudinally, and washed with saline. RNA from the harvested colons of 3 S and 3 S.LEW congenic rats were prepared for the microarray study.

first: Xi

last: Cheng


title: miR-132 mediates renal fibrosis: miRNA profiling of foxd1-derivative interstital cells derived from murine fibrotic kidneys compared to healthy kidneys

status: Public on Feb 16 2016

city: Leiden

first: Roel

last: Bijkerk

address: Albinusdreef 2

department: Nephrology

institute: LUMC

summary: Chronic kidney disease is associated with progressive renal fibrosis, where perivascular cells give rise to the majority of α-SMA positive myofibroblasts. We sought to identify pericytic miRNAs that could serve as a target to decrease myofibroblast formation. We induced kidney fibrosis in FoxD1-GC;Z/Red-mice by unilateral ureteral obstruction (UUO) followed by FACS sorting of dsRed-positive FoxD1-derivative cells and miRNA profiling. MiR-132 selectively increased 21-fold during pericyte-to-myofibroblast formation whereas miR-132 was only 2.5-fold up in total kidney lysates (both in UUO and ischemia-reperfusion injury). MiR-132 silencing in UUO decreased collagen deposition (35%) and tubular apoptosis. Immunohistochemistry, western blot and qRT-PCR confirmed a similar decrease in interstitial α-SMA+ cells. Pathway analysis identified a rate-limiting role for miR-132 in myofibroblast proliferation that was confirmed in vitro. Indeed, antagomir-132 treated mice displayed a reduction in the number of proliferating, ki67+ interstitial myofibroblasts. Interestingly, this was selective for the interstitial compartment and did not impair the reparative proliferation of tubular epithelial cells, as evidenced by an increase in ki67+ epithelial cells, as well as increased (p-)RB1, Cyclin-A and decreased RASA1, p21 levels in kidney lysates. Taken together, silencing miR-132 counteracts the progression of renal fibrosis by selectively decreasing myofibroblast proliferation and could potentially serve as a novel antifibrotic therapy.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Total RNA obtained from FACS sorted mouse FoxD1-derivative interstitial cells from healthy or fibrotic kidneys

first: Anton

last: van Zonneveld


title: MicroRNA expression profile in macrophages from rheumatoid arthritis and osteoarthritis patients

status: Public on Feb 05 2016

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: In osteoarthritis (OA) and rheumatoid arthritis (RA), many pathological alterations result from aberrant macrophage hyperactivation in the inflamed synovial membrane, and inhibition of macrophage effector functions is a therapeutic strategy in both diseases.  Little is known, about the specific genetic circuits that are differentially deregulated in RA and OA macrophages. microRNA (miR) are short single stranded non-coding RNAs involved in the post-transcriptional regulation of gene expression. Altered expression of miRs has been described under various pathological conditions, including rheumatic and other autoimmune diseases. Here we compared the miR expression profile in macrophages isolated from OA and RA patients

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

overall_design: miR expression in OA and RA macrophages was analyzed using Exiqon miRCURY microarrays. Three biological replicates (patients) were analyzed. Two samples (RA vs OA) were hybridized per microarray.

first: Jesús

last: Ogando

first: Manuel

last: Tardáguila

first: Andrea

last: Díaz-Alderete

first: Alicia

last: Isategui

first: Vanessa

last: Miranda-Ramos

last: Cañete

first: José

middle: L

last: Pablos

first: Santos

last: Mañes


title: miR-132 mediates renal fibrosis

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

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

overall_design: Refer to individual Series


title: A short-term maternal separation in early neonate rats markedly increases intestinal permeability, induces bacterial translocation to systemic organs and impacts gene expression in the liver

status: Public on Feb 01 2016

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

summary: Intestinal paracellular permeability (IPP) is high at birth and is involved in gut barrier maturation and liver development. Chronic maternal separation (MS) in early life alters intestinal barrier function in adulthood. However, only transient MS commonly occurs in human newborns, but whether a single episode of MS in early postnatal days (PND) affects the maturation of the gut-liver axis has not been explored. The aim of the current study was to evaluate the effect of a single MS of short duration in neonate rats on epithelial barrier integrity in the gut and on gene expression in the liver. Male and female pups were separated from their dams for 4h or not (controls) at PND10 or PND20. Total intestinal paracellular permeability (IPP) was measured through mucosal-to-plasma passage of oral FITC-Dextran 4 KD with or without ML7, a blocker of myosin light chain kinase (MLCK), or Mifepristone (RU486), an antagonist of the glucocorticoid receptor. Dose response to dexamethasone (DEX) on IPP was studied at PND10 and PND20. Bacterial translocation (BT) was assessed in mesenteric lymph nodes (MLN), liver and spleen in the presence or absence of ML7. The hepatic transcriptome was studied using Agilent microarrays and qPCR on PND10 rats pretreated or not with ML7. At PND10, control pups showed basal BT to MLN while liver and spleen were sterile. A short-term MS procedure increased IPP and plasma corticosterone levels, resulted in BT to the liver and spleen and had a clear impact on the hepatic transcriptome. Most notably, several genes involved in cell division were downregulated by MS. In PND10 rats, MS-induced increase of IPP and BT were blocked by ML7 or RU486, thus demonstrating a role of the MLCK pathway and of increased plasma levels of corticosterone in these effects of MS. All these effects of MS were absent in PND20 rats. Consistently, PND20 rats were found less sensitive to DEX exposure than PND10 rats. These results show that the early life period is a critical window for a short-term mother-infant separation, which can alter the development of the gut-liver axis and facilitate bacterial passage to systemic organs.

overall_design: Liver gene expression was measured from 10 day-old female Wistar rats subjected (n=5) or not (n=4) to a 4h-maternal separation.

