title: Identify potential maternal genes of Bombyx mori using Digital Gene Expression Profiling

status: Public on Feb 28 2018

city: Zhenjiang

first: Pingzhen

last: Xu

state: Jiangsu

address: sibaidu road 16

department: School of Biotechnology,

country: China

institute: Jiangsu University of Science and Technology

type: Expression profiling by high throughput sequencing

summary: Maternal genes present in mature oocytes and play a crucial role in the early development of the silkworm. Although maternal genes have been widely studied in many species, there are limited research in Bombyx mori. High-through experimental technology provides a practical way for genome-wide study. Here we show a transcriptome study on silkworm eggs. Unfertilized eggs from five different stages of early development were used for detecting the change situation of gene expression. The expressed genes showed different patterns over time. Maternal genes were annotated according to homology analysis with Drosophila melanogaster. In our result, more than a half expressed maternal genes were fall into four expression patterns and showed downward trend over time. The function annotation of material genes showed that they were related to transcription factor activity, growth factor activity, nucleic acid binding, RNA binding, ATP binding, ion binding and so on. In additional, twenty-two gene clusters including material genes were identified from 18 scaffolds. Altogether, we plotted a profile for maternal genes of Bombyx mori using digital gene expression profiling method. It will provide a base for mother-specific signature research and improve the understanding of early development of silkworm.

overall_design: To analyze the differentially expressed genes,in particular the maternal genes,related to embryonic development from 0h to 24h after unfertilized embryos spawning, the silkworm unfertilized embryos are used for RNA-Seq.

first: M

last: Zhang

first: S

last: Qin

first: G


title: The UzcRS two-component system integrates regulatory input from a diverse set of auxiliary regulators

status: Public on Feb 20 2018

city: Livermore

first: Dan

last: Park

state: CA

address: 7000 East Ave

department: BBTD

country: USA

institute: Lawrence Livermore National Lab

summary: The UzcRS two-component system in Caulobacter crescentus functions as a global activator of an extracytoplasmic stress response pathway and is induced by the metals U, Zn and Cu.  Unexpectedly, a screen for mutations that affected the activity of the UzcR-regulated urcA promoter (PurcA) revealed four previously uncharacterized proteins whose inactivation led to metal-independent induction of PurcA.  Using molecular genetics and functional genomics, we found that these auxiliary regulators regulate PurcA expression by modulating the activity of UzcRS through distinct mechanisms.  The membrane protein UzcX, whose expression is positively regulated by UzcR, forms a regulatory complex with UzcS, providing a mechanism of feedback inhibition within the UzcRS circuit.  UrtAP, an ABC transporter with a periplasmic metallo-aminopeptidase domain, negatively regulates UzcRS activity and antagonizes metal dependent stimulation by virtue of its enzymatic activity.  Lastly, two MarR family transcription factors, MarR1 and MarR2, synergistically regulate UzcRS activity by repressing the expression of the membrane proteins UzcY and UzcZ, respectively, which function as UzcRS activators.  In addition to modulating basal UzcRS activity, UzcY and UzcZ enhance the U/Zn/Cu sensitivity of UzcRS, shifting its responsiveness to more environmentally-relevant metal concentrations.  Collectively, these data suggest that UzcRS functions as the core-signaling unit within a multicomponent signal transduction pathway that includes an unusually diverse set of auxiliary regulators.

overall_design: Gene expression profiles of ΔuzcR, ΔuzcX ΔuzcR,  ΔurtAP ΔuzcR, ΔmarR1 ΔuzcR, ΔmarR2 ΔuzcR strains were determined in triplicate


title: Iron acquisition system and cell shape of host bacteria commonly respond to the carriage of three plasmids belonging to different incompatibility groups.

status: Public on Feb 17 2018

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

type: Expression profiling by genome tiling array

summary: Plasmids are one of the important mobile genetic elements in bacterial evolution. In this study, to evaluate the generality of the impact of plasmid carriage on host cell between different plasmids, we compared the response of Pseudomonas putida KT2440 to harboring three natural plasmids; RP4 (IncP-1, multidrug resistance, 60,099-bp), pCAR1 (IncP-7, carbazole-degradative, 200,231-bp) and NAH7 (IncP-9, naphthalene-degradative, 82,232-bp). We prepared two sets of plasmid-harboring strains from independent conjugation events to elucidate the reproducibility of the impact of the plasmid carriage. As results, the fitness was reduced by the carriage of RP4 and pCAR1 in liquid medium, while it was unaffected or even improved for NAH7-harboring strains. RP4-harboring KT2440 formed smaller colonies than the plasmid-free strain on solid medium (1.6% agar). The host cells were elongated by the carriage of the all plasmids, respectively. Copy number determination by quantitative PCR showed that the amount of each plasmid DNA in the host cell did not differed drastically. Whole genome resequencing showed that 13 SNPs (RP4), 24 SNPs (pCAR1) and 5 SNPs (NAH7) were the total differences between the two substrains for each plasmid-harboring strains. Transcriptome analyses showed that the impact of plasmid carriage was constantly larger in RP4-harboring strain than the other two plasmid-harboring strains. Genes involved in metal acquisition and metabolism were commonly affected by the carriage of the three plasmid. Indeed, plasmid-harboring strains showed greater growth inhibition than plasmid-free strains under iron-limiting condition. This feature could become future target to control plasmid spreading.

overall_design: Transcriptome analysis was performed using Pseudomonas putida KT2440 harboring one of the three plasmid (RP4, pCAR1, NAH7), respectively. RNA maps of the donor or the plasmid-free strain were used as controls. Biologically duplicated data were obtained.

first: Yurika

last: Takahashi


title: Efficacy of the highly selective focal adhesion kinase inhibitor BI 853520 in adenocarcinoma xenograft models is linked to a mesenchymal tumor phenotype [mRNA]

status: Public on Feb 27 2018

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary:
mRNA expression profiling of untreated CDX samples and correlation with sensitivity data derived from treatments with BI 853520.

Focal adhesion kinase (FAK), a non-receptor tyrosine kinase, has attracted interest as a target for pharmacological intervention in malignant diseases. Here, we describe BI 853520, a novel ATP-competitive inhibitor distinguished by high potency and selectivity. In vitro, the compound inhibits FAK autophosphorylation in PC-3 prostate carcinoma cells with an IC50 of 1 nmol/L and blocks anchorage-independent proliferation of PC-3 cells with an EC50 of 3 nmol/L, whereas cells grown in conventional surface culture are 1000-fold less sensitive. In mice, the compound shows long half-life, high volume of distribution and high oral bioavailability; oral dosing of immunodeficient mice bearing subcutaneous PC-3 prostate adenocarcinoma xenografts resulted in rapid, long-lasting repression of FAK autophosphorylation in tumor tissue. Daily oral administration of BI 853520 to nude mice at doses of 50 mg/kg was well tolerated for prolonged periods of time. In a diverse panel of 16 subcutaneous adenocarcinoma xenograft models in nude mice, drug treatment resulted in a broad spectrum of outcomes, ranging from group median tumor growth inhibition values >100% and tumor regression in subsets of animals to complete lack of sensitivity. Biomarker analysis indicated that high sensitivity is linked to a mesenchymal tumor phenotype, initially defined by loss of E-cadherin expression and subsequently substantiated by gene set enrichment analysis. Further, we obtained microRNA expression profiles for 13 models and observed that hsa-miR-200c-3p expression is strongly correlated with efficacy (R2 = 0.889). BI 853520 is undergoing evaluation in early clinical trials.

overall_design: In total 47 cell line derived xenografts were analyzed from 16 individual cell lines with either 2 or 3 biological replicates.

first: Norbert

last: Schweifer

first: Christian

last: Haslinger


title: Expression data from leaflets of domesticated tomato and wild-related Solanum pennellii plants subjected to water stress

status: Public on Feb 21 2018

city: Espinardo - Murcia

first: Francisco

middle: Borja

last: Flores

state: Murcia

address: P.O. Box 164

department: Stress Biology and Plant Pathology

country: Spain

institute: CEBAS-CSIC

summary:
Transcriptomics study which main goal is to elucidate the programme of gene expression triggered by water stress in leaflets of the drought-tolerant wild-related tomato Solanum pennellii (acc. PE47) compared with domesticated tomato (S. lycopersicum, cv. P73).
In this study we used S. lycopersicum (Sl) (cv. P73) and S. pennellii (Sp) (acc. PE47) species displaying remarkable divergences regarding drought tolerance, to investigate the physiological and molecular responses in leaves of plants grown without stress (control) and after four days of water withholding (water stress, WS), when plant water loss was significant but  leaves did not show visual dehydration symptoms yet. Significant physiological differences between species were found, showing Sp leaves higher ability to avoid water loss. Leaf transcriptomic analysis showed important constitutive expression differences between Sp and Sl, including genes with unknown function. In relation to the genes specifically induced by drought in Sp, those linked to stomatal closure, cell wall and primary carbohydrate metabolism and, specially, nitrogen metabolism were identified. Thus, genes linked to NH4+ assimilation, GOGAT/GS cycle and the GDH- and GABA-shunt were specifically induced  by water stress in leaves of Sp. Our results showed also the up-regulation in Sp of genes involved in JA biosynthesis pathway, which were induced in both conditions, whereas genes involved in ET biosynthesis were specifically induced under WS. Regarding ET signaling, ERF genes were up-regulated by WS in Sp, hinting at the importance of these transcriptional regulators in the drought response of Sp.

