title: Chicken meat quality: muscle transcriptional profiles of chickens with high and low breast meat ultimate pH

status: Public on Feb 01 2017

city: Nouzilly

first: Cécile

last: Berri

address: Centre INRA Val de Loire

country: France

institute: INRA

summary: The processing ability of chicken meat is highly related to its ultimate pH (pHu), which is mainly determined by the amount of glycogen in the muscle at death. The molecular mechanisms involved in variations of those traits for chicken remain to be fully described. For that purpose, two chicken lines were divergently selected on breast meat pHu, i.e. the pHu- and the pHu+ lines. In this study, Chicken Genome Arrays (60 K) were used to compare muscle gene expression profiles of chickens from both lines. The final goal of this experiment is to identify biomarkers of low and high-pHu chicken meat. This study was supported by INRA and the French Ministry of Agriculture through the RFI CASDAR #1309 OPTIVIANDE.

overall_design: Breast muscle transcriptomics profiles of chickens issued from divergent selection (6th generation) caracterized by low  (average pHu = 5.55; n = 15 chickens) and  high breast meat ultimate pH (average pHu = 6.34; n = 16 chickens)

first: Stéphane

last: Beauclercq

first: Christelle

last: Hennequet-Antier

first: Sandrine

last: Lagarrigue

first: Marco

last: Moroldo

first: Elisabeth

last: Le Bihan-Duval

first: Anne

last: Collin

first: Jérôme

last: Lecardonnel


title: miR-193a-3p is a key tumor-suppressor in ulcerative colitis-associated colon cancer and promotes carcinogenesis through regulation of IL17RD.

status: Public on Apr 28 2015

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

country: USA

institute: University of Viginia

type:
Expression profiling by array
Other

summary: Patients with ulcerative colitis (UC) are at increased risk for colorectal cancer although mechanisms remain poorly understood. We sought to evaluate the role of miRNAs in neoplasia development in this high-risk population

overall_design: RNA was extracted from formalin fixed paraffin embedded tissue from  controls (n=12), UC without neoplasia (UC, n=9), UC-associated neoplastic tissue (UCN, n=10; HGD-4, CRC-6) and adjacent tissue (n=9). miRNA array analysis was performed using the Nanostring nCounter System v1

first: Joel

last: Pekow

first: Katherine

last: Meckel

first: Urszula

last: Dougherty

first: Xindi

last: Chen

first: Anas

last: Almoghrabi

first: Reba

last: Mustafi

first: Fatma

last: Buton

first: John

last: Hart

first: David

last: Rubin

last: Kwon

first: Marc

last: Bissonnette


title: Expression profiling of long noncoding RNAs and mRNAs in mouse kidney tissue

status: Public on Dec 01 2016

city: Beijing

first: Qinghua

last: Cui

address: 38 Xueyuan Road

country: China

institute: Peking University

summary: Long noncoding RNA profile in the mouse left kidney and right kidney.

overall_design: In the study presented here, we mixed the three mouse left kidneys and three mouse right kidneys and identified the genome-wide expression level of lncRNAs.

first: Cui

last: Qinghua

first: Yang

last: Jichun


title: Multiple Low-dose Challenges in a Rhesus Macaque AIDS Vaccine Trial Result in an Evolving Host Response that affects Protective Outcome

status: Public on Sep 30 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Using whole-blood transcriptional profiling, we investigated differences in the host response to vaccination and challenge in a rhesus macaque AIDS vaccine trial. Samples were collected from animals prior to and after vaccination with live irradiated vaccine cells secreting the modified endoplasmic reticulum chaperone gp96-Ig loaded with SIV peptides, either alone or in combination with a SIV-gp120 protein boost. Additional samples were collected following multiple low-dose rectal challenge with SIVmac251. Animals in the boosted group had a 73% reduced risk of infection. Surprisingly, few changes in gene expression were observed during the vaccination phase. Focusing on post-challenge comparisons, in particular for protected animals, we identified a host response signature of protection comprised of strong interferon signaling after the first challenge, which then largely abated after further challenges. We also identified a host response signature, comprised of early macrophage-mediated inflammatory responses, in animals with undetectable viral load five days after the first challenge, but which had unusually high viral titers after subsequent challenges. Statistical analysis showed that prime-boost vaccination significantly lowered the probability of infection in a time-consistent manner throughout several challenges. Given that humoral responses in the prime-boost group were highly significant pre-challenge correlates of protection, the strong innate signaling after the first challenge suggests that interferon signaling enhances vaccine-induced antibody responses and is an important contributor to protection from infection during repeated low-dose exposure to SIV.

overall_design: 36 Indian-origin outbred, young adult, male and female rhesus macaques divided into thre vaccination groups of 12 animals each. Groups were balanced for Mamu-A*01 (three in each group), Mamu-B*08 (one in each group), and for susceptible and resistant TRIM5α alleles. There were no Mamu-B*17+ animals. The prime group (PG) received Gp96 SIV Ig vaccine 292 cells that were transfected with plasmids encoding gp96-Ig, SIVmac251 rev-tat-nef, Gag and gp160 (35). They were injected intraperitoneally with 107 irradiated gp96SIVIg vaccine cells in HBSS, which secrete 10 μg of gp96SIVIg per 24 h. For the prime-boost group (PBG), 100 g of rSIVgp120 protein was added to the vaccine cells. The control group received 292-gp96 Ig cells not transfected with SIV antigens. After a 32-week vaccination phase, which consisted of priming in weeks 0, 6, and 25 and (for the PBG only) additional boosts in weeks 6 and 25, all animals were subject to up to seven weekly low-dose intrarectal challenges starting at 33-week with SIVmac251 at a dosage of 120 TCID50. Whenever an animal had detectable viral load (>50 copies/ml of plasma) at 5 days post challenge, it was considered viremic, further challenges were suspended, and only viral load screening continued on a weekly basis. Whole blood samples (preserved in PAXgene tubes) were collected 2 weeks prior to the first prime, 1 week after the first prime, 2 weeks before and 1 week after the third prime, 1 week before the first challenge, for newly infected animals five days into the corresponding study week and from viremic animals four days into the study week (also denoted as challenge 2 and challenge 3).  Total RNA was isolated from Paxgene tubes using Paxgene Blood RNeasy Mini Kits (Qiagen) following the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

first: Christian

last: Selinger

first: Natasa

last: Strbo

first: Louis

last: Gonzalez

first: Lauri

last: Aicher

first: Jeffrey

middle: M

last: Weiss

first: G

middle: L

last: Law

first: Robert

middle: E

last: Palermo

first: Eckhard

middle: R

last: Podack

middle: G


title: Fibroblast growth factor 21 reflects liver fat accumulation and dysregulation of signalling pathways in the liver of C57BL/6J mice

status: Public on Aug 09 2016

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Fibroblast growth factor 21 (Fgf21) has emerged as a potential plasma marker to diagnose non-alcoholic fatty liver disease (NAFLD). To study the molecular processes underlying the association of plasma Fgf21 with NAFLD, we explored the liver transcriptome data of a mild NAFLD model of aging C57BL/6J mice at 12, 24, and 28 months of age. The plasma Fgf21 level significantly correlated with intrahepatic triglyceride content. At the molecular level, elevated plasma Fgf21 levels were associated with dysregulated metabolic and cancer-related pathways. The up-regulated Fgf21 levels in NAFLD were implied to be a protective response against the NAFLD-induced adverse effects, e.g. lipotoxicity, oxidative stress and endoplasmic reticulum stress. An in vivo PPARalpha challenge demonstrated the dysregulation of PPARalpha signalling in the presence of NAFLD, which resulted in a stochastically increasing hepatic expression of Fgf21. Notably, elevated plasma Fgf21 was associated with declining expression of Klb, Fgf21’s crucial co-receptor, which suggests a resistance to Fgf21. Therefore, although liver fat accumulation is a benign stage of NAFLD, the elevated plasma Fgf21 likely indicated vulnerability to metabolic stressors that may contribute towards progression to end-stage NAFLD. In conclusion, plasma levels of Fgf21 reflect liver fat accumulation and dysregulation of metabolic pathways in the liver.

overall_design: Male C57Bl/6J mice were divided to 3 dietary intervention groups: Control (AIN-93W), 30% calorie restriction (CR; AIN-93W-CR) and medium fat (MF; AIN-93W-MF; 25% energy from fat). Dietary interventions started at the age of 9 weeks and sacrifice was performed at the age of 6, 12, 24 and 28 months. We performed various measurements on metabolic parameters and gene expression analysis. This entry represents the microarray data.