first: Nabila

last: Moussaoui

first: Viorica

last: Braniste

first: Afifa

last: Ait-Belgnaoui

first: Yannick

last: Lippi

first: Soraya

last: Sekkal

first: Maïwenn

last: Olier

first: Vassilia

last: Théodorou

first: Eric

last: Houdeau


title: Transcriptome signatures for robustness of Lactococcus lactis

status: Public on Dec 24 2015

city: Ede

first: Annereinou

last: Dijkstra

address: Kernhemseweg 2

institute: NIZO food research

sample_organism: Lactococcus cremoris subsp. cremoris SK11


title: Large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination at the IgH locus in a cell-type specific manner

status: Public on Jan 31 2016

city: Boston

first: Guray

last: Kuzu

address: 185 Cambridge Street

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by genome tiling array

summary:
In this study, we compare the chromatin structure of the Ig heavy (IgH) chain locus (performing MNase digestion) in three murine cell types rendered recombinationally inactive by loss of a RAG recombinase: (i) RAG2-/- Pro-B cell lines, where the entire IgH locus is poised and available for recombination, (ii) RAG1-/- Pro-T cell lines, lymphoid cells where the IgH locus is partly open but the V region does not rearrange, (iii) recombinationally inactive RAG2-/- mouse embryonic fibroblasts (MEFs), where the entire IgH locus is in a closed conformation and unavailable for rearrangement.
Our findings suggest that developmentally-regulated changes in nucleosome location and occupancy play a fundamental role in regulating V(D)J recombination, by creating and controlling the accessibility of recombination signal sequences.

overall_design: Comparison of nucleosome mapping at the IgH locus between Rag-deficient proB, MEFs and proT cells. Two independent biological replicates were assessed for each cell type.

first: Sandhya

middle: R

last: Pulivarthy

first: Mattia

last: Lion

first: Adam

middle: G

last: Matthews

first: Mark

last: Borowsky

first: John

last: Morris

first: Robert

last: Kingston

first: Jonathan

last: Dennis

first: Michael

middle: Y

last: Tolstorukov

first: Marjorie

last: Oettinger


title: Transcriptome comparison between thymic T cell subsets in wildtype and Caph2(I15N) mutant mice

status: Public on Sep 01 2015

city: Edinburgh

first: Andrew

middle: James

last: Wood

address: Crewe Road

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

summary:
This study aimed to look for transcriptional differences between stage-matched thymic T cell subsets isolated from wildtype and condensin II mutant mice
CD4+CD8+ cells from 8-12 week animals were separated according to the expression of CD71, in order to isolate proliferative and non-proliferative subsets

overall_design: Total RNA from FACS purified CD4+CD8+CD71+ and CD4+CD8+CD71- was isolated, and comparisons were drawn between immunophenotypically matched cells from wildtype and Caph2 mutant (I15N) mice.


title: Transcriptome signatures for robustness of Lactococcus lactis KF147

summary: Recently, we demonstrated that fermentation conditions strongly impact on subsequent survival of Lactococcus lactis strain MG1363 during heat and oxidative stress, two important parameters during spray drying. Moreover, employment of a transcriptome-phenotype matching approach revealed groups of genes associated with robustness towards heat and/or oxidative stress. To investigate if other strains have similar or distinct transcriptome signatures for robustness, we applied a similar transcriptome-robustness phenotype matching approach on the L. lactis strains IL1403, KF147 and SK11. These strains were employed in an identical fermentation regime as was performed earlier for strain MG1363 which consisted of twelve conditions, varying in the presence of salt and/or oxygen, as well as fermentation temperature and pH. In the exponential phase of growth, cells were harvested for transcriptome analysis and assessment of heat and oxidative stress survival phenotypes. The variation in fermentation conditions resulted in differences in heat and oxidative stress survival up to five 10-log units. Effects of the fermentation conditions on stress survival of the L. lactis strains were typically strain-dependent, although the fermentation conditions had mainly similar effects on the growth characteristics of the different strains. Association of transcriptomes and robustness phenotypes identified highly strain-specific transcriptome signatures for robustness, indicating that multiple mechanism exist to increase robustness and, as a consequence, robustness of each strain requires individual optimization. However, a relatively small overlap in the transcriptome responses of the strains was also identified and this generic transcriptome signature included genes previously associated with stress (ctsR and lplL) and novel genes, including nanE and genes encoding transport proteins. The transcript levels of these genes can function as indicators of robustness and could aid in selection of fermentation parameters, potentially resulting in more optimal robustness during spray drying.

overall_design: two connected loops, both containing samples derived on a single day (sample 1-6, sample 7-13)

first: Wynand

last: Alkema

first: Marjo

last: Starrenburg

first: Jeroen

last: Hugenholtz

first: Sacha

last: van Hijum

first: Peter

last: Bron


title: E16/E19 rat fetus microarray

status: Public on Nov 14 2015

city: Los Angeles

first: Zhong

last: Zheng

address: 675 Charles E Young Dr, South

institute: UCLA

summary:
Examine the global gene expression changes from E16 (day 16.5) to E19 (day 18.5) in fetal SD rat skin samples
E19 samples were renamed as E18 samples in the relative manuscript

overall_design: Four E16 samples were pooled and three E19 samples are pooled.

first: Kang

last: Ting

first: Chia

last: Soo


title: Transcriptome signatures for robustness of Lactococcus lactis IL1403

first: Annereinou

last: Dijkstra


title: Gene expression signatures following nerve injury in a rat model (0.5h-9h)

status: Public on Aug 01 2015

city: Nantong

first: Shiying

last: Li

address: 19 Qixiu Road

institute: Nantong University

summary: We used microarrays to distinguish the gene expression differences among different time points after injury

overall_design: We generated L4-6 dorsal root ganglia (DRG) tissues (0.5cm) at 0.5h, 3h, 6h and 9h after sciatic nerve resection

last: LI

first: Xiaosong

last: Gu


title: Peripheral blood mononuclear cells gene expression reflects adaptive response and metabolic damage associated to the intake of diets with an unbalanced proportion of macronutrients