sample_organism:
Solanum lycopersicum
Solanum pennellii

overall_design: Domesticated tomato (cv. P73) and wild-related tomato S. pennellii (acc. PE47) plants were cultivated by pairs in pots with substrate. Eighteen pots with plants having 2-3 full-developed leaves for domesticated tomato, and 3-4 full-developed leaves for wild-related tomato were selected (18 P73 plants and 18 PE47 plants in total).  Nine couples divided into three biological replicates were maintained in standard culture conditions (control) while the other nine, also divided into three biological replicates, were subjected to water stress treatment by withholding watering during four days (water stress, WS). RNA isolated from leaflets coming from three individual pooled plants (biological replicates) was used in hybridization to one chip, resulting in total 12 chips: three replicates of P73 control, three replicates of PE47 control, three replicates of P73 WS and three replicates of PE47 WS. The biotinilated cRNA was hybridized to GeneChip® Tomato Genome Array of Affymetrix interrogating 10209 sequences. The intensity value of each probe in the array were processed and normalized according to the Robust Multichip Average (RMA) method to obtain an individual intensity value for each probeset.  First filtering, normalization and second filtering of probes yield a final list of 5050 sequences (working list).  A statistical analysis based in multiple test corrections was performed using the FDR test on the working list.  Genes with an FDR < 0.05 and a fold change (ratio value) of ≥ 2.0 when comparing genotypes in the same experimental condition were identified as differentially expressed genes. A final list of 535 genes was accomplished with the above conditions.  The annotation of probe sets was obtained from Affymetrix and loaded in the Partek Genomics Suite software (Partek Incorporated, St. Louis, USA).  For the functional study of DEGs MapMan software was used (http://mapman.gabipd.org).  The Slyc_AFFY_SGN_BUILD2_070709 database was loaded and used for this functional analysis.  The statistical analysis followed was of Willcoxon Rank Sum test with Benjamini-Hochberg correction.

first: Irene

last: Albaladejo

first: Isabel

last: Egea

first: Victoriano

last: Meco

first: Angel

last: Sevilla

first: Maria

middle: C

last: Bolarin

middle: B


title: Are small RNAs involved in the regulation of nitrogen metabolism in haloarchaea?

city: San Vicente del Raspeig

first: Julia

last: Esclapez

state: Alicante

address: Crta San Vicente del Raspeig s/n

department: Biochemistry

institute: University of Alicante

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs have been studied in detail in Bacteria and Eukarya domain, but in the case of Archaea domain the knowledge is scarce and the physiological function of the majority is still uncertain. To extend the knowledge of sRNAs in Archaea domain and its possible role in the regulation of the nitrogen assimilation metabolism in haloarchaea, Haloferax mediterranei has been used as a model microorganism. Bioinformatic approach has allowed to predict 295 putative sRNAs genes in the genome of H. mediterranei, 88 of which have been verified by means  of RNA-seq. The secondary structure of putative sRNAs and its possible targets have been identified. Curiously, some of them present as possible targets genes related to the nitrogen assimilation, as glutamate dehydrogenase or regulatory nitrogen protein PII. Analysis of RNA-seq data has also revealed differences in the expression pattern of 16 sRNAs according to the nitrogen source. Consequently, RNomic and the bioinformatic approaches used in this work have allowed the identification of new sRNAs in Hfx. mediterranei, some of which show different expression pattern depending on the nitrogen source. It suggests that these sRNAs could be involved in the regulation of nitrogen assimilation, being able to constitute important gene regulatory network.

overall_design: microRNAs were isolated from Hfx. Mediterranei cultures grown in the presence of two different nitrogen sources, nitrate and ammonium, to mid-exponential phase.

first: Gloria

last: Payá

first: Vanesa

last: Bautista

first: Mónica

last: Camacho

first: Natalia

last: Castejón-Fernández

first: Luís

middle: A

last: Alcaraz

first: María

middle: J

last: Bonete

middle: M


title: H9 human embryonic stem cells and Isthmic organizer (IsO) like cells

city: Seoul

first: Dong-Wook

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Physiol.

country: South Korea

institute: Yonsei University College of Medicine

summary: Identify gene expression patterns of isthmic organizer (IsO) like cells derived from human embryonic stem cells.

overall_design: The total of 6 samples were analyzed which could be grouped into 2 groups (control and IsO group)

first: Junwon

last: Lee

first: Sang-Hwi

last: Choi

first: Dae-Sung


title: The Evolutionarily Conserved AU-Dinucleotide at the 5’ End of U1 snRNA is Critical for the Biogenesis and Functionality of U1 snRNP

status: Public on Feb 22 2018

city: Ithaca

first: Jeffrey

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

summary: Splicing is initiated by a productive interaction of pre-mRNA and the U1 snRNP, which dictates the formation a short RNA duplex between the 5’ splice site of a pre-mRNA and the 5’ end of the U1 snRNA.  A long-standing puzzle has been why the AU dincucleotide at the 5’-end of the U1 snRNA shows strict conservation, despite the absence of an apparent role in duplex formation.  To explore this conundrum, we varied this AU dinucleotide into to all possible permutations and analyzed the resulting molecular, biochemical, and physiological consequences.  This led to the findings that the AU dinucleotide governs the precision of transcription start site, the methylation status of the U1 snRNA 5’-cap, appropriate maturation of a functional U1 snRNP, and its subsequent utilization in the splicing pathway.  Our data also provide an insight as to why the identity of the AU dinucleotide is strongly favored during evolution.

overall_design: Splicing sensitive microarrays for S. cerevisiae (Agilent AMADID #: 019521) were used to monitor global changes in splicing in the background of U1 snRNA (snR19) variant compared to wild type


title: CpdA is involved in amino acid metabolism in Shewanella oneidensis MR-1

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

institute: Tokyo University of Pharmacy and Life Sciences

summary: Cyclic 3',5'-adenosine monophosphate (cAMP) phosphodiesterase (CPD) is an enzyme that catalyzes the hydrolysis of cAMP, a signaling molecule affecting diverse cellular and metabolic processes in bacteria. Some CPDs are also known to function in cAMP-independent manners, while their physiological roles remain largely unknown. Here, we investigated physiological roles of CPD in Shewanella oneidensis MR-1, a model environmental bacterium, and report that CPD is involved in amino-acid metabolism. We found that a CPD-deficient mutant of MR-1 (ΔcpdA) showed decreased expression of genes for the synthesis of methionine, S-adenosylmethionine, and histidine and required these three compounds to grow in minimal media. Interestingly, deletion of adenylate cyclases in ΔcpdA did not restore the ability to grow in minimal media, indicating that the amino acid requirements were not due to the accumulation of cAMP. These results suggest that CPD is involved in the regulation of amino acid metabolism in MR-1 in a cAMP-independent manner.

overall_design: Total 8 samples, 4 biological replicates for each sample

first: Takuya

last: Kasai

first: Kazuya

last: Watanabe


title: Comparative transcriptional profiling of Arabidopsis yda11 mutant and wild-type plants after infection with Plectosphaerella cucumerina

status: Public on Feb 19 2018

city: Madrid

first: Sara

last: Sopeña Torres

address: Campus Montegancedo - Autovia M40 km.38

institute: Centro de Biotecnologia y Genomica de Plantas (UPM-INIA)

summary: Comparative transcriptomic analysis of Arabidopsis thaliana yda11 plants (in Col-0 background), and wild-type plants (Col-0) non-infected or infected with the necrotrophic fungal pathogen Plectosphaerella cucumerina BMM (PcBMM)

overall_design: Gene expression was measured in 3-week-old Arabidopsis yda11 plants and in wild-type plants (Col-0) at 1 and 3 days after inoculation (1 and 3 dpi) with P. cucumerina BMM (PcBMM) or after treatment with water (non-infected or mock treatment). Three independent experiments were performed.