first: Fenni

last: Rusli

first: Joris

last: Deelen

first: Evi

last: Andriyani

first: Mark

middle: V

last: Boekschoten

first: Carolien

last: Lute

first: Erik

middle: B

last: van den Akker

last: Müller

first: Marian

last: Beekman

first: Wilma

middle: T

last: Steegenga


title: Root and shoot performance of Arabidopsis thaliana exposed to elevated CO2: a physiologic, metabolic and transcriptomic response.

status: Public on Jan 02 2017

city: pamplona

first: Ivan

last: Jáuregui Mosquera

state: Navarra

address: Campus de Arrosadia, s/n,  Dpto. Ciencias del Medio Natural

country: Spain

institute: Universidad Pública de Navarra

summary:
In this study we explain the physiological, biochemical and gene expression mechanisms adopted by ammonium nitrate-fed Arabidopsis thaliana plants growing under elevated [CO2], highlighting the importance of root-to-shoot interactions in these responses
A transcriptomic analysis enabled the identification of photoassimilate allocation and remobilization as fundamental process used by the plants to maintain the outstanding photosynthetic performance. Moreover, based on the relationship between plant carbon status and hormone functioning, the transcriptomic analyses provided an explanation of why phenology accelerates in elevated [CO2] conditions.

overall_design: Arabidopsis thaliana, Columbia 0 ecotype (col 0) plants grown under hydroponic conditions. The nitrogen (N) source was NH4NO3 at 0.75 mM concentration. 5 weeks exposure to CO2 treatments, previous to first flower were buds visible (see Supplemental Figure 1 for the image of the plants), in 3.9 growth stage ontology from the scale described by Boyes (2001).

first: Iván

last: Jáuregui

first: Pedro

last: Aparicio-Tejo

first: Concepción

last: Avila

first: Marina

last: Rueda-López

first: Iker

last: Aranjuelo


title: Disease severity is associated with differential gene expression at the early and late phases of infection in non-human primates infected with different H5N1 highly pathogenic avian influenza viruses

status: Public on May 27 2014

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

country: Japan

institute: Japanese Science and Technology Agency

summary: Occasional transmission of highly pathogenic avian H5N1 influenza viruses to humans causes severe pneumonia with high mortality. To better understand the mechanisms via which H5N1 viruses induce severe disease in humans, we infected cynomolgus macaques with six different H5N1 strains isolated from human patients and compared their pathogenicity and the global host responses to the virus infection. Although all H5N1 viruses replicated in the respiratory tract, there was substantial heterogeneity in their replicative ability and in the disease severity induced, which ranged from asymptomatic to fatal. A comparison of global gene expression between severe and mild disease cases indicated that interferon-induced up-regulation of genes related to innate immunity, apoptosis, and antigen processing/presentation in the early phase of infection was limited in severe disease cases, although interferon expression was up-regulated in both severe and mild cases. Furthermore, co-expression analysis of microarray data, which reveals the dynamics of host responses during the infection, demonstrated that the limited expression of these genes early in infection led to a failure to suppress virus replication and to the hyperinduction of genes related to immunity, inflammation, coagulation, and homeostasis in the late phase of infection, resulting in a more severe disease. Our data suggest that the attenuated interferon-induced activation of innate immunity, apoptosis, and antigen presentation in the early phase of H5N1 virus infection leads to subsequent severe disease outcome.

overall_design:
Bronchial brushes  for microarray studies were obtained from female cynomolgus macaques infected with influenza viruses. Three animals per group were inoculated with one of three H5N1 influenza viruses (VN3028II, VN30259 or VN3040).
The early phase of infection refers to timepoints Pre (prior to infection), 1, and 3 days post-infection. The late phase of infection refers to days 5 and 7 post-infection.  Samples collected prior to infection (labeled as Pre) served as control data for each infection group.

first: Yukiko

last: Muramotmo

first: Jason

last: Shoemaker

first: Le

last: Mai

first: Yasushi

last: Itoh

first: Daisuka

last: Tamura

first: Yuko

last: Sakai-Tagawa

first: Hirotaka

last: Imai

first: Ryuta

last: Uraki

first: Ryo

last: Takano

first: Eiryo

last: Kawakami

first: Mutsumi

first: Kiyoko

last: Okamoto

first: Hirohito

last: Ishigaki

first: Hitomi

last: Mimuro

first: Chihiro

last: Sasakawa

last: Matsuoka

first: Takeshi

last: Noda

first: Satoshi

last: Fukuyama

first: Kazumasa

last: Ogasawara

first: Hiroaki

last: Kitano


title: miRNA expression profiling in myocardial tissue by caloric restriction initiated in different aged mice

status: Public on Nov 17 2016

city: Nanjing

first: yunlu

last: sheng

state: Jiangsu

address: 300 Guangzhou Road

department: Department of Gerotology

institute: The First Hospital Affiliated to Nanjing Medical University

summary: Using the highly sensitive miRNA array, we assessed the effect of CR, beginning in different ages, on modulating miRNAs expression in the heart and found miRNAs were related to cardiac aging and changed differently after 3 months CR during aging.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, 6 samples from young, middle-aged, and old mice with or without caloric restriction (CR) were used to acquire the miRNA expression profiling thus to elucidate the possible molecular pathways underlying the observed different effects of CR on cardiac aging.

first: Yunlu

last: Sheng

first: Min

last: Huang


title: Transcriptomes of whole blood and PBMC in chickens.

status: Public on Jul 22 2016

city: Rennes

first: Colette

last: DESERT

address: 65 Rue de St Brieuc

institute: Agrocampus INRA UMR1348 PEGASE

summary:
The gene expression profiles of chicken whole blood (WB) and peripheral blood mononuclear cells (PBMC) have been characterized and compared by microarray analysis.
This study  highlights the respective advantages of each blood cell subset and show that whole blood is more suitable for large scale studies and allows for the exploration of biological processes which are so far poorly investigated.

overall_design: Whole blood and PBMC from four male broilers (9 weeks old) were collected and isolated before -80°C conservation.

first: C

last: Désert

first: E

last: Merlot

first: T

last: Zerjal

first: B

last: Bed’hom

first: S

last: Härtle

first: A

last: Le Cam

first: P

middle: F

last: Roux

last: Baeza

first: F

last: Gondret

first: M

middle: J

last: Duclos

last: Lagarrigue


title: Analysis of gene expression in leaves of Medicago truncatula plants inoculated with arbuscular mycorrhizal fungi and plants fertilized with phosphate

status: Public on Apr 26 2016

city: Göteborg

first: Cornelia

last: Spetea

address: Carl Scottbergsgata 22B

department: Biological and Environmental Sciences

country: Sweden

institute: Gothenburg University

summary: Arbuscular mycorrhizas (AM) are the most common symbiotic associations between plant’s root compartment and fungi. They can provide both nutritional benefit (mostly inorganic phosphate) leading to improved growth and non-nutritional benefits including defense responses to environmental cues throughout the host plant, which in return delivers carbohydrates to the symbiont. However how transcriptional changes occurring in AM leaves differ from those induced by phosphate fertilization is poorly understood. We investigated systemic changes in the leaves of mycorrhized Medicago truncatula compared to non-mycorrhized control plants, and in phosphate fertilized plants compared to control plants.

overall_design: Leaves were harvested 4 weeks post inoculation from control, mycorrhized and phophate fertilized plants. Three biological replicates and 1-2 technical replicates were analyzed.

first: Lisa

last: Adolfsson


title: Long ncRNA in HCC cells

status: Public on Dec 01 2013

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

summary:
Normal human hepatocytes and 3 different HCC cell lines have been analyzed for the global expression of long non coding RNA (lncRNA).
Total RNA was extracted from each sample using RNeasy Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was assessed by Nanodrop ND-1000 and Bioanalyser2100.    DNA microarray  The Human Long Non-coding RNA Array was manufactured by Roche NimbleGen. Each array represents all long transcripts, both protein coding mRNAs and lncRNAs (long non-coding RNAs) in the human genome. More than 22000 lncRNAs are collected from the authoritative data sources including NCBI RefSeq, UCSC, RNAdb, lncRNAs from literatures and UCRs. Fluorescent cDNA targets were prepared using NimbleGen One-Color DNA Labeling Kit. Microarray hybridization was performed at 42°C for 16-20 hours in NimbleGen Hybridization System. After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.     Data Analysis  Raw data were extracted as pair files by NimbleScan software (version 2.5). NimbleScan software’s implementation of RMA offers quantile normalization and background correction. The Probe level (*_norm_RMA.pair) files and Gene summary (*_RMA.calls) files were produced. The gene summary files were imported into Agilent GeneSpring Software (version 10.0) for further analysis. Differentially expressed genes and non-coding RNA were identified through Fold-change screening. Unsupervised hierarchical clustering, GO analysis and Pathway analysis was performed using the Agilent GeneSpring GX software (version 10.0).