status: Public on Dec 07 2015

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: Gene expression studies in peripheral blood mononuclear cells (PBMC) can provide knowledge that would be difficult to obtain using other types of biological samples, as these cells can reflect overall response of the body to a specific stimulus, such as diet. Here, we aimed to study the impact of sustained intake of isocaloric diets with an unbalanced macronutrient proportion (rich in fat or protein) on PBMC gene expression in rats using transcriptomics, to better understand the effects of these diets on metabolism and health. Macronutrient diet composition (especially increased protein content) affected PBMC gene expression. An important effect was observed in immune response-related genes. High protein (HP) diet produced an activation of genes mainly related to antigen recognition/presentation, whereas the high fat (HF) diet was more related to a decreased expression of these genes. Key energy homeostasis genes (mainly involved in lipid metabolism) were also affected, reflecting a nutritional adaptive response to the diets. Decreased Dhrs3 and increased Pref-1/Dlk1 expression observed in HP-fed animals reflects a lower lipogenic capacity. In addition, HF diet affected the expression of genes related to insulin resistance/signaling (Msra/Slc9a6, Asb6), hypoxia (Akap12), cardiovascular problems (Ethe1, Lr11), cognitive impairment (Tmcc2) and tumorigenesis (Ddx17, Phb, Rnasen/Drosha, and Tsc2). HP diet also impaired the expression of genes related to glucose metabolism and insulinemia (Glut-4/Slc2a4, Sfxn5, Slc16a1), but positively affected genes involved in liver function (Clec4f and St6galnac3) and cardiovascular protection (Sort1). In conclusion, gene expression analysis in PBMC can provide information that could be useful to detect metabolic deviations and health consequences of diets with an unbalanced macronutrient composition.

overall_design: 2 months-old male Wistar rats received a low fat control diet, or a high fat (HF) diet, or a high protein (HP) diet for 4 months, respectively. At the end of the intervention, prior to the sacrifice of the animals, peripheral blood samples (1.5-2.5 mL) were collected from the safena vein, using heparin in NaCl (0.9%) as anticoagulant. Immediately after blood collection, peripheral blood mononuclear cells (PBMC) were isolated by Ficoll gradient separation.   Total RNA was isolated from PBMC, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 4x44K microarrays.

first: Ruben

last: Diaz

first: Jaap

last: Keijer

first: Oliver

last: Paula


title: Transcriptome signatures for robustness of Lactococcus lactis SK11


title: Expression profiles of dnaA null, rok null, and dnaA null; rok null mutants

status: Public on Jun 13 2015

city: Cambridge

first: Alan

middle: D.

last: Grossman

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

summary: To identify potential targets of co-regulation by DnaA and Rok, we compared the transcriptional profiles of dnaA null, rok null, and dnaA null rok null mutants.  Because a dnaA null mutant requires an oriC- strain background, we used an oriC- oriN+ background for all strains, to allow direct comparisons.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: We compared biological triplicates for each of the following strains: dnaA null (CAL2074), rok null (CAS196), dnaA null rok null (CAS192), and dnaA+ rok+ (CAL2083; control).

first: Charlotte

last: Seid

middle: D


title: Post-natal age is a critical determinant of the neonatal host response to sepsis

status: Public on Jul 06 2015

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: Neonates manifest a unique host response to sepsis even among other children. Preterm neonates may experience sepsis soon after birth or during often protracted birth hospitalizations as they attain physiologic maturity. We examined the transcriptome using genome-wide expression profiling on prospectively collected peripheral blood samples from infants evaluated for sepsis within 24 hours after clinical presentation. Simultaneous plasma samples were examined for alterations in inflammatory mediators. Group designation (sepsis or uninfected) was determined retrospectively based on clinical exam and laboratory results over the next 72 hours from the time of evaluation. Unsupervised analysis showed the major node of separation between groups was timing of sepsis episode relative to birth (early, <3 days or late, >3 days). Principal component analyses revealed significant differences between patients with early or late sepsis despite the presence of similar key immunologic pathway aberrations in both groups. Unique to neonates, the uninfected state and host response to sepsis is significantly affected by timing relative to birth. Future therapeutic approaches may need to be tailored to the timing of the infectious event based on post-natal age.

overall_design:
We used human microarrays to detail the molecular profile of the events that occur following sepsis in hospitalized neonates
Please note that 'uninfected chorio' represents babies who were not infected but had chorioamnionitis exposure

first: James

last: Wynn

first: Scott

middle: O

last: Guthrie

first: Hector

last: Wong

first: Patrick

last: Lahni

first: Ricardo

last: Ungaro

first: M

middle: C

first: Henry

middle: V

last: Baker

first: Lyle

last: Moldawer


title: Identifying genes and pathways that respond differently to dietary C:P between old (~700-yr-old) and young (~10-yr-old) resurrected Daphnia pulicaria genotypes that differ in C and P physiology

status: Public on Jun 01 2015

city: Notre Dame

first: Jacqueline

state: Indiana

address: 019 Galvin Life Science Center

institute: University of Notre Dame

summary: How does environmental change drive phenotypic evolution? We addressed this question using Daphnia genotypes separated by ~1600-years of evolution in a Minnesota lake using methods in resurrection ecology (i.e., reviving dormant eggs from sediments) and found substantial genetic and physiological differentiation. These shifts are highly correlated with anthropogenic environmental change, specifically phosphorus (P)-driven eutrophication. Here, we explore transcriptomic changes that may underlie the observed shifts in P use physiology (see poster by Fricsh et al for a detailed explanation). We compared the transcriptomes of two ancient and two contemporary genotypes in ancient (i.e., low P; LP) and contemporary (i.e., high P; HP) conditions using an 11000-gene microarray. Ancient and contemporary genotypes differed in the number of differentially expressed genes in the HP (mean ± SD; 645 ± 112.95) and LP (1071 ± 211.63) treatments. These results indicate considerable transcriptomic variation between ancient and contemporary genotypes in both dietary treatments, with stressful (LP) conditions invoking differential expression of more genes (t= -2.51; P= 0.04). Moreover, ancient and contemporary genotypes exhibited markedly different transcriptomic responses to dietary treatments. Contemporary genotypes upregulated 84.5 ± 28.99 while ancient genotypes upregulated 413.5 ± 26.16 genes (t= 164.5; P= 0.003). Similarly, ancient (127.5 ± 101.1) and contemporary (316 ± 98.99) genotypes differed significantly in the number of genes downregulated between the HP and LP treatments (t= 125.66; P= 0.005). These results indicate substantial regulatory shifts may underlie the striking physiological differences observed. Further analyses of gene families that were differentially expressed (DE) between ancient and contemporary genotypes revealed several gene families already known to be important in mitigating stoichiometric imbalances driven by P availability. Agglomerative hierarchical cluster analyses of DE loci between ancient and contemporary genotypes indicating age-based clustering will be presented. Together, our theoretical framework based on elemental supply, and unique model system enabled a millennial-scale exploration of the environmental contribution to phenotypic evolution.