last: Sopeña-Torres

first: Lucía

last: Jordá

first: Clara

last: Sánchez-Rodríguez

first: Eva

last: Miedes

first: Viviana

last: Escudero

first: Sanjay

last: Swami

first: Gemma

last: López

first: Mariola

last: Pislewska-Bednarek

first: Ines

last: Lassowskat

first: Justin

first: Yangnan

last: Gu

first: Sabine

last: Haigis

first: Danny

last: Alexander

first: Sivakumar

last: Pattathil

first: Antonio

last: Muñoz-Barrios

first: Pawel

last: Bednarek

first: Shauna

last: Somerville

first: Paul

last: Schulze-Lefert

first: Michael

middle: G

last: Hahn

first: Dierk

last: Scheel

last: Molina


title: Identification of miRNAs that regulate vestibular compensation

first: Munyoung

last: Chang

address: 102 Heukseok-ro, Dongjak-gu

department: Otorhinolaryngology-Head and Neck Surgery

institute: Chung-Ang University College of Medicine

summary: To investigate which miRNAs regulate the vestibular compensation after unilateral vestibular deafferentiation (UVD), we have performed microarray for miRNAs as a discovery platform. UVD induces breakdown of the activity of ipsilesional vestibular nuclei and an unbalance of activity between bilateral vestibular nuclei. Vestibular compensation is a course of rebalancing of activities of bilateral vestibular nuclei. It takes place mainly in medial vestibular nucleus. This study was performed using seven week-old-male Sprague–Dawley rats. Based on our previous experiment about vestibular compensation course, we set two time points for harvesting medial vestibular nuclei: 4hr and 4 days after unilateral vestibular deafferentiation. Twenty four animals were divided into two experimental groups: UVD group undergoing UVD at left side (n = 12); and SO group undergoing sham operation (SO) at left side (n=12). Six animals of each group were anesthetized deeply and euthanized at 4 hr or 4 days after surgery, respectively. Medial vestibular nucleus at left side was harvested. Medial vestibular nucleus from three animals became one sample for microarray. Sequentially two samples were obtained for each time point in one group. Microarray for miRNAs was performed using the Agilent Rat miRNA Microarray 8x15K platforms. Considering the fold change of normalized signal intensities between two time points in UVD group and between UVD and SO groups at the same time, miR-31a-5p, 133a-3p, 133b-3p, 204-5p, 206-3p, 218a-5p, 219a-5p, 221-3p and 497-5p were selected as the candidate miRNAs. This result was validated by quantitative reverse transcription-PCR.

overall_design: Unilateral vestibular deafferentiation induced miRNAs expression in medial vestibular nucleus of Sprague–Dawley rat was measured at 4hr and 4 days after unilateral vestibular deafferentiation. Comparing these results with the results from the sham operation group, the candidate miRNAs that might regulate vestibular compensation were selected.

first: Mun

middle: Y

first: Moo

middle: K

last: Park


title: AAV-mediated RNAi of traumatic brain injury-induced genes in the rat hippocampus

status: Public on Feb 16 2018

city: Northbrook

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: To address the hypothesis that silencing deleterious or protective injury-induced genes in the rat hippocampus will reduce or increase the numbers of injured hippocampal neurons, alter cellular pathways essential for neuronal function and improve or worsen functional outcome after traumatic brain injury (TBI), we evaluated the effects of silencing neuronal nitric oxide synthase (nNOS) and glutathione peroxidase-1 (GPx-1) expression in the injured rat hippocampus.

overall_design: Two weeks post-TBI/post-AAV treatment, hippocampal pyramidal neurons were laser captured for comparative whole genome microarray analysis.

first: Deborah

last: Boone

first: Jeanna

last: Crookshanks

middle: T

first: Karen

middle: E

last: Torres

first: Helen

middle: L

last: Hellmich


title: Gene expression profile of Candida albicans SC5314 in response to sanguinarine exposure

city: Shanghai

first: Hua

last: Zhong

address: No. 325, Guohe Road

institute: Second Military Medical University

summary: Transcriptional profile of Candida albicans comparing sanguinarine treated cells with untreated cells.

overall_design: Wild type Candida albicans strain SC5314 was selected to perform the gene expression microarray. Two-condition experiment, DMSO treated cells vs. sanguinarine treated ones. Biological replicates: 3 control treated with DMSO, 3 sanguinarine treated, independently grown and harvested. One replicate per array.

first: Gan-Hai

last: Hu


title: Antagonistic roles of TGF-β ligands during cardiac regeneration in zebrafish

city: Giessen

first: Sven

last: Reischauer

state: Hessen

address: Auweg 129

department: Cardiology/Angiology

country: Germany

institute: Medical Clinic I - JLU

summary: we are comparing sham-injured zebrafish heart samples with 4 days post cryoinjured zebrafish heart samples.

overall_design: pool of 10X sham-injured zebrafish heart compared to pool of 10X 4 days post cryoinjured zebrafish hearts

first: Deepika

last: Dogra

first: Suchit

last: Ahuja

first: Hyun-Taek

last: Kim

first: Didier

middle: R

last: Stainier


title: Next Generation Sequencing Facilitates Quantitative Analysis of hpoR mutant and wild-type strains Transcriptomes in Mycobacterium smegmatis

status: Public on Feb 18 2018

city: Wuhan

first: Weihui

last: Li

address: 1 str Sizisan

institute: Huazhong Agricultural University

summary: Compare the gene expression difference between hpoR knockout strains and wild-type strains by RNA sequencing in Mycobacterium smegmatis. The goal of this study is that detection HpoR acts as a transcriptional factor and regulates the target genes expression.

overall_design: Two samples in triplicate are analyzed. The control sample is the wild-type strains in Mycobacterium smegmatis.

first: Zhengguo

last: He


title: Transcriptomic analysis of Pancreatic Stellate Cells (PSC) and pancreatic cancer cells

city: Barcelona

first: Eva

last: Vaquero

address: Carrer Villarroel 170

institute: Hospital Clínic

summary:
Transcriptomic analysis of Wild Type (WT) and heterozygous (HT) PSC in order to study how the heterozygosis of our gene of interest affect the gene expression pattern of this cell population.
Transcriptomic analysis of pancreatic cancer cells that were previously stimulated with conditioned media from both WT and HT PSC, in order to study the effect of PSC secreted factors on cancer cells transcriptome.

overall_design: WT and HT PSC were isolated from WT and HT mice respectively and kept in culture for two weeks until they were activated. Pancreatic cancer cells were treated for 24h with control media or with conditioned media from WT PSC or HT PSC. Once PSC were activated and cancer cells were treated, we isolated their mRNA.

first: Irene

last: Sangrador

first: Sebastià

last: Franch-Expósito

first: Antoni

last: Castells


title: Comparative transcriptional profiling of Arabidopsis CA-YDA line and wild-type plants after infection with Plectosphaerella cucumerina

first: Sara

last: Sopeña Torres

summary: Comparative transcriptomic analysis of Arabidopsis thaliana lines expressing a constitutively active YDA protein (CA-YDA; in La-0 background), and wild-type plants (La-0) non-infected or infected with the necrotrophic fungal pathogen Plectosphaerella cucumerina BMM (PcBMM)

overall_design: Gene expression was measured in 18-days old Arabidopsis thaliana plants expressing a constitutively active YDA protein (CA-YDA) and in wild-type plants (La-0) at 1 day after inoculation (1 dpi) with P. cucumerina BMM (PcBMM) or after treatment with water (non-infected or mock treatment). Three independent experiments were performed.

last: Sopeña-Torres

first: Lucía

last: Jordá

first: Clara

last: Sánchez-Rodríguez

last: Miedes

first: Viviana

last: Escudero

first: Sanjay

last: Swami

first: Gemma

last: López

first: Mariola

last: Pislewska-Bednarek

first: Ines

last: Lassowskat

first: Justin

last: Lee

first: Yangnan

last: Gu

first: Sabine

last: Haigis

first: Danny

last: Alexander

first: Sivakumar

last: Pattathil

first: Antonio

last: Muñoz-Barrios

first: Pawel

last: Bednarek

first: Shauna

last: Somerville

first: Paul

last: Schulze-Lefert

first: Michael

last: Hahn

first: Dierk

last: Scheel

last: Molina


title: Expression profiles of Bacillus subtilis strains deleted for or ectopically expressing dnaA, sda, and spo0A during exponential growth and after treatment with HPUra.

city: Cambridge

first: Alan

last: Grossman

state: MA

address: 31 Ames St.

department: Biology

institute: MIT

summary: The objective of the study was to determine the role of dnaA in regulating gene expression, and the extent to which the effects are mediated by sda and spo0A.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
To identify transcriptional targets for DnaA, we compared a strain lacking dnaA (AIG200) with a strain where dnaA was reintroduced under an IPTG-inducible promoter (Pspank-dnaA; TAW5). Because a dnaA null mutant cannot replicate from oriC, we used an oriC- oriN+ background for these strains. RNA was analyzed from cultures growing exponentially in minimal media, and after treatment with the hydroxyl-phenyl-azo-uracil (HPUra), which inhibits DNA polymerase.
In order to determine the effect during exponential growth of deleting sda on gene expression, and the role of sda in mediating the transcriptional effects of dnaA, we analyzed RNA from wild type cells (AG174), an isogenic sda-null (BB668), and the following oriC- oriN+ strains that either lack or inducibly express dnaA and sda: TAW86 (dnaA- Pspank-sda), TAW97 (Pspank-dnaA Pspank-sda), TAW121 (Pspank-dnaA sda-), and TAW118 (dnaA- sda-). Because Sda indirectly inhibits Spo0A, we also analyzed RNA from a spo0A strain (TAW106; Pspank-dnaA, spo0A).
For all experiments, at least three biological replicates were performed.