overall_design: Long ncRNA expression has been assessed in normal and malignant hepatocytes to assess differences in expression

first: Chiara

last: Braconi


title: Gene expression changes in blood RNA after swimming in a pool

status: Public on Sep 07 2015

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary:
Trihalomethanes (THM) are a class of disinfection by-products in chlorinated waters linked to deleterious health effects in humans although biological mechanisms are unclear. We aimed to study short-term changes in blood gene expression of adult recreational swimmers associated with physical activity and THM exposure.
Adult volunteers (18-50 years, non-smokers, non-asthmatics) swam 40 minutes in an indoor chlorinated pool in Barcelona. Blood samples and THM measurements in exhaled breath were collected before and 5 min/1h after swimming, respectively. Physical activity intensity was calculated as metabolic equivalents (METs). Gene expression in whole blood RNA was evaluated using Illumina HumanHT-12v3 Expression-BeadChip. Linear mixed models, Gene Set Enrichment Analyses-GSEA and mediation analyses were used.
The study population comprised 37 before-after pairs, with mean age 31 years (SD: 6.0), 60% female, and average changes before-after swimming of 1.75 METs (SD: 1.36) and 0.23 µg/m3 of exhaled bromoform (SD: 0.23). Among THM, bromoform yielded the strongest effect on gene expression changes. Eighty eight probes were associated with bromoform, 326 probes with MET and 77 probes overlapped. In mutually adjusted models, 15 probes remained significant for MET after False Discovery Rate (FDR). Although not FDR significant, in 23 nominally significant probes (p-value <0.05), fulfilling criteria for exploring mediation, 29.5 to 53.4% of MET effect was mediated by exhaled bromoform. Individual genes in this subset and the GSEA of the mutually adjusted gene lists of bromoform and MET were associated with pathways related to inflammatory/immune response and to several cancers.
In this first study evaluating short-term gene expression changes associated with swimming in a chlorinated pool, changes in gene expression were observed in association with physical activity with part of this effect mediated through bromoform exposure. Identified genes were correlated with inflammatory, immune response and cancer pathways. These results need replication in larger studies.

overall_design: Expression profile differences were determined between total RNA extracted before and after exposure to trihalomethanes present in swimming pool water for 40 minute from whole blood samples from 33 healthy human individuals.

first: Lucas

middle: A

last: Salas

first: Laia

last: Font-Ribera

first: Mariona

last: Bustamante

first: Joan

middle: O

last: Grimalt

first: Sarah

last: Bonnin

first: Maria

last: Aguilar

first: Heidi

last: Mattlin

first: Manuela

last: Hummel

first: Anna

last: Ferrer

first: Manolis

last: Kogevinas

first: Cristina

last: Villanueva


title: Brain transcriptome profiles in mouse model simulating features of post-traumatic stress disorder

status: Public on Apr 20 2015

city: Fort Detrick

first: seid

last: muhie

state: MD

address: 568 Doughten Dr

department: Systems Biology Enterprise

institute: USACEHR

summary: Social stress mouse models were used to simulate human post-traumatic stress disorder (PTSD).  C57B/6 mice exposed to SJL aggressor mice exhibited behaviors accepted as PTSD-in-mouse phenotype: 'frozen' motion, aggressor’s barrier avoidance, startled jumping, and retarded locomotion.  Transcripts in hippocampus, amygdala, medial prefrontal cortex, ventral striatum (nucleus acumbens), septal region, corpus striatum, hemi-brain, blood, spleen and heart of stressed and control C57B/6 mice were analyzed using Agilent’s mouse genome-wide arrays.

overall_design:
C57B6 mice were exposed to SJL aggressor mice for periods of 5 days and 10days (6 hours each day) to induce anxiety/stress which parallels to PTSD in human
Organs, blood and brain regions were collected after 24 hours and 1.5 week of post 5 days social defeat period; and 24 hour and 6 weeks post 10 days social stress period.

first: Seid

last: Muhie

first: Rasha

last: Hammamieh

first: Marti

last: Jett


title: Global gene expression profiling of the effect of probiotics supplementation in dairy cows

status: Public on Nov 21 2015

city: Greensboro

first: Mulumebet

last: Worku

state: North Carolina

address: 1601 E market Street

department: Animal Sciences

summary: In animal production, the use of probiotics supplements to promote animal health is increasing. The objective of this study was to assess the impact of probiotics administration on global gene expression in dairy cows. Lactating Holstein-Friesian cows (n=10) from the North Carolina Agricultural and Technical State University dairy herd were used for the study. Treatment was a 50 ml oral drench of FASTtrak microbial pack (Probiotics) (Conklin Company, Kansas City, MO) at the recommended dose in sterile endotoxin-free water or sterile endotoxin-free water only (control). This treatment was carried out for 60 days. Whole blood was collected at the beginning (Day 0) and end of the study (Day 60) for microarray analysis.  We employed microarray expression profiling as a discovery platform to identify genes with potential association with probiotics supplementation in cows. Gene expression analysis identified 10,859 differentially expressed genes- 1168 upregulated genes and 9691 downregulated gene. Results for pathway analysis showed significant pathways associated with innate immunity such as the Toll-like receptor (TLR) pathway, inflammation response and Wingless (Wnt) signaling pathway. Real-time PCR was used to validate the expression of the Wnt signaling pathway and immune response genes. Probiotic treatment impacted global gene expression, and particularly, the expression of immune response and Wnt signaling pathway genes.  Oral administration of probiotics to dairy cows impacts global gene expression and particularly the expression of innate immune genes in dairy cows.

overall_design: Ten animals were enrolled in the study and an initial blood sample was collected (Day 0). Animals (n=5) received either oral supplement of a commercial probiotic under the name FASTtrak microbial pack (Conklin Company, Kansas City, MO) or water only (control animals) for 60 days. Blood samples were collected at the end of the study from probiotics-treated and control animals for RNA extraction and microarray analysis. In vitro effect of lipopolysaccharide (LPS), endotoxin treatment was evaluated using blood samples collected from probiotics-treated animals (Day 60 samples) to serve as a positive control array.  A pooled sample was generated by taking an equal concentration of RNA from experimental animals in each group. Pooled samples from each group were hybridized on Agilent one-color bovine v2 bovine (v2) 4x44K array slides.

last: Adjei-Fremah

first: Hamid

last: Ismail

first: Kingsley

last: Ekwemalor

first: Emmanuel

last: K. Asiamah


title: Interferon and ribavirin treatment in a rhesus macaque model of novel Middle East respiratory syndrome coronavirus (MERS-CoV) infection (hCoV-EMC)

status: Public on Sep 06 2013

first: Michael

last: Katze

summary: Microarray analysis of lungs (right lower lobe) on day 3 post-infection with MERS-CoV with and without treatment beginning 8 h post-infection with intravenous type I interferon (IFN) and ribavirin (RBV).  Dosages are as follows: IFN a2b 5 million IU/kg s.c. q8, RBV loading dose 30mg/kg i.v.; Maintenance doses: IFN 5 MIU/kg s.c. q16; RBV, 10mg/kg i.m. q8.

overall_design: Six 4-6 year-old rhesus macaques were infected with 7x10e6 TCID50 total (4x10e6 intratracheal, 1x10e6 oral, 1x10e6 intranasal, 1x10e6 intraocular).  Treatment was initiated at 8h post-infection  with intravenous type I interferon (IFN) and ribavirin (RBV). Dosages are as follows: IFN a2b 5 million IU/kg s.c., RBV loading dose 30mg/kg i.v.; Maintenance doses: IFN 5 MIU/kg s.c. q16; RBV, 10mg/kg i.m. q8.  Three animals received IFN-a2b and ribavirin, while 3 animals received mock treatments with comprable volumes of saline delivered in the same routes.  On day 3 post-infection animals were necropsied and lower right lung tissue gene expression was analyzed by microarray.