overall_design: 2 ~700-yr-old clones (SC1X & SC3X), 2 ~10-yr-old clones (SC4B & SC15A), two dietary treatments (C:P~120 and C:P~800) of Scenedesmus algae. Exposed for 3 days.

first: Punidan

last: Jeyasingh


title: Genetic and physiological mechanisms underlying genotype by dietary stoichiometry interactions in Daphnia

summary: Understanding the fitness consequences of correlated shifts in ecological parameters is a central challenge in contemporary biology. We studied two genotypes of the waterflea, Daphnia pulex that exhibit striking genotype x environment (GxE) interaction in response to shifts in phosphorus (P) supply, which also alters dietary carbon (C) content. Genotype1 (G1) had higher fitness under a LoC:HiP (C:P~100) diet, while Genotype2 (G2) performed better in C:P~800 diet. Dual 14C/33P radiotracer assays clearly show that this GxE interaction is driven by physiological differences in the processing of C and P. G1 was more efficient in C processing, while G2 was more efficient in P use. Microarrays revealed that the genotypes differed in the expression of 6057 genes. Most of these genes were involved in pathways already known to be sensitive to stoichiometric imbalances. Our study provides the first step to couple functional genomics with ecologically explicit frameworks to understand the complexity of processes underlying GxE interactions.

overall_design: 2 genotypes of Daphnia pulex, two dietary treatments (high and low phosphorus Scenedesmus algal, C:P= 100, and 800, respectively), exposed 6hours and 3days


title: Unraveling the rat blood genome-wide transcriptome after oral administration of Lavender oil by a two-color dye-swap DNA microarray approach

status: Public on Apr 02 2015

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: Lavender oil (LO) is commonly used oil in aromatherapy, with well-defined volatile components linalool and linalyl acetate, in non-traditional medicine. To understand and demonstrate the potential positive effects of LO on the body, we have established an animal model for investigating the orally administered LO effects genome-wide in the rat tissues. In this data submission, we investigate the effect of LO ingestion in the blood. These results are the first such inventory of genes that are affected by lavender essential oil (LO) in the blood of an animal model, forming the basis for further functional analysis and investigation.

overall_design: Briefly, rats were administered LO at 5 mg/kg (usual therapeutic dose in humans) followed by screening of differentially expressed genes in the tissues, using a 4×44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA) in conjunction with a dye-swap approach.

first: Motohide

last: Hori

first: Hiroko

last: Kubo

first: Junko

last: Shibato

first: Tomomi

last: Saito

first: Tetsuo

last: Ogawa

first: Seiji

last: Shioda

first: Randeep

last: Rakwal


title: Quantitative transcriptomic analysis of wild type and metabolic mutants of Clostrdidium acetobutylicum ATCC824 under different physiological conditions

status: Public on Jul 01 2015

city: Toulouse

first: Philippe

last: Soucaille

address: 135 avenue de Rangueil

institute: INSA Toulouse

summary:
Transcriptomic analysis was applied to acidogenic, solventogenic and alcohologenic steady-state C. acetobutylicum cells for understanding the regulation of the metabolism of this organism.
Used microarray is Clostridium acetobutylicum ATCC824 transcriptional 44k v4, correspondance to GPL10908

overall_design: Phosphate-limited continuous cultures of C. acetobutylicum were performed under acidogenesis (pH 6.3, 995 mM of carbon from glucose), solventogenesis (pH 4.4, 995 mM of carbon from glucose) and alcohologenesis (pH 6.3, 498 mM of carbon from glucose and 498 mM of carbon from glycerol). Samples were collected for three biological replicates from one control strain and three metabolic mutants, respectively.  Total RNA of 36 samples was extracted using an RNeasy Midi kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions with the supplementation of DNase treatment using RNase-Free DNase Set (Qiagen). Agilent microarray for Clostridium acetobutylicum ATCC 824 (4x44K AMADID 024247) was used. The RNAs were labeled with a Low Input Quick Amp Labeling kit and hybridized following a one-color microarray-based gene expression analysis protocol.

first: Minyeong

last: Yoo

first: Gwénaëlle

last: Bestel-Core


title: microRNAs expression in kidneys from normal, cisplatin induced AKI rats and those with the restoration of MSCs

status: Public on Mar 11 2015

city: Zhenjiang

first: Yuan

last: Zhu

address: xuefu road

institute: Jiangsu Key Laboratory of Medical Science and Laboratory Medicine

summary: The availability of mesenchymal stem cells in kidney injury repair has been demonstrated. However, the underlying molecular mechanism remains not well understood. Herein, we profiled the altered microRNAs in renal tissiues from cisplatin-induced acute kidney injury (AKI) rats administrated with or without rat bone marrow mesenchymal stem cells, normal kidneys as control. Sprague Dawley rats were administrated with PBS by caudal vein after 24h peritoneal injection of 6mg/mg cisplatin, short for g2. 1×106 MSCs were injected to rats after 24h peritoneal injection of cisplatin, short for g3. Kidneys from healthey rats were used as control, short for g1. Renal tissues were collected at day 5 after treatment. There were 44 micorRNAs changed with significance between g2 and g3, among which 36 microRNAs upregulated and 8 microRNAs downregulated.

overall_design: Cisplatin induced microRNAs expression in kidneys were profiled after administrated with PBS or MSCs for 4 days. In g2 and g3,three independent experiments were performed, while two in g1.