first: Tracy

last: Washington

first: Janet

last: Smith

middle: D


title: microRNA expression profiling in tumor prostate samples from recurrent and non-recurrent cases

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We investigated the relative miRNA levels in primary prostate cancer samples from patients that had a subsequent recurrence event versus patients that did not. For one of the top miRNAs arising from this analysis, miR-33a, we carried out further investigation, including miRNA levels in normal and tumor prostate samples as well as PCa cell lines. Then, we performed a detailed functional analysis of mir-33a in LNCaP and VCaP PCa cells and evaluated proliferative, invasive and anchorage independent growth potential of cells upon overexpression and knockdown of miR-33a.

overall_design: Two groups of tumor samples from prostate cancer patients: recurrent versus non-recurrent. Recurrence was defined as two consecutive serum PSAs greater than 0.2 ng/ml. Patients were followed for until PSA recurrence or at least 4 years (for non-recurrent cases).

last: Ittmann

first: Mustafa

last: Ozen

first: Yiqun

last: Zhang


title: Transcriptomic analyses of IXR1 gene deletion in Saccharomyces cerevisiae and its increased resistance to cisplatin treatment.

city: A Coruña

first: Angel

last: Vizoso-Vázquez

address: Púa da Fraga, 10

department: Cellular and Molecular Biology Department

institute: University of A Coruña

summary: Ixr1 is a transcriptional factor from Saccharomyces cerevisae with high affinity to cisplatin-DNA adducts through their two HMG-box DNA binding domains. Its transcriptional regulation  is essential in the cytotoxicity caused by cisplatin, although the molecular mechanisms supporting this function are not understood. We present a transcriptome analysis discriminating between RNA changes induced by cisplatin which are dependent or independent of the Ixr1 function.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: The S. cerevisiae strain W303 (MATa ade2-1 can1-100 leu2-3,112 trp1-100 ura3- 52) and its derivative W303-Δsky1 previously described (Rodríguez- Lombardero et al., 2012) have been used in these analyses. Biological replicates of cultures and treatments were run in triplicate.  The yeast cells were pre-cultured over night in 10mL of complete synthetic medium (SD) prepared as previously described (Zitomer and Hall, 1976). The following day the cells were inoculated at initial OD600 of 0.4 in 70 mL SD and grown in 250 mL Erlenmeyer flasks at 30 ºC and with agitation at 250 rpm. When cells reached OD600 of 0.6, the cultures from each strain were divided in two aliquots of 25 mL (control and cisplatin treatment). A stock solution of cisplatin 6 mM in dimethyl sulfoxide (DMSO) was prepared and the drug was added to the treated cultures at a final concentration of 600 microM. An equivalent volume of DMSO was added to the control cultures. The treatment was done at 30ºC and with agitation at 250 rpm during four hours in darkness. RNA was extracted from a number of cells corresponding to OD600 of 3 with the AurumTM Total RNA Mini Kit (Bio-Rad) and following the manufacturer’s instructions. The RIN parameter (RNA Integrity Number) evaluated with the 2100 was near to the value 9 in all the samples.

first: Ángel

first: Mónica

last: Lamas-Maceira

first: M

middle: I

last: González-Siso

first: Manuel

last: Becerra

last: Cerdán


title: Foxc1 ablated mice are anhidrotic and recapitulate features of human miliaria sweat retention disorder

city: Baltimore

first: Chang-Yi

last: Cui

state: MD

address: 251 Bayview Blvd Suite 100, 10C222

department: NIA

institute: NIH

summary: Sweat glands are critical for thermoregulation. The single tubular structure of sweat glands has a lower secretory portion and an upper reabsorptive duct leading to the secretory pore in the skin. Genes that determine sweat gland structure and function are largely unidentified. Here we report that a Fox family transcription factor, Foxc1, is obligate for appreciable sweat duct activity in mice. When Foxc1 was specifically ablated in skin, sweat glands appeared mature, but the mice were severely hypohidrotic. Morphological analysis revealed that ducts were blocked by hyperkeratotic or parakeratotic plugs. Consequently, lumens in ducts and secretory portions were dilated, and blisters and papules formed on the skin surface in the knockout mice. The phenotype was strikingly similar to human sweat retention disorder miliaria. We further found that Foxc1 deficiency ectopically induced the expression of keratinocyte terminal differentiation markers in the luminal duct cells, which most likely contributed to keratotic plug formation. In summary, Foxc1 regulates sweat duct luminal cell differentiation, and mutant mice may provide a model for miliaria.

overall_design: Wild Type vs Foxc1 cKO mouse footpads

first: Changyi

first: Piao

last: Yulan


title: microRNA data in cardiomyocytes isolated from rat at 1 versus 10 day of age

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

institute: Shanghai University

summary: This study was to identify microRNAs responsible for postnatal cardiomyocyte proliferation.

overall_design: Total RNAs were extracted from cardiomyocytes isolated from rat at 1 versus 10 day of age (n=4 per group), and then subjected to microRNA array analysis (Agilent Rat miRNA, Design ID: 031189).

first: Junjie

last: Xiao

first: Xiangqing

last: Kong


title: Proteasome degradative activity regulates CD8+ T lymphocyte metabolism and fate specification

city: La Jolla

first: Christella

last: Widjaja

state: ca

address: 9500 Gilman Drive #0063

department: Medicine

institute: UCSD

summary: Pre-effector and pre-memory cells resulting from the first CD8+ T cell division in vivo exhibit low and high rates of proteasome degradative activities, respectively. These proteasome-induced metabolic consequences were mediated in part by asymmetric segregation of Myc during cell division. Taken together, these results suggest proteasome activity as a regulator of CD8+ T lymphocyte metabolism and fate specification.

overall_design: Transcriptome of biological duplicates of isolated CD8+CD44+ mouse lymphocytes treated with vehicle control, proteasome inhibitor, and proteasome activator were analyzed.

first: Patrick

last: Metz

first: Anthony

last: Phan

first: Jeffrey

middle: N

last: Savas

first: Gerjan

last: de Bruin

first: Yves

last: Leestemaker

first: Kathleen

last: Fisch

first: Aaron

last: Chang

first: Hermen

middle: S

last: Overkleeft

first: Huib

last: Ovaa

first: John

last: Yates III

first: Ananda

middle: W

last: Goldrath


title: ADARs regulate small RNAs mapped to edited sequences

status: Public on Feb 23 2018

city: Salt Lake City

first: Brenda

last: Bass

state: Utah

address: 15 N Medical Drive East, Rm 4800

institute: University of Utah

summary: Cellular RNAs containing double-stranded RNA (dsRNA) structures are subject to A-to-I RNA editing by the adenosine deaminases that act on RNA (ADARs). While A-to-I editing can alter mRNA coding potential, most editing is observed in non-coding sequences, the function of which remains poorly characterized. To correlate small RNA population with expression patterns of ADARs and hyperedited RNAs (editing-enriched regions: EERs) defined and characterized in a separate RNAseq analysis, we re-analyzed existing smallRNAseq datasets of a wildtype strain and a strain lacking ADARs (adr-1;adr-2). Analysis of primary siRNAs from mixed-stage worms revealed that ADARs impact siRNA biogenesis from EERs. We then analyzed primary and secondary RNAs mapping to EERs from embryo-stage or L4-stage worms and observed that ADAR effects on siRNA levels are dependent on developmental stage.

overall_design:
For mixed-stage wildtype (N2) and adr-1;adr-2 samples, small RNAs with 5' monophosphates sequenced on Illumina HiSeq2000 (see GSE28888) were mapped to 1523 EERs defined in GSE79375, excluding those mapping to annotated miRNA or 21U-RNA loci. For embryo and L4-staged samples (from PMID: 21909095), small RNAseq using  5'phosphate independent protocols were likewise mapped to 1523 EERs, excluding those mapping to annotated miRNA or 21U-RNA loci.