first: Angela

last: Rasmussen

first: Atsushi

last: Okumura

first: Arndt

last: Benecke

first: Darryl

last: Falzarano

first: Emmie

last: DeWit

first: Vincent

last: Munster

first: Heinrich

last: Feldmann


title: Integrated Clinical, Pathologic, Virologic, and Transcriptomic Analysis of H5N1 Influenza Virus-Induced Viral Pneumonia in the Rhesus Macaque

status: Public on Apr 11 2012

summary: Viral pneumonia has been frequently reported during early stages of influenza virus pandemics and in many human cases of highly pathogenic avian influenza (HPAI) H5N1 virus infection. To better understand the pathogenesis of this disease, we produced non-lethal viral pneumonia in rhesus macaques by using an HPAI H5N1 virus  (A/Anhui/2/2005; referred to as Anhui/2). Infected macaques were monitored for 14 days, and tissue samples were collected at 6 time points for virologic, histopathologic and transcriptomic analyses.

overall_design: Thirteen colony-bred male or female rhesus macaques (Macaca mulatta), aged from 2.5 to 3.5 years and ranging in weight from 2.8 to 4.4 kg,  were used for experiments. Twelve macaques were individually  infected intratracheally with 10^7 EID50 of Anhui/2 in 4 ml of phosphate-buffered saline (PBS). At 6 h, 12 h, 1 d, 3 d, 6 d, and 14 d post-infection (p.i.), two animals per time-point were euthanized under anesthesia and necropsies were performed. Lung samples were collected and stored in RNAlater (Ambion, Austin, USA) at -80°C for RNA analyses.  The remaining macaque (mock-infected) was inoculated with 4 ml of PBS intratracheally and euthanized at 6 h p.i. Lung tissues from the mock-infected animal were collected and stored as described.

first: Kyoko

last: Shinya

first: Yuwei

last: Gao

first: Cristian

last: Cilloniz

first: Yasuhiro

last: Suzuki

first: Masahiro

last: Fujie

first: Guohua

last: Deng

first: Qiyun

last: Zhu

first: Shufang

last: Fan

first: Akiko

last: Makino

first: Yukiko

last: Muramoto

first: Satoshi

last: Fukuyama

first: Daisuke

last: Tamura

first: Takeshi

last: Noda

first: Amie

last: Eisfeld

first: Hualan

last: Chen

first: Yoshihiro

last: Kawaoka


title: Neuropeptides:developmental signals in placode progenitor formation

status: Public on Apr 25 2014

city: London

first: David

last: Chambers

state: London

address: Guy's Campus

department: Wolfson CARD

country: United Kingdom

institute: King's College Londonn

summary: Few families of signaling factors have been implicated in the control of development. Here we identify the neuropeptides nociceptin and somatostatin, a neurotransmitter and neuroendocrine hormone, as a class of developmental signals in chick and zebrafish. We show that signals from the anterior mesendoderm are required for the formation of anterior placode progenitors with one of the signals being somatostatin. Somatostatin controls ectodermal expression of nociceptin and both peptides regulate Pax6 in lens and olfactory progenitors. Consequently, loss of somatostatin and nociceptin signaling leads to severe reduction of lens formation. Our findings not only uncover these neuropeptides as developmental signals, but also identify a long-sought-after mechanism that initiates Pax6 in placode progenitors and may explain the ancient evolutionary origin of neuropeptides, pre-dating a complex nervous system.

overall_design: We used progenitors for anterior and posterior sensory placodes dissected from chick embryos HH5-7; these were either processed immediately or cultured for 5 hrs to hybridise to Affymetrix chick array. We aimed to identify genes that are co regualted with Pax6, a key regulator of lens and olfactory progenitor cells. Pax6 is normally present in anterior, but not posterior placode precursors, but upregulated in both after 5 hrs culture.

first: Andrea

last: Streit

first: Laura

last: Lleras-Forero

first: Monica

last: Tambalo

first: Nicolas

last: Christophorou

first: Corinne

last: Houart


title: Development of gene expression for stress in heat- and shake-induced injury in the rat jejunum

status: Public on Sep 18 2014

first: peng

last: yin

state: Other

address: China Agricultural University (CAU), Beijing 100193, PR China

institute: CAU-BUA TCVM Teaching and Researching Team, College of Veterinary Medicine, China Agricultural University

summary: To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish radiation dose across an exposure range relevant for medical decision-making in a radiological emergency.   Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples.  The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy).  Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern.

overall_design: Heat and shake stress induced gene expression in rat jejunum was measured with or without 3 days stressed (Control and S3d groups) The conditions of the treatment for rats were as follows: 35°C with a vibration of 0.1 × g for 3 days， 2 h/day in a temperature shake. each group had 3 sample replications,  and each sample were mixed by 3 rats total RNA

first: Peng

last: Yin


title: Functional and cellular constraints that shaped the PPARg binding landscape in human and mouse macrophages: human expression

status: Public on Dec 01 2011

city: Chicago

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

institute: University of Chicago

summary: Genome-wide comparisons of transcription factor binding sites in different species allow for a direct evaluation of the evolutionary constraints that shape transcription factor binding landscapes. To gain insights into the evolution of the PPARg-dependent transcriptional network we obtained binding data for PPARg, RXR and PU.1 in human macrophages and compared the profiles to matching data from mouse macrophages. We found that PPARg binding was highly divergent and only 5% of the PPARg bound regions were occupied in both species. Despite the low conservation of PPARg binding sites, conserved PPARg target genes contribute more than 30% to the functional target genes identified in human macrophages. In addition conserved target genes are strongly enriched for lipid metabolic functions. We detected the lineage-specification factor PU.1 at the majority of human PPARg binding sites. This confirmed the juxtaposed binding configuration found in mouse macrophages and demonstrated the preservation of tissue-specific adjacent PPARg-Pu.1 binding in the absence of individual binding site conservation. Finally, based on this of PPARg and PU.1 binding between human and mouse we suggest a mechanism by which PU.1 facilitates PPARg binding site turnover in macrophages.

overall_design: Comparison of RNAs level in Rosiglitazone (RSG) and vehicle (DMSO) treated PMA differentiated THP-1 cells over a timecourse from 0.5h to 12h

first: E

last: Liu


title: RNA expression changes in MDA-MB-231 cells following MEK inhibition

status: Public on Apr 01 2015

city: San Francisco

first: Wolfgang

middle: Michael

last: Korn

state: CA

address: 2340 Sutter Street

institute: UCSF

summary: Molecular responses to MEK inhibition in cancer cells are complex and dynamic. We performed a time-series experiment to measure global RNA expression changes following treatment with the MEK inihibor U0126

overall_design: MDA-MB-231 human breast cancer cells were grown in low-serum conditions. Treatment with U0126 was initiated in the presence of EGF. RNA was harvested at multiple time points during the course of 48 hours.

first: Olga

last: Mirzoeva

first: Rina

last: Gendelman

last: Heiser

first: Nora

last: Bayani

first: Nicholas

last: Wang

first: Richard

last: Neve

first: Heidi

last: Feiler

first: Philippe

last: Gascard

first: Paul

last: Spellman

first: Wen-Lin

last: Kuo

first: Joe

last: Gray

first: W


title: Gallus gallus white isthmus transcriptome

city: Nouzilly

first: Joel

last: Gautron

address: UR83 Recherches avicoles

institute: INRA

summary:
The Del-Mar 14K chip was used to interrogate differential expression of transcripts in the white isthmus (WI) compared with the  adjacent magnum (Mg) and uterine (Ut) segments of the hen oviduct. Differential expression of genes common to both  comparisons (WI/Mg and WI/Ut) was detected for 204 annotated proteins. Of these, 58 genes were overexpressed in both WI/Mg and WI/Ut, and are therefore considered to be the most interesting candidates for WI - specific functions.  Additionally,  general analysis revealed 135 clones hybridizing to overexpressed transcripts (WI/Mg + WI/Ut), and corresponding to 102 NCBI annotatated non-redundant Gallus gallus gene ID~s. This combined analysis revealed that structural proteins highly over-expressed in white isthmus were collagen X (COL10A1), Fibrillin (FBN1)  and Cysteine Rich Eggshell  Membrane Protein (CREMP). In addition, genes encoding collagen-processing enzymes were over-expressed, as were  proteins known to regulate disulfide cross-linking,  suggesting that coordinated upregulation of gene networks in the white isthmus is associated with eggshell membrane fibre formation.  IPA interactome analysis reinforces the key role of the estrogen receptor and SMAD3 in mediating gene regulation during eggshell membrane synthesis. These results will assist with development of selection strategies to improve eggshell quality and food safety of the table egg.
Keywords: Laying hen, eggshell, oviduct, Isthmus expression, cDNA microarray, indirect cDNA labelling, Alexa Fluor dyes