first: Hui

last: Qian

first: Wen

last: Xu

first: Yong

last: Yan


title: Expression analysis of kairomone responsive genes in Daphnia pulex

status: Public on May 13 2015

city: Utsunomiya

first: Hitoshi

last: Miyakawa

state: Tochigi

address: 350 Mine-machi

institute: Utsunomiya University

type: Expression profiling by genome tiling array

summary: Investigation of gene expression level changes in Daphnia pulex MFP strain between in the presence or absence of Chaoborus kairomone.

overall_design: 12 samples (4 conditions x 3 replicates) in one 12-plex NimbleGen array GPL11278

first: Taisen

last: Iguchi


title: Transcriptomic analysis of prefrontal medial cortex, hippocampus and nucleus accumbens of alcohol-preferring and nonpreferring rats

status: Public on Jan 17 2015

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

summary:
Animal models provide opportunity to study neurobiological aspects of human alcoholism.  Changes in gene expression have been implicated in mediating brain function, including reward system and addiction.  The current study aimed to identify novel genes that may underlie ethanol preference.  Microarray analysis comparing gene expression in nucleus accumbens (NAc), hippocampus (HP) and prefrontal medial cortex (mPFC) was performed in two rat strains selected for extreme levels of ethanol preference - Warsaw High Preferring (WHP) and Warsaw Low Preferring (WLP).  The identified candidate genes may underlie differential ethanol preference in rat model of alcoholism.

This study was supported through funding from the following grants: Polish Scientific Committee Grant 2011/03/N/NZ29/05222, Polish Ministry of Science and Higher Education Grants “Iuventus Plus” (IP2011 030371) and N N519 657940.

overall_design: This is analysis of 18 RNA samples, including 9 technical replicates.  Two strains of rats selected for extreme levels of ethanol preference (low preferring WLP and high preferring WHP) were compared.  Three brain areas (nucleus accumbens, prefrontal medial cortex and hippocampus) were studied.  For each brain area, 6 RNA samples (including 3 technical replicates) were analyzed.  Each RNA sample consist of of equal amounts of total RNA from 3 male rats.  Comparisons: Nucleus accumbens of WHP vs. Nucleus accumbens of WLP; Prefrontal medial cortex of WHP vs. Prefrontal medial cortex of WLP; Hippocampus of WHP vs. Hippocampus of WLP. 3 biological replicates in each comparison.

first: Joanna

last: Goscik

first: Wanda

last: Dyr.

first: Martyna

last: Murat

first: Grzegorz

last: Juszczak

first: Danuta

last: Ryglewicz

first: Artur

middle: H

last: Swiergiel

first: Marek

last: Wieczorek

first: Roman

last: Stefanski

first: Pawel

last: Lisowski


title: Increase in membrane cholesterol of neurons in culture recapitulates Alzheimer’s disease early phenotypes.

status: Public on Jan 15 2015

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

institute: INSERM U1127-CNRS UMR7225-UPMC

summary: Levels of membrane-associated cholesterol were shown to be increased in the brain of individuals with sporadic Alzheimer’s disease (AD) and correlated with the severity of the disease. We previously found that heavy membrane cholesterol burden promotes amyloid precursor protein (APP) endocytosis and processing, leading to increased amyloid-A) secretion. We hypothesized that such an increase of cholesterol could trigger sporadic AD. We thus acutely loaded the plasma membrane of neurons in culture with cholesterol to reach the 30 % increase observed in AD brains. We showed by multiplex electro-chemiluminescence immuno-assay that transient membrane cholesterol loading produced a significant increase of A42 secretion. We also found that early endosomes were enlarged and more prone to aggregation using confocal and electron microscopy and that APP vesicular transport in neuronal processes was slowed down using fluorescence live-imaging. In addition, treatment of neurons with cholesterol induced changes in gene expression profile that are reminiscent of early AD. This model of membrane cholesterol increase in cultured neurons reproduces most of early AD changes and could thus be relevant for deciphering early mechanisms and design new targets for sporadic AD.

overall_design: In this study, we loaded the plasma membrane of neurons with 30% more cholesterol and observed the effects on gene expression. We compared gene expression of primary hippocampal neurons treated or not with  cholesterol using 4 independant replicates in each group.

first: Catherine

last: Marquer

first: Jeanne

last: Lainé

first: Linda

last: Hanbouch

first: Camille

last: Lemercier-Neuillet

first: Nathalie

last: Pierrot

first: Koen

last: Bossers

first: Mickael

last: Le

first: Fabian

last: Corlier

first: Caroline

last: Benstaali

first: Frederic

last: Saudou

first: Gopal

last: Thinakaran

first: Jean-Noël

last: Octave

first: Charles

last: Duyckaerts

first: Marie-Claude

last: Potier


title: Macrophage gene expression associated with remodeling of the prepartum rat cervix: Microarray and pathway analyses

status: Public on Jan 27 2015

city: Colton

first: Abigail

middle: Elisa

last: Dobyns

state: CA

address: 2255 Cahullia St, apt #69

department: Perinatal Biology

institute: Loma Linda University

summary:
As the critical gatekeeper for birth, prepartum remodeling of the cervix is associated with increased resident macrophages (Mφ), proinflammatory processes, and extracellular matrix degradation. This study tested the hypothesis that expression of genes unique to Mφs characterizes the prepartum from unremodeled nonpregnant cervix.
Perfused cervix from prepartum day 21 postbreeding (D21) or nonpregnant (NP) rats, with or without Mφs, had RNA extracted and whole genome microarray analysis performed.  By subtractive analyses, expression of 194 and 120 genes related to Mφs in the cervix from D21 rats were increased and decreased, respectively.  In both D21 and NP groups, 158 and 57 Mφ genes were also more or less up- or down-regulated, respectively.

overall_design: Gene expression from four groups: D21 pregnant or non-pregnant rat cervix, with or without macrophages. Comparing the with and without macrophage groups can show genes that are expressed only in macrophages.

middle: E

first: Ravi

last: Goyal

first: Lauren

last: Carpenter

first: Tom

last: Freeman

first: Lawrence

last: Longo

first: Steven

last: Yellon


title: Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia

status: Public on Mar 07 2015

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

institute: Ghent University

summary:
Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli.
Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of non-lineage specific genes was conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families.