This series includes two samples re-analyzed from GSE28888 and eight samples re-analyzed from PubMed ID 21909095. These eight samples from PubMed ID 21909095 have not been deposited in GEO or SRA or any other public database  and were obtained upon request from the authors. Included on this record are alignment files of reads aligned to EERs (in SAM format) and processed data for all re-analyzed samples.

first: Daniel

middle: P

last: Reich

first: Katarzyna

last: Tyc


title: Expression data from postnatal piglet retina, investigating how sialyllactose benefit retina development and vision

city: Beijing

first: yujie

last: shi

address: No.5 building No.5 Road Dijin

institute: Nestle research center- Beijing hub

summary:
Sialyllactose supplementation in pig milk replacer could promote cognitive functions in postnatal piglet behaviour experiment. There are 2 groups of 3-day-old postnatal piglets, feeding basal level and sialyllactose. After 35 days  feeding, sialyllactose group showed better performance in behaviour experiment.
We used microarrays to detail the global programme of gene expression underlying the nervous system development and memory formation.

overall_design: There are 2 treatment groups and 9 replicates for each group. The 2 treatment groups are control group feeding basal level and sialyllactose supplement group. Pig retina tissues were collecteded for RNA extraction and hybridization on Affymetrix microarrays.

first: Yujie

last: Shi


title: Whole genome pooled shRNA screen to characterize Raptinal-induced apoptosis in the MIA PaCa-2 cell line

city: Urbana

first: Kathryn

last: Partlow

address: 1301 West Gregory Drive

institute: University of Illinois, Urbana-Champaign

summary: The goal of the study was to characterize the mechanism by which Raptinal induces apoptosis using a genome-wide pooled shRNA screen.  Following drug treatment, the abundance of the shRNA constructs were determined and compared between DMSO and Raptinal-treated samples. Constructs depleted in Raptinal samples versus DMSO control, are expected to potentiate Raptinal-induced apoptosis by down regulating anti-apoptotic proteins. In contrast, shRNA constructs enriched upon Raptinal treatment are expected to target pro-apoptotic proteins, whose down regulation confers protection from Raptinal-induced apoptosis. Follow up experiments were performed on enriched shRNAs in order to validate potentially novel pro-apoptotic proteins.

overall_design: Cells were treated with Raptinal (1.25-1.8 micromolar) or DMSO vehicle control over a 20 day period. After every 2-3 days of drug treatment, cells were allowed to recover in drug-free medium and treatment repeated for a total of 3 rounds over the 20 day period. Two biological replicates of Raptinal-treatment were performed and one biological replicate of DMSO vehicle control was performed. Cell passaging was performed on a scale sufficient to maintain >100 fold library representation. At the end of the 20 days, total RNA was extracted and shRNA abundances determined.

first: Rahul

last: Palchaudhuri

middle: C

first: Paul

last: Hergenrother

first: Michael

last: Lambrecht

first: Rachel

last: Botham


title: Different target specificities of haptoglobin and hemopexin define their sequential role as primary and backup protective systems against hemoglobin toxicity

status: Public on Feb 25 2018

city: Zurich

first: Christian

middle: Andreas

last: Schaer

address: Raemistrasse 100

country: Switzerland

institute: University Hospital Zurich

summary:
Hemoglobin (Hb) released from red blood cells during hemolysis is a trigger of oxidative vascular damage with endothelial cells being a primary target. The Hb and heme scavenger proteins haptoglobin (Hp) and hemopexin (Hx) have been characterized as a sequential defense system with Hp as the primary protector and Hx as a backup when all Hp is depleted during more severe or prolonged hemolysis. The paradigm of sequential protection by the two scavengers is based on observational patient data proposed by Mueller-Eberhardt. In this study we present a mechanistic rationale for these clinical observations using a novel in vitro model of Hb triggered endothelial damage. We identified oxyHb(Fe2+) transformation to ferric Hb(Fe3+), free heme transfer from ferric Hb(Fe3+) to lipoprotein and subsequent oxidative reactions in the lipophilic phase.
The accumulation of toxic lipid peroxidation products liberated during oxidation reactions lead to endothelial damage characterized by a specific gene expression pattern, reduced cellular ATP and monolayer disintegration. Quantitative analysis of key biochemical and functional parameters allowed us to precisely define the mechanisms and concentrations required for Hp and Hx to prevent this toxicity. In the case of Hp we defined an exponential relationship between Hp availability relative to oxyHb(Fe2+) and related protective activity. This exponential relationship demonstrates that large Hp quantities are required to prevent Hb toxicity. In contrast, the linear relationship between Hx concentration and protective activity allows for significant protection by the backup scavenger during conditions of large excess of free oxyHb(Fe2+) that occurs when all Hp is consumed. The diverse protective function of Hp and Hx in this model can be explained by the different target specificities of the two proteins.

overall_design: A two color common reference design was chosen with 4-12 independent biological replicates of each condition. Each experimental sample (Cy5 labeled) was hybridized against a non-treated reference sample (Cy3 labeled).

middle: A

first: Jeremy

last: Deuel

first: Dominik


title: MicroRNA microarray between smoking-induced human bronchial epithelial cell (HBEC)-derived extracellular vesicles (EVs) and non-treated HBEC-derived Evs

city: chuo-ku

first: Yu

last: Fujita

address: 5-1-1 Tsukiji

department: Research of Molecular Functions and Targets

institute: National Cancer Center Research Institute

summary: To identify exosomal miRNAs that regulate smoking-induced lung myofibroblast differentiation, we conducted a miRNA microarray between smoking-induced HBEC-derived EVs and non-treated HBEC-derived EVs.

overall_design: Cigarette smoke extract (CSE) was prepared for smoking exposure model in vitro. Forty milliliters of cigarette smoke was drawn into the syringe and slowly bubbled into sterile serum-free cell culture media in a 15-ml BD falcon tube. One cigarette was used for the preparation of 10 mL of solution. CSE solution was filtered (0.22 μm) to remove insoluble particles and was designated as a 100% CSE solution. We analyzed the role of CSE induced HBEC-derived EVs in the airway microenvironment. After HBECs were incubated in the non-FBS containing medium with or without a low-concentration CSE (1.0%) for 2 days, we collected conditioned medium (on day 4, 6) and isolated EVs by ultracentrifugation. After then, we collected exosomal RNA and analyzed exosomal microRNA microarray.

first: Takahiro

last: Ochiya


title: Real-time quantitative PCR analysis of human monocyte cells treated invitro with purified angiotensin type 1 receptor auto antibody

first: Peter

middle: M

last: Abadir

state: Maryland

address: 5501 Hopkins Bayview Circle. Rm 1a62

department: Geriatrics

institute: Johns Hopkins University

summary: Human Peripheral blood mononuclear cells were purified from older volunteers' blood and were cultured for 24 hrs in the presence or abscence of angiotensin type 1 receptor autoantibody (AT1RaAb 7ug/ml). In brief:  PBMCs were isolated from heparinized venous blood by Ficoll-Hypaque density gradient centrifugation (86). PBMCs from older individuals cultured in six-well plates (0.5 x 106 cells/ml) were divided into two groups: control group and treatment group. The treatment group was incubated with purified AT1R-aAb (Eagle bioscience, Noshua, New Hampshire) for 24 hours. Supernatant was collected and cells harvested after a total culture period of 24 hours.  RNA extraction, RT2 profiler assay and pathway analysis:  Control and AT1R-aAb treated monocytes and lymphocytes from participants were prepared for RNA isolation. Total cellular RNA was isolated using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany). cDNA was synthesized at 37°C for 60 minutes and the reaction was stopped by heating the reaction mix to 94 °C. PCR cycling parameters are 10 minutes at 95°C and 40 cycles of 15 seconds at 95°C and 60 seconds at 60°C. All primers for the polymerase chain reaction (PCR) were purchased from Operon Technologies, Inc. (Alameda, CA). We performed quantitative PCR with an Mx-3000P Real Time PCR System Instrument and SYBR Green florescent reagents (Stratagene, La Jolla, CA). QPCR to determine AT1R expression was performed using the TaqMan gene expression assay mix (Applied Biosystems) after reverse transcription of RNA with the high-capacity cDNA archive kit (Applied Biosystems, Foster City, CA). To avoid DNA contamination in RT-PCR assays, samples were extensively processed using DNase 1 digestion. Gene expression profiling for inflammation and autoimmunity target genes was performed using RT2 profiler PCR arrays (SuperArray, Frederick, MD) following the manufacturer's instructions. In brief, 1 μg RNA was reverse transcribed with the RT2 profiler PCR array first strand synthesis assay (SuperArray, Frederick, MD) followed by real-time PCR with RT2 real-time PCR master mix Sybr green (SuperArray, Frederick, MD). PCR data from the treated and untreated cells were analyzed by the QIAGEN SuperArray group and the results reported as differential gene expression and statistical significance, fold change and p-value respectively.

overall_design: qPCR gene expression profiling.  Monocytes from three donors were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was pooled prior to gene expression analysis.

first: Neal

last: Fedarko


title: Gene expression in diabetes-prone (NZO/HiBomDife) and diabetes-resistant (C57BL/6.V-Lepob/ob) mouse strains

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary:
Mouse strains like NZO and B6-ob/ob differ in their susceptibility to diet-induced diabetes. Comparison of the islet transcriptomes leads to genes that are either involved in protection or apoptosis of pancreatic islet cells upon carbohydrate challenge.
Genes being upregulated in NZO can be seen as drivers of beta cell failure, while genes upregulated in B6-ob/ob are most likely involved in beta cell protection.

overall_design: Male NZO and B6-ob/ob mice were kept on a carbohydrate-free high-fat diet until the age of 18 wks. Afterwards, diet was switched to a carbohydrate-containing diet to induce glucolipotoxic stress. After 48 h pancreatic islets were isolated for transcriptome analysis.

first: Oliver

last: Kluth

first: Annette

last: Schürmann


title: Heart profiling HMDP

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Identify genes in the heart whose expressions under genetic regulation in the hybrid mouse diversity panel.  The hybrid mouse diversity panel is comprised of classical inbred and recombinant inbred wild type mice.  The RMA values of genes were used for genome wide association as described in Bennett et al Genome Research 2010.  These data used to identify candidate genes at loci associated with atherosclerosis.