Keywords: Expression profiling by array

overall_design: A balanced block hybridization design (Dye switch) was used where half of the samples were labelled with Alexa® 555 fluorescent dye and the other half with Alexa® 647. A total of 16 microarray slides were used for hybridization to 32 samples that correspond to four tissue contrast (White isthmus versus magnum and uterus versus white isthmus).

first: J

first: MT

last: Hincke

first: A

last: Brionne

first: L

last: Cogburn

first: C

last: Hennequet-Antier

first: Y

last: Nys


title: Evidence for a rheostat that determines neuronal survival after traumatic brain injury

status: Public on Dec 20 2010

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: To investigate the determinants of neuronal survival after traumatic brain injury, we compared the transcriptional profiles of dying (Fluoro-Jade-positive) and immediately adjacent surviving (Fluoro-Jade-negative) neurons from the CA3 subfield of the rat hippocampus 24 hours after experimental TBI. We found that hippocampal neurons that survive TBI invariably express high levels of genes that have cellular functions involved in survival, regeneration, development, proliferation, neuronal plasticity such as cAMP response element binding protein (CREB), brain-derived-neurotrophic factor (BDNF) and mitogen-activated protein kinase 1 (MAPK1). Dying neurons express high levels of genes involved in aberrant cell cycle progression, immune response, inflammation, oxidative stress and apoptosis such as Interleukin-1β (IL-1β), caspase 3 and B-cell linker (BLNK). We conclude that shifting the balance between the global levels of these proteins with pharmacotherapeutic drugs that induce expression of cell survival associated genes, is expected to alter the cellular rheostat that determines cell survival or cell death.

overall_design: Replicate pooled samples (approximately 600 laser capture microdissected hippocampal neurons per sample of dying neurons (labeled with Fluoro-Jade, a fluorescent stain for degenerating CNS neurons) and surviving neurons (Fluoro-Jade-negative) were hybridized in duplicate to rat Agilent whole genome arrays.

first: Helen

last: Hellmich

first: Deborah

middle: K

last: Boone

first: Karen

last: Torres


title: Gene expression profiling in the Cynomolgus macaque Macca fascicularis shows variation within the normal birth range.

status: Public on Nov 01 2011

city: Al ain

first: Starling Emerald

last: Bright David

address: Tawam Medical Campus

department: Anatomy

country: United Arab Emirates

institute: United Arab Emirates University

summary: To understand the effect of an adverse early life environment within  the normal birth range we have utilised a non human primate model Macca fascicularis and employed microarray. We have identified 1973 genes which were differentially expressed in the three tissue types namely umbilical cord, neonatal liver, and skeletal muscle.

overall_design: Using microaary,  we compard tissues from neonates in the average birth weight (50-75th centile) to those of lower birth weight (5-25th centile).

first: B

middle: S

last: Emerald


title: Understanding Streptococcus suis serotype 2 infection in pigs through a transcriptional approach

status: Public on Oct 26 2010

city: Wuhan

first: Liu

middle: Man

last: li

address: Shizishan Road Number 1, Hongshan Area, Wuhan , Hubei Provience, China

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

summary:
Streptococcus suis serotype 2 is an important pathogen of pigs, and the disease it causes is characterized by meningitis, septicaemia and pneumonia with high mortality. The pathogen is also an emerging zoonotic agent and threatens humans that are exposed to pigs or their by-products.
We investigated the response of PBMC (Peripheral Blood Mononuclear Cell), brain and lung tissues to infection with S. suis 2 strain SC19 by using the Affymetrix Porcine Genome Array.

overall_design: Six piglets free of S. suis 2 were allocated randomly to the infected group and the uninfected group. Each piglet of the infected group was intravenous injection with Streptococcus suis 2 strain SC19 at a dose of 3×105 colony-forming units (CFU). Each piglet of the noninfected group was treated similarly with an identical volume of PBS as control. At 24 h after challenge, the pigs were slaughtered and their brains, lungs and PBMC were collected with RNase-free equipment for microarray analysis.

first: Manli

last: Liu

first: Liurong

last: Fang

first: Tiansi

last: Long

first: Huanchun

last: Chen

first: Shaobo

last: Xiao


title: Transcriptional comparison of cynomolgus macaques (Macaca fascicularis) following infection with Lassa or Lujo viruses

status: Public on Aug 29 2014

city: Seattle

last: Katze

address: Rosen Building 960 Republican St.

institute: University of Washington

summary: Microarray analysis of PBMC from cynomolgus macaques collected longitudinally over the course of infection with Lassa-Josiah, Lassa-Z132, Lassa-SorombaR, or Lujo viruses (n=3 animals/infection condition).

overall_design: 3 macaques from each group were infected intramuscularly with 10^4 PFU of Lassa-Josiah, Lassa-Z132, Lassa-SorombaR, or Lujo viruses.  PBMC were collected at days 1, 4, 7, 10, 13, and 29 (for surviving animals).  We performed microarray analysis on PBMC samples using Agilent rhesus macaque arrays on all samples, as well as on PBMC from 3 uninfected animals for use as a control.

first: Angela

last: Rasmussen

first: Nicolas

last: Tchitchek

first: David

last: Safronetz

first: Heinrich

last: Feldmann


title: Rhesus macaque model of hCoV-EMC respiratory infection

status: Public on Aug 29 2013

summary: Microarray analysis of peripheral blood mononuclear cells (PBMCs), lungs, and lung lesions collected over the course of hCoV-EMC infection of 6 rhesus macaques.

overall_design: 6 rhesus macaques were infected intratracheally with hCoV-EMC. PBMCs were collected at days 0, 1, 3, and 6, and lungs were collected from serial sacrifices of 3 animals each at day 3 and day 6. Infection produced a mild-moderate, self-limiting respiratory infection, and was not lethal. We performed microarray analysis (using Agilent Rhesus arrays) on all lungs, lung lesions, and PBMCs collected for the study.

first: Arndt

last: Benecke

first: Atsushi

last: Okumura

first: Emmie

last: DeWit

first: Vincent

last: Munster


title: Genome wide binding of Insensitive in w[1118] embryos

status: Public on Apr 04 2013

city: New York

first: Jakub

middle: Orzechowski

last: Westholm

state: NY

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan-Kettering Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq for Drosophila Insensitive, together with IgG control. Chromatin extracted from 2.5-6h w[1118]  embryos and 6.5-12h w[1118]  embryos.

overall_design: Samples from two time points were analyzed:  2.5-6h embryos and 6.5-12h embryos. In each time point there is one Insv ChIP sample and one IgG control sample.

first: Qi

last: Dai

first: Eric

last: Lai


title: High-througput Bacteria one hybrid (B1H) selections for all Drosophila homeodomain proteins

status: Public on Nov 13 2010

city: Worcester

first: Scot

last: Wolfe

state: MA

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

summary: In many metazons, such as humans and Drosophila, homeodomain proteins comprise the second largest family of sequence specific transcription factors.  In Drosophila, homeodomains play an important role in development.  Many homeodomain proteins display a high level of homology across metazons, presumably due to importance of their functional roles.  We comprehensively characterized the DNA binding preferences of all 84 Drosophila homeodomain transcription factors which contain a single DNA binding domain.  Previously, we employed a  bacterial one hybrid (B1H) assay to select for 20 to 40 high affinity transcription factor binding sites [Noyes et al. (2008). Cell. 133(7):1277-1289].  In this system, E. coli are transfected with two plasmids.  One plasmid encodes the DNA binding domain of a homeodomain fused to two zinc finger domains and the omega subunit of RNAP.  The other plasmid is drawn from a library of prey plasmids which contain a 10bp randomized transcription factor binding site (TFBS) region in the promoter of the reporter gene His3.  The E. coli strain used is a His3 homolog and omega subunit knock out strain.  If a transcription factor has high affinity for a TFBS, more His3 will be produced, leading to the production of more histidine and an increase in the growth rate.  If the transcription factor does not bind with sufficient affinity to the TFBS, little or no histidine will be produced resulting in little or no growth.  The stringency of the B1H system can be tuned using the chemicals IPTG and 3-AT.  IPTG induces production of the chimeric transcription factor, and 3-AT is a competitive inhibitor of the enzyme encoded by His3.  One of the advantages of the B1H system is that the transcription factor does not have to be purified and that many experiments can be easily conducted in parallel.  In this study, in stead of picking 20 to 40 colonies and sequencing their TFBSs, we used high-throughput Illumina sequencing to sequence the selected sites of all of the colonies growing on a plate.  This provided quantitative data regarding the growth rate of cells possessing each selected TFBS variant, which is a function of the affinity of the transcription factor for the binding site.   With this quantitative data, we can build more accurate models of transcription factor binding.