overall_design: Whole transcriptome dual color arrays were used to discover differentially expressed genes following sub-lethal exposure to five cyanobacteria in D. pulex. RNA was  isolated from eight independent and concurrently replicated exposures of Daphnia to control and five cyanobacteria conditions. RNA was hybridized to microarrays using a standard, control vs. treated design that included dye swaps. Cyanobacteria were Anabaena (ANA), Aphanizomenon (Aph), Cylindrospermopsis (Cyl), Nodularia (Nod) and Oscillatoria (Osl).

first: Michael

last: Pfrender

first: Jacqueline

last: Lopez

first: Dieter

middle: I

last: De Coninck

first: Colin

last: Janssen

first: Joseph

last: Shaw

first: Karel

middle: A

last: De Schamphelaere


title: A DNA Microarray Analysis of Rat Intestine, Spleen and Liver Transcriptome after Oral Administration of Lavender Oil

status: Public on Nov 26 2014

first: RANDEEP

last: RAKWAL

summary: Lavender oil (LO) – a commonly used oil in aromatherapy with well defined volatile components linalool and linalyl acetate – use in non-traditional medicine is increasing globally. To understand and provide evidence for the potential positive effects of LO on the body, we have established an animal model for investigating in this current study, orally administered LO effects genome-wide in rat intestine, spleen and liver. The rats were administrated LO at 5 mg/kg (usual threaupeutic dose in humans) followed by screeing of differentially expressed genes in the tissues utlilizing a 4x44K whole genome rat chip (Agilent microarray platform) in conjunction with a dye-swap approach, one of the novelties of this study. Fourteen days after treatment (LO) and in comparison with a control group (sham), a total of 156 and 154 up (>1.5 fold)- and down (<0.75 fold)-regulated genes, 174 and 66 up- (>1.5 fold)- and down (<0.75 fold)-regulated genes, and 222 and 322 up- (>1.5 fold)- and down (<0.75 fold)-regulated genes showed differential expression at the mRNA level, in the intestine, spleen and liver, respectively. Reverse transcription-polymerase chain reaction (RT-PCR) validation of highly up- and down-expressed genes revealed the regulation of Papd4, Lrp1b, Alb, Cyr61, Cyp2c, and Cxcl1 genes, by LO, as examples in these tissues. Using bioinformatics functionally categorization of differentially expressed genes was done by their Gene Ontology (GO) revealing their diverse functions and potential roles in LO-mediated effects in rat. Present results are a first such inventory of genes affected by the essential oil of Lavender (LO) in an animal model.

overall_design: Rats were administrated LO at 5 mg/kg (the usual threaupeutic dose in humans) followed by the screeing of differentially expressed genes in the intestine, spleen, and liver utlilizing a 4x44K whole genome rat chip (Agilent) and the dye-swap approach.

first: Hiroko

last: Kubo

first: Junko

last: Shibato

first: Tomomi

last: Saito

first: Tetsuo

last: Ogawa

first: Randeep

last: Rakwal

first: Seiji

last: Shioda


title: Microarray analysis on livers of young Nile rats fed palm fruit juice

status: Public on Jan 13 2015

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

summary:
Microarray analysis on livers of young (three weeks old) Nile rats (Arvicanthis niloticus) fed with either a high carbohydrate diet only (percentage energy from carbohydrate:fat:protein = 70:10:20, 16.7 kJ/g) or a high carbohydrate diet supplemented with palm fruit juice (PFJ) (415 ml of 13000 ppm gallic acid equivalent (GAE) for a final concentration of 5.4 g GAE per kg diet or 2.7 g per 2000 kcal)
PFJ (415 ml of 13000 ppm gallic acid equivalent (GAE) for a final concentration of 5.4 g GAE per kg diet or 2.7 g per 2000 kcal) was supplemented to young Nile rats (Arvicanthis niloticus) given a high carbohydrate diet (percentage energy from carbohydrate:fat:protein = 70:10:20, 16.7 kJ/g) to observe for possible anti-diabetic effects. Livers were harvested four weeks after the feeding regimen for gene expression studies. Results from the microarray data analysis carried out show that rats given PFJ had down-regulated insulin signalling, consistent with anti-diabetic effects observed in vivo.

overall_design: Total RNA obtained from livers of young Nile rats (Arvicanthis niloticus) given PFJ in a high carbohydrate diet (four weeks after the feeding regimen) were compared to controls (three replicates in the treatment group versus four replicates in the control group)

first: K

last: Hayes

first: Ravigadevi

last: Sambanthamurthi


title: PRR7 is a novel NMDA-dependent inhibitor of c-Jun ubiquitination in neurons

status: Public on Oct 25 2014

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Elevated c-Jun levels result in apoptosis and are evident in neurodegenerative disorders such as Alzheimer's disease and dementia and after global cerebral insults such as stroke and epilepsy. NMDA receptor (NMDAR) antagonists block c-Jun upregulation and prevent neuronal cell death following excitotoxic insults. However, little is known about the molecular mechanisms that regulate c-Jun abundance in neurons. Here we show that PRR7, a component of synaptic junctions, can upregulate c-Jun levels by inhibiting its ubiquitination in neurons. PRR7 interacts with the GLUN1 subunit of NMDARs and is upregulated in the nucleus following NMDAR activation. We show that PRR7 interacts with the E3 ligase SCFFBW7 (FBW7) and blocks the FBW7-mediated ubiquitination of c-Jun. PRR7 overexpression increases c-Jun-dependent transcriptional activity and promotes neuronal death. Microarray assays indicate  that both Prr7 knockdown or overexpression alter the abundance of c-Jun-regulated transcripts associated with cellular viability as well as synaptic function. Moreover, Prr7 knockdown attenuates NMDA-mediated excitotoxicity in primary neuronal cultures. Our results show that PRR7 links NMDAR activity to c-Jun function and provide insight into the processes that underlie NMDA-dependent excitotoxicity.

overall_design: Four biological replicas of each of the four conditions: NO = not transduced with virus; NT = transduced with control lentiviruses containing a non-targeting shRNA sequence; KD = transduced with lentiviruses expressing PRR7-specific shRNAs; OE= transduced with lentiviruses to overexpress PRR7.