overall_design: GWAS for expression in Heart of inbred strains

first: Aldons

middle: J

last: Lusis

first: Brian

last: Bennett

first: Anatole

last: Ghazalpour


title: Ventromorphins: A new class of small molecule activators of the canonical BMP signaling pathway

status: Public on Feb 14 2018

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Here we describe three new small-molecule activators of BMP signaling found by high throughput screening of a library of ~600,000 small molecules. Using a cell-based luciferase assay in the BMP4-responsive human cervical carcinoma clonal cell line, C33A-2D2, we identified three compounds with similar chemotypes, each ventralized zebrafish embryos and stimulated increased expression of the Bmp target genes, bmp2b and szl. Because these compounds ventralize zebrafish embryos, we have termed them “ventromorphins.” As expected for a BMP pathway activator, they induce the differentiation of C2C12 myoblasts to osteoblasts. Affymetrix RNA analysis confirmed the differentiation results and showed that ventromorphin treatments elicits a genetic response similar to BMP-4 treatment. Unlike isoliquiritigenin (SJ000286273), a flavone that maximally activates the pathway after 24 hours of treatment, all three ventromorphins induced SMAD1/5/8 phosphorylation within 30 minutes of treatment and achieved peak activity at 30 minutes or 1 hour, indicating that their direct responses are consistent with activated BMP signaling.

overall_design: This study compares the effects of three drugs on myoblasts to that of BMP4.

first: Jamie

last: Genthe

first: Jaeki

last: Min

first: Dana

last: Farmer

first: Anang

last: Shelat

first: Jose

last: Grenet

first: Wenwei

last: Lin

first: Karen

last: Vrjens

first: Taosheng

last: Chen

first: R

last: Guy

first: Wilson

last: Clements

first: Martine

middle: F

last: Roussel


title: Serum microRNA screening and functional studies reveal miR-483-5p as a potential driver of fibrosis in systemic sclerosis

status: Public on Feb 15 2018

city: Utrecht

first: Eleni

last: Chouri

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht, Utrecht University

summary:
To investigate the miRNA signature in the serum of systemic sclerosis (SSc) patients. The levels of 758 miRNAs were evaluated in the serum of 26 SSc patients as compared to 9 healthy controls by using an Openarray platform. Patients fulfilling the ACR/EULAR 2013 classification criteria were classified in relation to the extent of skin fibrosis as limited cutaneous (lcSSc) or diffuse cutaneous SSc (dcSSc); patients fulfilling the classification criteria without skin fibrosis will be referred to as non-cutaneous SSc (ncSSc).
MicroRNAs (miRNAs) are regulatory molecules, which have been addressed as potential biomarkers and therapeutic targets in rheumatic diseases. Here, we investigated the miRNA signature in the serum of systemic sclerosis (SSc) patients and we further assessed their expression in early stages of the disease.The levels of 758 miRNAs were evaluated in the serum of 26 SSc patients as compared to 9 healthy controls by using an Openarray platform. Three miRNAs were examined in an additional cohort of 107 SSc patients and 24 healthy donors by single qPCR. MiR-483-5p expression was further analysed in the serum of patients with localized scleroderma (LoS) (n=22), systemic lupus erythematosus (SLE) (n=33) and primary Sjögren’s syndrome (pSS) (n=23). The function of miR-483-5p was examined by transfecting miR-483-5p into primary human dermal fibroblasts and pulmonary endothelial cells.30 miRNAs were significantly increased in patients with SSc. Of these, miR-483-5p showed reproducibly higher levels in an independent SSc cohort and was also elevated in patients with preclinical-SSc symptoms (early SSc). Notably, miR-483-5p was not differentially expressed in patients with SLE or pSS, whereas it was up-regulated in LoS, indicating that this miRNA could be involved in the development of skin fibrosis. Consistently, miR-483-5p overexpression in fibroblasts and endothelial cells modulated the expression of fibrosis-related genes.Our findings showed that miR-483-5p is up-regulated in the serum of SSc patients, from the early stages of the disease onwards, and indicated its potential function as a fine regulator of fibrosis in SSc.

overall_design: Serum RNA was extracted from 35 donors; 9 healthy (HC), 8 non-cutaneous SSc (ncSSc), 9 limited cutaneous (lcSSc) and 9 diffuse cutaneous SSc (dcSSc) patients

first: Marzia

last: Rossato

first: Timothy

last: Radstake


title: Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Here we describe a method for fabricating a primary human Small Intestine-on-a-Chip (Intestine Chip) containing epithelial cells isolated from healthy regions of intestinal biopsies. The primary epithelial cells are expanded as 3D organoids, dissociated, and cultured on a porous membrane within a microfluidic device with human intestinal microvascular endothelium cultured in a parallel microchannel under flow and cyclic deformation. In the Intestine Chip, the epithelium forms villi-like projections lined by polarized epithelial cells that undergo multi-lineage differentiation similar to that of intestinal organoids, however, these cells expose their apical surfaces to an open lumen and interface with endothelium. Transcriptomic analysis also indicates that the Intestine Chip more closely mimics whole human duodenum in vivo when compared to the duodenal organoids used to create the chips. Because fluids flowing through the lumen of the Intestine Chip can be collected continuously, sequential analysis of fluid samples can be used to quantify nutrient digestion, mucus secretion and establishment of intestinal barrier function over a period of multiple days in vitro. The Intestine Chip therefore may be useful as a research tool for applications where normal intestinal function is crucial, including studies of metabolism, nutrition, infection, and drug pharmacokinetics, as well as personalized medicine.

overall_design: Total RNAs extracted from Intestine-on-Chip, Organoid-on Chip and Caco2 Gut-on-Chip biological samples and were submitted for microarray analysis.

first: Magdalena

last: Kasendra

first: Alessio

last: Tovaglieri

first: Donald

last: Ingber


title: PTEN Deficiency Promotes Pathological Vascular Remodeling of Human Coronary Arteries

city: Aurora

first: Mary

last: Weiser-Evans

state: Colorado

address: 12700 East 19th Ave

department: Department of Renal Medicine and Hypertension

institute: University of Colorado Denver

summary:
Gene expression profiles of Rat aortic smooth muscle clonal isolates of PTEN knock-down and control wild-type.
We used Affymetrix microarrays to detail the global program of gene expression changes between PTEN deficient and wild type smooth muscle cells.  We identified distinct classes of up- and down-regulated genes during this process.

overall_design: Infection of Rat VSMC's with retroviral shRNA specific to PTEN or non-targeting control in order to compare the gene expression under basal, low serum, conditions.

last: Moulton


title: Expression data from MCAO or Sham operated rat blood [miRNA]

city: Bunkyo-ku

first: Ayako

last: Takuma

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

summary:
In the search for stroke biomarkers, miRNAs are gaining attention. To investigate novel miRNAs that work as stroke biomarkers, we used Middle Cerebral Artery Occlusion model of rats.
By using microarray analysis and comparing with Sham operated rats, we extracted the miRNAs whose expressions are alterated by stroke.

overall_design: 6 Sprague-Dawley rats were subjected to Middle Cerebral Artery Occlusion (MCAO) or Sham operation (n=3), and the miRNA expression in the blood was compared between the two grosup.

first: Yoshikazu

last: Saito

first: Arata

last: Abe

first: Tomiko

last: Asakura

first: Keiko


title: Immuno-related transcripts in biliary tract cancers

city: Glasgow

first: Chiara

last: Braconi

address: Switchback road

department: Wolfson Wohl Cancer Research Centre

country: United Kingdom

institute: University of Glasgow

summary: Tumour and adjacent components from human resected biliary tract cancers were characterised for the expression of immunorelated transcripts

overall_design: 22 cases were microdissected to achieve tumour and adjacent tissue. RNA was obtained for 22  tumour (T) with matched adjacent tissue (N).


title: Expression data from MCAO or Sham operated rat blood [mRNA]

summary:
To analyze the gene expression alteration after stroke, we used Middle Cerebral Artery Occlusion model of rats. By comparing with Sham operated rats, we extracted the mRNAs whose expressions are alterated by stroke.
Using microarray analysis, we aimed to grasp the overall expression alteration of mRNA in blood after stroke.

overall_design: 6 Sprague-Dawley rats were subjected to Middle Cerebral Artery Occlusion (MCAO) or Sham operation (n=3), and the mRNA expression in the blood was compared between the two group.


title: Peste des Petits Ruminants Virus Attachment and Entry into Caprine Endometrial Epithelial Cells Profoundly Effects Early Cellular Gene Expression

city: Yangling

first: Bo

last: Yang

address: 22 Xinong Rd, College of Veterinary Medicine 4316

department: College of Veterinary Medicine,

institute: Northwest A&F University

summary: In addition, to obtain a comprehensive view of the effects of PPRV early infection on target cells, microarray analyses revealed significant differences in the regulation of cellular gene expression between infection and control cells.