overall_design: All 84 of the Drosophila homeodomain proteins that contain a single DNA binding domain were analyzed using the B1H assay.  The same selection stringency was used for all experiments (10uM IPTG and 5mM 3-AT).  All experiments were run for 36 to 48 hours.  10 mutants were also assayed: 3 Caup, 3 Bcd and 4 En mutants.  The bait plasmid omegaUV2zf was used in all but 3 cases.  In this instances, a slightly different bait plasmid, omegaUV5zf, with a stronger promoter was used.   Thirty different replicates were performed in order to insure that sufficient number of reads were obtained for each protein.  In total, 126 experiments were performed.

first: Michael

middle: H

last: Brodsky


title: Gene expression profiling of M. mulatta (Rhesus macaques) infected with H1N1 and pH1N1 influenza

status: Public on Oct 01 2012

city: Minato

first: Yoshihiro

last: Kawaoka

address: Shirokanedai 4-6-1

institute: Japanese Science and Technology Agency

summary: Annually, influenza A viruses circulate the world causing wide-spread sickness, economic loss, and death. One way to better defend against influenza virus-induced disease may be to develop novel host-based therapies, targeted at mitigating viral pathogenesis through the management of virus-dysregulated host functions. However, mechanisms that govern aberrant host responses to influenza virus infection remain incompletely understood. We previously showed that the pandemic H1N1 virus influenza A/California/04/2009 (H1N1; CA04) has enhanced pathogenicity in the lungs of cynomolgus macaques relative to a seasonal influenza virus isolate (A/Kawasaki/UTK-4/2009 (H1N1; KUTK4)). Here, we used microarrays to identify host gene sequences that were highly differentially expressed (DE) in CA04-infected macaque lungs, and we employed a novel strategy – combining functional and pathway enrichment analyses, transcription factor binding site enrichment analysis and protein-protein interaction data – to create a CA04 differentially regulated host response network. This network describes enhanced viral RNA sensing, immune cell signaling and cell cycle arrest in CA04-infected lungs, and highlights a novel, putative role for the MYC-associated zinc finger (MAZ) transcription factor in regulating these processes.

overall_design: Lung tissues used for microarray studies were obtained from 13 female cynomolgus macaques infected with influenza viruses. 6 animals were inoculated with influenza A/California/04/2009 and 6 animals were inoculated with influenza A/Kawasaki/UTK-4/2009. 1 uninfected animal served as a negative control. On days 3 and 7 post-infection (p.i.), lung tissues were harvested from the middle and lower lung lobes of 3animals in each infection group (N = 26 total samples were collected, 3 samples were removed from the study due to low RNA quality).  All but 3 samples were collected from visually apparent virus-induced gross lesions. Two lung tissue samples were obtained from middle and lower lobes of the uninfected animal at the start of the experiment.

first: Jason

last: Shoemaker

first: Satoshi

last: Fukuyama

first: Amie

last: Eisfeld

first: Yukiko

last: Muramoto

first: Shinji

last: Watanabe

first: Tokiko

last: Matsuoka

first: Hiroaki

last: Kitano


title: Dicer-2 processes diverse viral RNA species

status: Public on Jan 31 2013

city: Wilmington

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: RNA silencing pathways play critical roles in gene regulation, virus infection, and transposon control. RNA interference (RNAi) is mediated by small interfering RNAs (siRNAs), which are liberated from double stranded (ds) RNA precursors by Dicer and direct the RNA-induced silencing complex (RISC) to target transcripts. Recent efforts have uncovered important principles governing small RNA (smRNA) sorting into RISC, yet mechanisms defining substrate selection by Dicer proteins remain uncharacterized. Methodology: To better characterize Dicer-2 substrates in Drosophila, we examined the antiviral RNAi response, which generates virus-derived siRNAs from viral RNA. Using high-throughput sequencing, we found that diverse viruses were uniquely targeted; substrates included dsRNA replication intermediates and intramolecular RNA stem loops. smRNA distribution patterns from viral and synthetic dsRNA precursors were highly reproducible, and machine learning techniques identified characteristics of precursor molecules and smRNA duplexes important in determining relative smRNA abundance. Significance: To our knowledge, this study provides the first description of the rules governing Dicer-2 substrate selection, which has important implications for exogenous RNA silencing technologies and the development of smRNA-based antiviral therapeutics.

overall_design: virus-derived siRNA (vsiRNA) expression comparison between control and 4 different virus-infected cells in control as well as 5 different RNAi pathway protein knock-downs in Drosophila dl1 cells

first: Leah

last: Sabin

first: Pramod

last: Thekkat

first: Jamie

last: Yang

first: Gregory

last: Hannon

first: Brian

middle: D

last: Gregory

first: Matthew

last: Tudor

first: Sara

last: Cherry


title: Comparative transcriptomic analysis of acute host responses during 2009 pandemic H1N1 influenza infection in mouse, macaque, and swine

status: Public on Aug 14 2012

last: Katze

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

sample_organism:
Macaca fascicularis
Sus scrofa
Mus musculus

platform_organism:
Macaca mulatta
Sus scrofa
Mus musculus

overall_design: Refer to individual Series


title: Binding site turnover produces pervasive quantitative changes in TF binding between closely related Drosophila species

status: Public on Feb 18 2010

city: Berkeley

last: Eisen

address: Stanley Hall 304B

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary:
[original title] Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.
We demonstrate extensive quantitative changes in binding of six factors that control early embryonic patterning between two closely related Drosophila species

sample_organism:
Drosophila melanogaster
Drosophila yakuba

overall_design: ChIP-Seq based binding measurements of six transcription factors in embryos of two Drosophila species, D.melanogaster and D.yakuba.

first: Robert

last: Bradley

first: Xiao-Yong

last: Li


title: Comparative transcriptomic analysis of acute host responses during 2009 pandemic H1N1 influenza infection in mouse, macaque, and swine (macaque dataset)

first: Michael

summary:
Background: The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non-human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular pathways were impacted by pH1N1 virus across independent infection models remains to be further defined. To address this, we have performed a comparative transcriptomic analysis of acute host responses to a single pH1N1 influenza virus, A/California/04/2009 (CA04), in the lung of mice, macaques and swine.

Results: Despite similarities in the clinical course, we observed differences in inflammatory molecules elicited, and the kinetics of their gene expression changes across all three species. The retinoid X receptor (RXR) signaling pathway controlling pro-inflammatory and metabolic processes was differentially regulated during infection in each species, though the heterodimeric RXR partner, pathway associated signaling molecules, and gene expression patterns differed in each species.