first: Dana

last: Savariego

first: Matous

last: Hrdinka

first: Sanda

last: Kreutz

first: Bryen

last: Jordan


title: Expression profiling of rat heart and blood after amiodarone treatment

status: Public on Mar 23 2015

city: Agripolis - Legnaro (PD)

first: Mery

last: Giantin

state: Padova

address: Viale Università, 16

department: Dip. Biomedicina Comparata e Alimentazione

country: Italy

institute: University of Padova

summary: In the present study, an oligonucleotide microarray platform was used to compare expression profiles of heart and blood in rats treated with amiodarone against respective controls. Male Sprague-Dawley (CD) rats, which were 10 weeks old and weighed 290-320 grams at the beginning of the study, have been treated for ten days with amiodarone by oral route at a dose of 300mg/Kg/die. The study has been constituted by a control group, which received the vehicle (methylcellulose 1%, w/v), and by a treatment group (10 animals for both groups). For each tissue sample, total RNA has been individually extracted and evaluated. For each tissue, three pools/group (2 pools composed of 3 animals and the last one by 4) have been used for microarray analysis. A modulation of 600 genes in heart and 8300 genes in blood has been obtained.

overall_design: In this study, we analyzed the gene expression profiles of 6 pools (3 composed of control rats and 3 composed of rats treated with amiodarone) for each tissue (blood and heart) using the Agilent-014879 Rat oligo microarray platform (12 arrays, no replicates) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal remaining, after all the FE processing steps have been completed, is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal. The heart and blood samples were normalized separately.

first: Nicola

last: Bocchini

first: Serena

last: Ferraresso


title: Down-regulation as the dominant hippocampal gene expression profile with voluntary resistance wheel running by DNA microarray analysis

status: Public on Oct 09 2014

first: RANDEEP

last: RAKWAL

summary: Exercise improves brain function enhancing neuronal plasticity and cognitive enhancement. For voluntary resistance wheel running (RWR) exercise, with a load of 30% of body weight, we reported enhancement of neurogenesis and spatial memory associated with hippocampal brain-derived neurotrophic factor (BDNF) signaling compared to wheel running (WR) without a load (Lee et al., 2012; Lee et al., 2013). Despite these new evidences, mechanisms for RWR-induced improvement of hippocampal function remained to be clarified. In the present study, we have utilized the high-throughput DNA microarray approach to gain deep insight into molecular mechanisms underlying these changes that could be novel targets of RWR-induced hippocampal plasticity. To do so, whole genome (4x44K) high-density oligonucleotide microarrays were used to monitor the expression level of gene transcripts in the hippocampus of rats voluntary running for 4 weeks in comparison with sedentary animals. These rats showed a significant decrease in average running distance although average work levels immensely increased 12-fold in the RWR group, resulting in muscular adaptation for the fast-twitch plantaris muscle. DNA microarray analysis revealed that 122 (sedentary x WR) and 157 (sedentary x RWR) genes were up-regulated (> 1.5-fold change) as compared with 97 (sedentary x WR) and 467 (sedentary x RWR) down-regulated genes (< 0.75-fold change). Functional categorization using the Ingenuity Pathway Analysis (IPA) revealed expression pattern changes in the major categories of disease and disorders, molecular functions and physiological system development and function. Among these, RWR up-regulated genes such as NFATc1, AVPR1A and FGFR4, which are crucial role for neuronal development and its functions. The down-regulated inflammatory cytokines (IL1B, IL10, IL2RA, TNF) and chemokines (CXCL1, CXCL9, CXCL10, CCL2, CCL13, CCR4) might be important to neuronal dysfunction and vulnerability. Taken together, these gene candidates are suggested to play a critical role in hippocampal plasticity. This is a first study presenting not only new information into the voluntary RWR influenced transcriptome in the rat hippocampus, but also provides a hypothesis for the RWR influenced enhancement in brain function.

overall_design: 10-week-old male Wistar rats were randomly allocated to three groups: (1) housed in standard cages and used as non-active controls (sedentary, n = 10), (2) wheel running with no resistance (WR, n = 8), and (3) housed in cages with resistance running wheels with an adjustable resistance (RWR, n = 8). Rats of both running wheel groups (WR and RWR) were housed individually and had free access to a specially designed running wheel apparatus for 24 h/day. Between 08:00 and 12:00 on the day after the final day of exercise, the animals were immediately decapitated using a guillotine. The hippocampi were rapidly dissected, snap frozen in liquid nitrogen and stored at —80°C prior to further analysis. The deep-frozen hippocampi were transferred to a precooled (in liquid nitrogen) mortar and ground with a pestle to a very fine powder with liquid nitrogen. Total RNA was extracted and validated followed by checking subsequently synthesized cDNA by RT-PCR. A rat 4x44K whole genome oligo DNA microarray chip was used for global gene expression analysis using the hippocampi. Fluorescently labeled targets of Sed, WR and RWR samples were hybridized to the same microarray slide with 60-mer probes. A flip labeling (dye swap or reverse labeling with Cy3 and Cy5 dyes) procedure was followed to nullify the dye bias associated with unequal incorporation of the two Cy dyes into cDNA. Briefly, to select differentially expressed genes, we identified genes that were up regulated in chip 1 (Cy3/Cy5 label for sedentary and WR, respectively) but down regulated in chip 2 (Cy3/Cy5 label for WR and sedentary, respectively) for the hippocampus. The same selection criteria were applied for chips 3-4 (sedentary and RWR). Hybridization and wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an agilent microarray scanner. The functional and network analysis were generated through the use of IPA (Ingenuity® Systems, www.ingenuity.com). To validate gene changes in array data and test the BDNF signaling-related molecules and expression of select transcripts were determined by quantitative real-time RT-PCR.

first: Min-Chul

last: Lee

first: Koshiro

last: Inoue

first: Hideaki

last: Soya


title: Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia

status: Public on Oct 02 2014

first: Jacqueline

last: Lopez

summary: In this study we use nimblegen high-density arrays to examine gene expression regulation in a common-garden experiment varying thermal environments. We report genome-wide patterns of gene expression in two heat tolerant southern and two heat-sensitive northern clones of Daphnia pulex exposed to either optimal (18°C) or substressful (28°C) temperatures.