overall_design: Gene expression profiling of Caprine Endometrial Epithelial Cells with PPRV infection for 1h or 24h and controls without PPRV infection.

first: JingYu

last: Wang

first: XueFeng

last: Qi


title: Transcriptional profiling of two Candida albicans isolates in different growth condition

city: San Michele all'Adige

first: Lisa

last: Rizzetto

address: via E. Mach 1

department: Research and Innovation Centre

country: Italy

institute: Fondazione Edmund Mach

summary: The study asked the question whether commensalism or pathogenicity of an opportunistic pathogen like Candida albicans, depend on strain specific traits or on the phenotypic and genomic plasticity of the genus as a whole. Transcriptional analysis performed upon different medium conditions (RPMI in presence or absence of FBS) indicated differentially expressed genes involved in adhesion, filamentous growth and biofilm formation. Both genome sequence and gene expression highlighted concordant changes in pathways related to invasiveness and filamentation. These results reflected marked differences in term of morphological features, environment adaptation and survival to phagocytosis. The results indicate that the genetic background of C. albicans may greatly affect its behaviour in terms of in vitro susceptibility to immune effector cells. Based on this approach, a more in depth understanding of fungal genetic makeup is achievable, thus allowing to establish the virulence potential of a given isolate and possibly to predict the outcome of C. albicans infection.

overall_design: Gene expression adaptation of two different C. albicans strains was measured at 1 hr and 24 hr after growth in presence of absence of 10% FBS. Three independent experiments were performed at each time (1 or 24 hours) using different starting material for each experiment.

first: Monica

last: Di Paola

first: Bruna

last: Colombari

first: Luisa

last: Berna

first: Carlotta

last: De Filippo

first: Andrea

last: Ardizzoni

first: Noemi

last: Tocci

first: Simona

last: Paulone

first: Paolo

last: Lionetti

first: Ivo

middle: G

last: Gu

first: Elisabetta

last: Blasi

first: Duccio

last: Cavalieri

first: Samuele

last: Peppoloni


title: Long-term dietary replacement of fish meal and fish oil in diets for rainbow trout: effects on intestinal and hepatic gene expression

city: Saint-Pée sur Nivelle

first: Viviana

last: Lazzarotto

address: Quartier Ibarron

country: France

institute: INRA

summary: In the context of replacing fish meal and fish oil in feeds for aquaculture, rainbow trout alevins received from first-feeding onwards, one of the three experimental diets: V (100% plant-based), C (mix of FM-FO & plant ingredients) or M (100% FM-FO based). The long term effects of such dietary replacement on the intestinal (mid gut) and hepatic transcriptome were studied in juveniles after a 7-month feeding trial at 7°C.

overall_design: The microarray analysis was performed on samples of RNA from intestine (mid gut) and livers of juveniles (n=8 per dietary group) sampled 48h after the last meal.

first: Françoise

last: Médale

first: Laurence

last: Larroquet

first: Geneviève

last: Corraze


title: Study of gene expression following Pim2 knockdown in FLT3-ITD-positive acute myeloid leukemia

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

summary:
The objective of the sudy is to explore the biological pathways controlled by Pim2 in FLT3-ITD positive AML
We used microarrays to investigate gene expression in the MOLM-14 AML cell line in which Pim2 knockdown was induced by RNA interference (doxycycline-inducible shRNA)

overall_design: MOLM-14 cells transduced by doxycycline-inducible scrambled or anti-Pim2 shRNA were cultured 72h in the presence of 200 ng/ml doxycycline. Total RNA was extracted with DNase I digestion (RNeasy Mini Kit used with the Bio-robot QIAcube). Biotinylated cDNAs were prepared from 100ng total RNA using the GeneChip® Whole Transcript Sense Target Labeling Assay Kit according to the standard Affymetrix protocol (Affymetrix, Santa Clara, CA, USA). Following fragmentation, 10ug of cDNA were hybridized for 16h at 45°C on GeneChip® Human Gene 2.0 ST arrays arrays (Affymetrix), washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

first: Jerome

last: Tamburini

first: Marie-Anne

last: Hospital


title: Immuno-related transcripts in the microenvironment of biliary tract cancers

first: Chiara

last: Braconi

summary: Adjacent components from human resected biliary tract cancers were characterised for the expression of immunorelated transcripts

overall_design: 53 cases were microdissected to achieve tissue adjacent to cancer. RNA was obtained from 53  adjacent tissues.


title: Caenorhabditis elegans infected with Enterococcus

city: Boston

first: Grace

middle: J.

last: Yuen

state: Massachusetts

address: 185 Cambridge Street, CPZN-7724, Simches Research Building

department: Molecular Biology

institute: Massachusetts General Hospital

summary:
Young adult N2 Caenorhabditis elegans were infected with Enterococcus faecalis or Enterococcus faecium for 8 h to determine the transcriptional host response to each enterococcal species.
Analysis of differential gene expression in C. elegans young adults exposed to four different bacteria: heat-killed Escherichia coli strain OP50 (control), wild-type E. faecalis MMH594, wild-type E. faecium E007, or Bacillus subtilis PY79 (sigF::kan). Samples were analyzed at 8 hours after exposure to the different bacteria. These studies identified C. elegans genes induced by pathogen infection. Brain-heart infusion agar plates (10 ug/ml kanamycin) were used.

overall_design: There are 13 samples total: 3 biological replicates of E. faecalis-infected animals, 3 biological replicates of E. faecium-infected animals, 4 biological replicates of heat-killed E. coli-fed controls, and 3 biological replicates of B. subtilis-fed controls. All treatments were performed in parallel except for two heat-killed E. coli-fed controls, Jos5531(OP504) and Jos5532(OP505), which were processed together on a different day from the other samples.

first: Frederick

last: Ausubel


title: Genome-wide profiling of DNA methylation and gene expression in radiation-induced rat mammary carcinomas

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Deciphering the genetic regulation of peripheral blood transcriptome in pigs through allele-specific expression analysis and expression genome-wide association study

status: Public on Feb 13 2018

city: Jouy-en-Josas

first: Jordi

last: Estelle

address: Domaine de Vilvert, Bat. GABI-320

institute: INRAE

summary: Efforts to improve resilience in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual's health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity. The objective of this work was to study the genetic architecture of variation in gene expression in the blood of healthy pigs using two approaches: an expression genome-wide association study (eGWAS) and allele-specific  expression (ASE) analysis. The blood transcriptomes of 60-day-old Large White pigs were characterized by expression microarrays for eGWAS (243 animals) and by RNA-Seq for ASE analysis (38 animals). Using eGWAS, the expression levels of 1,901 genes were found to be associated with expression quantitative trait loci (eQTLs). We recovered 2,839 local  and 1,752 distant associations (defined as single-nucleotide polymorphism, or SNP, located less or more than 1 Mb from expression probe, respectively). ASE analyses confirmed the extensive cis-regulation of gene transcription in blood, and revealed allelic imbalance in 2,286 SNPs, which affected 763 genes. eQTLs and ASE-genes were widely distributed on all chromosomes. By analyzing mutually overlapping eGWAS results, we were able to describe putative regulatory networks, which were further refined using ASE data. At the functional level, genes with genetically controlled expression that were detected by eGWAS and/or ASE analyses were significantly   involved in biological processes related to RNA processing and immune function. In particular, numerous distant and local regulatory relationships were detected within the major histocompatibility complex region on chromosome 7, revealing ASE for most class I and II genes. This study represents, to the best of our knowledge, the first genome-wide map of the genetic control of gene expression in porcine peripheral blood. These results represent an  important resource for the identification of genetic markers and blood biomarkers associated with variations in immunity traits in pigs, as well as any other complex traits for which blood is an appropriate surrogate tissue.

overall_design:
In this study our aim was to build a genome-wide map of the genetic control of gene expression in the blood of 60-day-old Large White pigs by combining eGWAS and ASE results.