Conclusions: By comparing transcriptional changes in the context of clinical and virological measures, we identified differences in the host transcriptional response to pH1N1 virus across independent models of acute infection. Antiviral resistance and the emergence of new influenza viruses have placed more focus on developing drugs that target the immune system. Underlying overt clinical disease are molecular events that suggest therapeutic targets identified in one host may not be appropriate in another.

overall_design: The goal of this experiment was to use global gene expression profiling to understand non-human primate lung cellular responses to pandemic H1N1 influenza A/California/04/2009 virus infection. Four- to fifteen-year-old cynomologous macaques were infected with CA04 virus (n = 4) under anesthesia through a combination of intratracheal (4 ml), intranasal (0.5 ml per nostril), conjunctival (0.5 ml per eyelid) and oral (1 ml) routes with a suspension containing 10^6 TCID50/ml (total infectious dose was 7x10^6 TCID50). Animals were euthanized on 1 and 6 days post-inoculation (n = 2 per time point), and total RNA was extracted from lung samples and analyzed by microarray. Pooled RNA from lungs of uninfected animals served as the reference.

first: Jennifer

last: Tisoncik Go

first: Sarah

middle: E

last: Belisle

first: Nicolas

last: Tchitchek

first: Terrence

middle: M

last: Tumpey

first: Wenjun

last: Ma

first: Juergen

last: Richt

first: Heinz

last: Feldmann


title: Functional annotation of genes differentially expressed between primary motor and prefrontal association cortices of macaque brain

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

summary: DNA microarray-based genome-wide transcriptional profiling and gene network analyses were used to characterize the molecular underpinnings of the frontal neocortical organization in rhesus macaque, with particular focus on the differences in the functional annotation of genes in the primary motor cortex and the prefrontal association cortex. Biofunctional analysis of the differentially expressed genes showed that the list of genes selectively expressed in the primary motor cortex were enriched with genes involved in development, oligodendrocyte function, and increased energy consumption, whereas the list of genes selectively expressed in the prefrontal association cortex were enriched with genes involved in cell morphology and calcium dynamics. These functional differences in selectively expressed genes may reflect the fundamental molecular structure of each cortex.

overall_design: Brain tissue was obtained from 4 adolescent rhesus monkeys (Macaca mulatta) aged between 2.6 and 2.7 years that had been bred in group cages without being subjected to any experimental treatment. Adequate measures were taken to minimize pain and discomfort, in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals (NIH Publication No. 80–23). The monkeys were perfused with 500–1000 ml of ice-cold saline containing heparin sodium (1000 U/ml, Novo Heparin; Leo Pharmaceutical Products, Ballerup, Denmark) through the ascending aorta within 15 min of an overdose injection of pentobarbital sodium (50 mg/kg, i.p., Somnopentyl; Kyoritsu Shoji, Tokyo, Japan). The 2 neocortical areas (M1 and A46) were identified by sulcal landmarks. We used the forelimb region of M1 for the present analysis, which is located around the superior genu of the central sulcus. A46 was obtained from both the upper and lower banks of the principal sulcus. Each area from the left hemispheres was dissected on crushed ice and immediately frozen in liquid nitrogen.

first: Noriyuki

last: Higo

first: Akira

last: Sato

first: Takao

last: Oishi

first: Yukio

last: Nishimura

first: Tatsuya

last: Yamamoto

first: Yumi

last: Murata

first: Kimika

last: Yoshino-Saito

first: Hirotaka

last: Onoe

first: Tadashi

last: Isa


title: Loqs-PD and R2D2 define independent pathways for RISC generation in Drosophila

status: Public on Feb 10 2011

city: Munich

first: Klaus

last: Förstemann

address: Feodor-Lynen 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilians University

summary: In Drosophila, siRNAs are classified as endo- or exo-siRNAs based on their origin. Both are processed from double-stranded RNA precursors by Dcr-2, then loaded into the Argonaute protein Ago2. While exo-siRNAs serve to defend the cell against viruses, endo-siRNAs restrict the spread of selfish DNA in somatic cells, analogous to piRNAs in the germ line. Endo- and exo-siRNAs display a differential requirement for double-stranded RNA binding domain proteins (dsRBPs): R2D2 is needed to load exo-siRNAs into Ago2 while the PD isoform of Loquacious (Loqs-PD) stimulates Dcr-2 during the nucleolytic processing of hairpin-derived endo-siRNAs. In cell culture assays, R2D2 antagonizes Loqs-PD in endo-siRNA silencing and Loqs-PD is an inhibitor of RNA interference. Loqs-PD can interact via the C-terminus unique to this isoform with the DExH/D-helicase domain of Drosophila Dcr-2, where binding of R2D2 has also been localized. Separation of the two pathways is not complete; rather, the dicing and Ago2-loading steps appear uncoupled, analogous to the corresponding steps in miRNA biogenesis. Analysis of deep sequencing data further demonstrates that in r2d2 mutant flies, siRNAs can be loaded into Ago2 but not all siRNA classes are equally proficient for this. Thus, the canonical Ago2-RISC loading complex can be bypassed under certain circumstances.

overall_design: Examination of small RNAs from two different mutant strains as well as the corresponding heterozygous controls

first: Julia

last: Hartig


title: Long-Term Programming of Antigen-Specific Immunity from Gene Expression Signatures in the PBMC of Rhesus Macaques Immunized with an SIV DNA Vaccine

status: Public on Feb 15 2012

first: Michael

last: Katze

department: Microbiology

summary: The primary objective of this study was to evaluate response to a SIV DNA-based vaccine that was adminstered via vivo electroporation (EP) in rhesus macaques to further understand the molecular correlates of protection against SIV. In this study, rhesus macaques were immunized with a DNA vaccine including individual plasmids encoding SIV gag, env, and pol alone, or in combination with a molecular adjuvant, plasmid DNA expressing the chemokine ligand 5 (RANTES), followed by EP. At eight month post-vaccination, animals were challenged with SIV. Standard immunological assays, flow-based activation analysis without ex vivo restimulation and high-throughput gene expression analysis were performed to determine the host response to each vaccine regimen.

overall_design: The overall study was designed to evaluate the response to a SIV-DNA vaccination administered to animals via intramuscular electroporation. Chinese rhesus macaques were divided into three treatment groups (n=6 animals per group): Control (no vaccination), DNA vaccine alone (pCSIVgag, pCSIVpol, pCSIVenv), DNA vaccine with RANTES adjuvant (pCSIVgag, pCSIVpol, pCSIVenv, pmacRANTES). Eight months following the last vaccination, animals were infected with 25 MID of SIVmac251 and response to infection was monitored. RNA for microarray analysis was isolated from fresh PBMCs that were isolated from individual animals and treated overnight with a pool of overlapping SIV pol peptides or mock treated. Samples for microarray analysis were taken longitudinally at 8 months post-vaccination (pre-SIV challenge; biological n=5-6 per group for each treatment; technical n=2 for each sample) and  at day 10 post-SIV challenge (n=5-6 per group for each treatment; technical n=2 for each sample).

first: Sarah

last: Belisle

first: Jiangmei

last: Yin

first: Devon

last: Shedlock

first: Anlan

last: Dai

first: Jian

last: Yan

first: Lauren

last: Hirao

first: Michele

last: Kutzler

first: Mark

middle: G

last: Lewis

first: Hanne

last: Andersen

first: Simon

last: Lank

first: Julie

last: Karl

first: David

last: O'Connor

first: Amir

last: Khan

first: Niranjan

last: Sardesai

first: Jean

last: Chang

first: Lauri

last: Aicher

first: Robert

last: Palermo

last: Weiner

last: Boyer


title: Aged animals generate a robust immune response against swine origin 2009 pandemic H1N1 influenza A virus

status: Public on Jun 06 2012

first: Michael

last: Katze

summary: In June 2009, the World Health Organization declared the first influenza pandemic of the 21st century, due to the emergence and rapid spread of new swine origin H1N1 influenza A virus. In contrast to seasonal influenza infections, which typically cause morbidity and mortality in the elderly, this virus caused severe infection in young adults and not the elderly. This phenomenon was attributed to the presence of cross-neutralizing antibodies acquired by older individuals from previous exposure to swine origin influenza. However, this hypothesis could not be empirically tested using clinical data. To address this question, we investigated viral replication and the development of the immune response in naï12 years old) and aged (20 to 24 years old) female rhesus macaques infected with A/California/04/2009 (H1N1), one of the circulating pandemic strains in 2009. We compared viral loads as well as the kinetics and magnitude of the adaptive immune response in peripheral blood and bronchoalveolar lavage samples (BAL) collected longitudinally for 99 days post-infection. Although, adult animals exhibited earlier T cell responses in peripheral blood, aged animals generated a robust T cell response with comparable kinetics and magnitude as those observed in young animals in BAL. Moreover, aged animals generated a higher hemagglutination inhibition titer compared to young animals. We also measured the concentration of several cytokines in BAL supernatant. With the exception of IL-8, which was higher in aged animals, we found no differences in IFNa, IFNb, TNFa, IL-1r, IL-6, IL-15, IL-17, or MCP1 levels. Finally, we compared gene expression infection using microarray analysis of BAL samples taken on days 0, 4, 7, 10, and 14 pi. Our analyses revealed that the largest difference in host response between aged and young animals was detected day 4 post-infection, with significant enrichment for genes associated with inflammation, the innate immune response, and T cell activation in aged animals. The ability of aged animals to generate a robust immune response, especially antibody response, following infection with 2009 H1N1 virus could explain the lack of morbidity normally observed with seasonal influenza viruses in this vulnerable population.