overall_design: Four competitive hybridizations of heat tolerant clones BW102 (hereafter B) and KSP3 (hereafter K),  and heat sensitive clones EB1 (hereafter E) and CHQ3 (hereafter   C) in response to thermal stress of either 18 degrees Celcius (here after 18) or 28 degrees (hereafter 28) in a loop design where each hybridization was replicated four times with two dye-swaps nested in each set of replicates.

first: Lev

last: Yampolsky

first: John

middle: K

last: Colbourne

first: Michael

last: Pfrender


title: Transcriptional network analysis reveals that AT1 and AT2 Angiotensin II receptors are both involved in the regulation of genes essential for glioma progression

status: Public on Dec 20 2014

city: São Paulo

first: Hatylas

last: Azevedo

state: Sao Paulo

address: Doutor Arnaldo Avenue, 455

department: Pediatrics

country: Brazil

institute: University of São Paulo

summary: Gliomas are aggressive primary brain tumors, presenting surgery limitations due to their highly infiltrative potential. The expression of Angiotensin II (Ang II) receptors in human astrocytomas was previously associated with a poor prognosis. Accordingly, this study was undertaken to reveal the molecular mechanisms underlying Ang II actions in gliomas through the transcriptomic analysis of glioma cells exposed to Ang II.   C6 glioma cells were treated with Ang II and specific antagonists of AT1 and AT2. Total RNA was isolated at three and six hours intervals and submitted to oligonucleotide microarray protocol. The differentially expressed genes were obtained by paired t-tests with p<0.05 and interpreted using Venn diagrams, functional enrichment and protein interaction network analyses. Validation of microarray results was carried out through qPCR experiments of selected genes.  We found a high number of significant genes with low fold changes in gene expression at the time intervals studied. These genes were regulated in a time dependent-manner, with most gene expression changes being exclusive to one of the time intervals evaluated. Our results indicated that blocking AT1 or AT2 changed the expression of genes involved in regulation of transcription, cell cycle, cell proliferation, differentiation, apoptosis, cell adhesion, cell migration, regulation of actin cytoskeleton, protein transport and protein ubiquitination. Additionally, the signaling pathways over-represented by the significant genes were ErbB, mTOR, MAPK, neurotrophin, insulin and Wnt. Finally, interactome analyses revealed hub genes associated with cell proliferation, survival, migration, transport, structural support, neurotrophin pathway, MAPK signaling and Wnt signaling.   Taken together, our findings implicate Ang II-transcriptional regulation in glioma progression by means of the modulation of genes participating in protumoral functions. This transcriptome pattern is observed upon Ang II activation of either AT1 or AT2 receptors, thereby highlighting the relevance of both receptor subtypes in glioma progression. Interactome analyses disclosed hub genes regulated by Ang II which may present higher control over their networks. These genes participate in biological functions that could enhance the degree of malignancy in gliomas and thus should be further explored.

overall_design: C6 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum, 100 Units/ml penicillin and 100 µg/ml streptomycin. Cells were seeded in cell culture dishes and incubated at 37°C/ 5% CO2 until becoming confluent. Then, these cells were pre-treated (30 minutes) with either AT1 receptor antagonist (Losartan: 10-5M) or AT2 receptor antagonist (PD123319: 10-5M) followed by Ang II treatment (10-7 M) according to the treatment scheme: Group 1 – control; Group 2 – cells only treated with Ang II; Group 3 – cells pre-treated (30 minutes) with Losartan and then treated with Ang II; Group 4 – cells pre-treated (30 minutes) with PD123319 and then treated with Ang II.                                                                                To identify which genes were significantly differentially expressed, paired t-tests (p<0.05) were performed in the following comparisons: Ang II x Control (3h); Ang II x Control (6h); Ang II +Los x Ang II (3h); Ang II +Los x Ang II (6h); Ang II +PD123319 x Ang II (3h); Ang II +PD123319 x Ang II (6h).

first: Hátylas

first: André

last: Fujita

first: Silvia

last: Bando

first: Priscila

last: Iamashita

first: Carlos

last: Moreira-Filho


title: In vitro ischemia triggers a transcriptional response to down-regulate synaptic proteins in hippocampal neurons.

status: Public on Jun 16 2014

city: Coimbra

first: Joana

middle: Filipa

last: Fernandes

state: -- Please Select --

address: Rua Larga, Faculdade de Medicina 2º andar, lab 206A Coimbra

department: Life Sciences

country: Portugal

institute: Center for Neuroscience and Cell Biology

summary: The present study has used whole-rat genome microarray expression profiling to identify genes whose expression is significantly altered in hippocampal neuronal cultures submitted to oxygen and glucose deprivation (OGD), an established in vitro model for cerebral global ischemia that is suitable for investigations at the molecular level. To do so, total RNA was extracted from hippocampal neuronal cultures at an early (7h) and delayed (24h) time point after OGD, as well as from control neurons. Analysis of gene ontology showed that OGD followed by 7h or 24h of recovery induces changes in the expression levels of genes related with inflammation, response to oxidative stress, metabolism, apoptosis, synaptic proteins and ion channels and, importantly, genes that show different expression levels are mainly specific to one of the two time points of recovery analyzed. The expression levels of several genes were confirmed by qPCR and were in good agreement with the microarray data, showing that the combined use of the OGD model and the microarray technology can be a useful tool for the study molecular mechanisms contributing to the neuronal demise after transient global ischemia.

overall_design: Ischemia induced gene expression in primary hippocampal neuronal rat cultures was measured at 7 and 24 hours after exposure to Oxygen and Glucose deprivation (OGD).  Three independent experiments were performed at each time (7 or 24 hours) as independent biological replicates.

first: Marta

last: Vieira

first: Laura

last: Carreto

first: Manuel

last: Santos

middle: B

last: Duarte

first: Ana

middle: L

last: Carvalho

first: Armanda