overall_design: 16 female rhesus macaques (Macaca Mulatta) 10-12 (Adult) and 20-24 years (Old/Aged) of age were used in these studies. Animals were infected with A/California/04/ 2009 H1N1 using a combinatory of intra-tracheal (4ml), intranasal (0.5 ml/nostril), and conjunctival (0.5 ml/eyelid) routes for a total dose of 7x106 TCID50 dose. Microarray analysis was performed on Bronchoalveolar lavage (BAL) samples collected on days 0, 4, 7, 10 and 14.  Note: One of the Day 0 array did not pass QC metrics so for this animal the average of the other Day 0 samples from that group was utilized. At the end of the study animals were released back to the colony.

first: Laurence

last: Josset

first: Ilhem

last: Messaoudi

first: Flora

last: Engelmann

first: Buyng

last: Park

first: Adolfo

last: García-Sastre


title: Rat lung gene expression during acute pulmonary embolism

status: Public on Sep 01 2009

city: Charlotte

first: John

last: Zagorski

state: NC

address: 1542 Garden Terrace, 301

department: Emergency Medicine

institute: Carolinas Medical Center

summary:
Rats were given pulmonary embolism by i.v. injection of 25 micron polystyrene microspheres or 0.01% Tween20 solution as vehicle control
Embolism of microspheres is irreversible and causes dose dependent pulmonary hypertension

Keywords: time course and dose response

overall_design: Rats received one of three treatments: 0.15 ml/100 grams weight of 0.01% Tween20 as "vehicle" control; 0.10 ml/100 grams of 10% microsphere suspension in 0.01% Tween20 = 1.3 million/100 grams = "PE1.3" dose; 0.15 ml/100 grams of 10% microspheres = 2.0 million/100 grams = "PE2.0" dose; rats were euthanized at either 2 hours or 18 hours after treatment

first: Jeffrey

last: Kline


title: Interplay between MAMPs-triggered and SA-mediated defense responses

status: Public on Jul 14 2007

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

summary:
The Arabidopsis Pathoarray 464_001 (GPL3638) was used to compare response of Col-0, pad4-1 (Zhou et al., 1998; Jirage et al., 1999) and sid2-2 (Wildermuth et al., 2001) to Pseudomonas syringae pv. tomato DC3000 hrcC mutant. SA production is drastically reduced in sid2 mutants. PAD4 is required for SA-mediated responses. The results suggested that the SA increase triggered by MAMPs is one major component in the MAMPs-triggered signaling mechanism.
Keywords: Responses of Arabidopsis to Pseudomonas syringae pv. tomato DC3000 hrcC mutant

overall_design: This experiment consists of three biological replicates of four samples (mock-inoculated_Col-0, hrcC-inoculated_Col-0_hrcC, hrcC-inoculated_pad4-1 and hrcC-inoculated_sid2-2). For each genotype, two leaves per plant were pooled from three pots to prepare total RNA.

first: Fumiaki

last: Katagiri


title: Identification and analysis of transgene-derived endo-siRNAs in Drosophila Schneider cells by Solexa sequencing.

status: Public on Sep 14 2009

first: Klaus

last: Förstemann

summary: Colonization of genomes by a new selfish genetic element is detrimental to the host species and must lead to an efficient, repressive response. In vertebrates as well as in Drosophila, piRNAs repress transposons in the germ line while endogenous siRNAs take on this role in somatic cells. For endo-siRNAs as well as for piRNAs, it is unclear how an efficient response can be initiated de novo. Our experiments establish that the endo-siRNA pathway will target artificially introduced sequences without the need for a pre-existing template in the genome. This response is also triggered in transiently transfected cells, thus genomic integration is not essential. Deep sequencing revealed that corresponding endo-siRNAs are generated throughout the sequence, but preferentially from transcribed regions.

overall_design: Examination of 3 different cell lines.

first: Stephanie

last: Esslinger


title: Analysis of the transcriptome of Dunaliella sp. by cDNA microarray

status: Public on Jan 01 2010

city: Seoul

first: MinJung

last: Kim

address: 17 Haengdang-dong, Seongdong-gu

department: Life Science

country: South Korea

institute: Hanyang University

summary:
Algae of the genus Dunaliella are known to be able to grow in a wide range of salinities. To investigate which genes may be important for growth under extremely low or high salinities, a survey of the Dunaliella sp. transcriptome was performed by microarray analysis. For the cDNA microarray 778 expressed sequence tags (ESTs) were generated from a cDNA library of Dunaliella sp. The cDNA microarray was used to compare the transcription profile of cells that were acclimated to extreme saline conditions (0.08 M and 4.5 M NaCl) with the transcription profile of cells acclimated to an intermediate salinity at 1.5 M NaCl. The comparative microarray analysis indicated that 211 out of the 778 ESTs differed in their expression levels more than two-fold in cells grown at extreme different salinity when compared to cells grown at intermediate salinity (1.5M NaCl). The sequences of these 211 cDNAs were classified into 169 non-redundant gene clusters. Of these genes, the expression of 36 genes was increased and 69 genes were suppressed in cells grown at low salinity. The expression of 49 genes was increased and 85 genes were suppressed in cells grown at high salinity. One-hundred thirty four genes have been revealed to show up- and down-regulation by high salinity (4.5M NaCl). Of the high salinity-regulated genes 52% were also influenced by low salinity (0.08M NaCl), revealing a dense overlap between low and high salt responses. Only 35 genes are regulated independently by low salt condition. Strong relationships, however, were observed in the expression of these extreme salinity-responsive genes based on Venn diagram analysis, which found 70 genes that responded to these two salinity conditions. Refined expression analysis using gene-specific primers and real-time PCR for selected transcripts was in agreement with microarray results for most genes tested. This study provides the first large-scale survey of the transcriptome in the microalga Dunaliella sp. and it provides a platform for further functional investigation of differentially expressed genes in Dunaliella.
Keywords: Low salt(0.08M NaCl) or high salt(4.5M NaCl)-acclimated cells

first: EonSeon

last: Jin


title: Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma

status: Public on Sep 08 2009

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Hepatocellular carcinoma (HCC) is a highly heterogeneous disease, and prior attempts to develop genomic-based classification for HCC have yielded highly divergent results, indicating difficulty in identifying unified molecular anatomy. We performed a meta-analysis of gene expression profiles in data sets from eight independent patient cohorts across the world. In addition, aiming to establish the real world applicability of a classification system, we profiled 118 formalin-fixed, paraffin-embedded tissues from an additional patient cohort. A total of 603 patients were analyzed, representing the major etiologies of HCC (hepatitis B and C) collected from Western and Eastern countries. We observed three robust HCC subclasses (termed S1, S2, and S3), each correlated with clinical parameters such as tumor size, extent of cellular differentiation, and serum alpha-fetoprotein levels. An analysis of the components of the signatures indicated that S1 reflected aberrant activation of the WNT signaling pathway, S2 was characterized by proliferation as well as MYC and AKT activation, and S3 was associated with hepatocyte differentiation. Functional studies indicated that the WNT pathway activation signature characteristic of S1 tumors was not simply the result of beta-catenin mutation but rather was the result of transforming growth factor-beta activation, thus representing a new mechanism of WNT pathway activation in HCC. These experiments establish the first consensus classification framework for HCC based on gene expression profiles and highlight the power of integrating multiple data sets to define a robust molecular taxonomy of the disease.

overall_design: Surgically resected 118 tumor tissues from patients with hepatocellular carcinoma (HCC)

first: Sebastian

last: Nijman

first: Masahiro

last: Kobayashi

first: Jennifer

last: Chan

first: Jean-Philippe

last: Brunet

first: Derek

last: Chiang

first: Augusto

last: Villanueva

first: Philippa

last: Newell

first: Amy

last: Camargo

first: Supriya

last: Gupta

first: Jamie

last: Moore

first: Matthew

last: Wrobel

first: Jim

last: Lerner

last: Reich

first: Kenji

last: Ikeda

first: Masashi

last: Hashimoto

first: Goro

last: Watanabe

first: Stacey

last: Gabriel

first: Scott

last: Friedman

first: Hiromitsu

last: Kumada

first: Josep

last: Llovet

first: Todd

middle: R

last: Golub