This submission represents eGWAS component of study.

first: T

last: Maroilley

first: G

last: Lemonnier

first: J

last: Lecardonnel

first: D

last: Esquerré

first: Y

last: Ramayo-Caldas

first: M

last: Mercat

first: C

last: Rogel-Gaillard

last: Estellé


title: Modulation of Navitoclax Sensitivity by Dihydroarteminisin-Mediated MCL-1 Repression

first: David

last: Finkelstein

summary: Poor prognosis BCR-ABL+ B-ALL leukemic cells are highly dependent on the expression of endogenous anti-apoptotic MCL-1. However, the survival of most normal blood cells (e.g. progenitors, lymphocytes, and granulocytes) and other normal cell types (e.g. cardiomyocytes and neurons) are also exquisitely dependent on Mcl-1 gene expression, suggesting that effective therapeutic inhibition of MCL-1 could be acutely toxic, especially when combined with standard chemotherapy. Therefore, as an alternative to MCL-1 inhibition, we have identified dihydroarteminisin (DHA), a water-soluble metabolite of the anti-malarial arteminisin, which induces the down-modulation of MCL-1 protein expression by triggering an endoplasmic reticulum stress response. The DHA induced repression of MCL-1 expression renders leukemic cells highly sensitive to synergistic cell death induced by BH3-mimetic agents such as navitoclax (ABT-263) in a mouse model of BCR-ABL+ B-ALL.  Furthermore, DHA also synergizes with navitoclax in human Ph+ ALL cell lines, and primary patient derived xenografts of Ph+ ALL. These data demonstrate that combining DHA with BH3-mimetic agents can improve therapeutic response in poor prognosis leukemia.

overall_design: We used microarrays to compare the DHA treatement to controls in mice.

first: Amit

last: Budhraja

first: Meghan

last: Tunis

first: Michelle

last: Churchman

first: Anisha

last: Kothari

first: Xue

last: Yang

first: Haiyan

last: Xu

first: Ewa

last: Kaminska

first: John

last: Panetta

first: Joseph

middle: T

last: Opferman


title: Differential gene expression of zebrafish melanocytes and melanomas (microarray)

city: Worcester

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas.

overall_design: Examination of gene expression in two different cell types

first: Arvind

last: Venkatesan

first: Craig

last: Ceol


title: Global gene expression profiling of radiation-induced rat mammary carcinomas

first: Kazuhiro

last: DAINO

summary: To investigate gene expression patterns in rat mammary carcinomas induced by ionizing radiation.

overall_design: Gene expression patterns were analyzed in radiation-induced rat mammary carcinomas and normal mammary gland tissues.

last: Daino

first: Shizuko

last: Kakinuma


title: Study of the function of COX19 by transcriptional profiling of Arabidopsis thaliana transformed with artificial microRNA to reduce expression of COX19

city: Santa Fe

first: Elina

last: WELCHEN

state: Santa Fe

address: Colectora Ruta Nac. Nº168 km. 0

country: Argentina

institute: Instituto de Agrobiotecnologia del Litoral

summary: Analysis of transcriptional profiling of Arabidopsis Col-0 leaves from wild-type and plants transformed with artificial microRNA to reduced expression of AtCOX19-1 and AtCOX19-2

overall_design: Two-condition experiment, Control vs. Silenced Plants. Biological replicates: 2 control, 2 silenced

first: Daniel

middle: H

last: Gonzalez

last: Welchen

first: Lucila

last: Garcia


title: Inflorescence development and the role of LsFT in regulating bolting in lettuce (Lactuca sativa L.)

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

summary: Lettuce (Lactuca sativa L.) is one of the most important leafy vegetable that is consumed during its vegetative growth. The transition from vegetative to reproductive growth is induced by high temperature, which has significant economic effect on lettuce production. However, the progression of floral transition and the molecular regulation of bolting are largely unknown. Here we morphologically characterized the inflorescence development and functionally analyzed the FLOWERING LOCUS T (LsFT) gene during bolting regulation in lettuce. We described the 8 developmental stages during floral transition process. The expression of LsFT was negatively correlated with bolting in different lettuce varieties, and was promoted by heat treatment. Overexpression of LsFT could recover the late-flowering phenotype of ft-2 mutant. Knockdown of LsFT by RNA interference dramatically delayed bolting in lettuce, and failed to respond to high temperature. Therefore, this study dissects the process of inflorescence development and characterizes the role of LsFT in bolting regulation in lettuce.

overall_design: mRNA profiles of SAM cells from bolting-sensitive line S39 and bolting-resistant line S24 at four critical developmental stage.

first: Zijing

last: Chen

first: Danfeng

last: Ge


title: Global DNA methylation profiling of radiation-induced rat mammary carcinomas

summary: To investigate DNA methylation patterns in rat mammary carcinomas induced by ionizing radiation.

overall_design: DNA methylation patterns were analyzed in radiation-induced rat mammary carcinomas and normal mammary gland tissues using CpG island microarray.


title: Transcriptional profile analysis of C. dubliniensis tlo mutants complemented with C. albicans TLO genes with and without peroxide

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

summary: The ability of C. albicans TLO genes to mediate oxidative stress responses was characterised by expressing CaTLO1 and CaTLO4 in a C. dubliniensis TLO null mutant. Each complemented strain was grown with and without peroxide. The transcript profile of peroxide vs no peroxide cultures was analysed in 4 biological replicates for both CaTLO1 and CaTLO4.

overall_design: 1 experiemental parameter was analysed in quadruplicate in two complemented mutants (∆∆tlo::TLO1 and ∆∆tlo::TLO4)


title: B cell development requires discrete regulation by PTEN-PI3K and mTOR pathways and the intricate interplay with IL-7 r-Stat5 signaling

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: IL-7 r and Stat5 signaling drives early B lymphopoiesis, but it remains poorly understood how Stat5-dependent and independent pathways contribute to this process. We report the discrete effects of PI3K and mTOR signaling on Stat5 signaling and B cell development. PI3K was not engaged by IL-7 in pro-B cells but was actively suppressed by PTEN to ensure proper IL-7 r expression, Stat5 signaling and pro-B cell survival. Further, IL-7-mediated mTORC1 activation, which was uncoupled from PI3K signaling, orchestrated a unique program in early B cell development in a Stat5-independent but Myc-dependent manner. mTORC1 was also required for immunoglobulin heavy chain rearrangement and Myc-driven lymphomagenesis. Finally, mTORC2 was not essential for early B cell development but contributed to peripheral B cell maturation. Altogether, genetic dissection of PI3K, mTORC1, and mTORC2 reveals the distinct effects of these seemingly related pathways on B cell development and the intricate interplay between PI3K, mTOR and IL-7 r-Stat5 signaling.

overall_design: We used microarrays to explore the gene expression profiles differentially expressed in untreated and IL-7 treated B220+CD43+IgM- pro-B cells from Cre^(ER)/Rptor^(fl/+) and Cre^(ER)/Rptor^(fl/fl) mice 7 days after tamoxifen treatment.

first: Hu

last: Zeng

first: Hongbo

last: Chi


title: Unique Circulating MicroRNA profiles in HIV Infection

city: San Francisco

first: Priscilla

last: Hsue

state: CA

address: 1001 Potrero Ave, Room 5G4

institute: University of California, San Francisco

summary: We aimed to determine the association between extracellular miRs and HIV infection, and have demonstrated unique expression profile of 29 miRs in HIV+ subjects and 34 miRs in elite controllers as compared to HIV- subjects. Elite HIV+ subjects are those  who are HIV+, not on antiretroviral therapy, and with HIV viral load <200 copies/mL.

overall_design: Single-center cross-sectional study

first: Venkata

last: Narla

first: Nirav

last: Bhakta

first: Jane

last: Freedman

first: Kahraman

last: Tanriverdi

first: Kristinalisa

last: Maka

first: Steven

last: Deeks

first: Peter

last: Ganz


title: Hormonal regulation of cervix transcript expression in the menstrual cycle

city: Beaverton

first: Ov

middle: D

last: Slayden

state: OR

address: 505 NW 185th Ave

department: Division of Reproductive Sciences

institute: Oregon National Primate Research Center; Oregon Health & Science University

summary: The aim of this study was to identify hormonally regulated genes and their related biological pathways in the rhesus macaque cervix during the menstrual cycle. The cervix is the gateway for gamete passage, which is driven by hormonal regulation with progesterone (P) suppressing the passage of gametes. Contraceptives that are progesterone based change the cervix. Progestogen only contraception is reported to act by suppressing ovulation and/or altering cervical mucus secretion. In order to further investigate novel contraceptive targets and their pathways, a microarray was used to discover genes in the cervix that are suppressed under varying lengths of exposure to progesterone throughout an artificial menstrual cycle.

overall_design: Adult ovariectomized rhesus macaques (Macaca mulatta) were treated sequentially with estradiol (E2) and then E2 plus progesterone (P) to create artificial menstrual cycles.  Reproductive tracts were collected in the artificial proliferative phase (PF; E2 alone; n=13) and in the artificial secretory phase (SP) after 1, 3, 7, and 14 days of P (n=4, 5, 5 and 10, respectively).

first: Kise

middle: R

last: Bond

first: M

last: Wilcox


title: P. aeruginosa PA14 mutant PA4496 biofilm vs wild-type biofilm

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: P. aeruginosa PA14 mutant strain PA4496 expression in biofilm cells relative to PA14 wild-type strain expression in biofilm cells. All samples cultured in LB with glass wool

overall_design:
Strains: P. aeruginosa PA14 wild-type, mutant PA4496
Medium: LB
Biofilm grown glass wool
Time: 7 hr
Cell type: biofilm

first: Yunho

last: Lee

middle: K


title: Effects of maternal zinc deficiency on placental development and function in mice

city: Adelaide

first: Rebecca

middle: L

last: Wilson

state: SA

address: Medical School North, Frome Rd

country: Australia

institute: University of Adelaide

summary:
Zinc is an essential micronutrient in pregnancy and zinc deficiency impairs fetal growth. We used a mouse model of moderate zinc deficiency to determine how zinc is important to placental morphogenesis.
Global placental gene expression at gestational day 18.5 was analysed using microarray to determine the effects of zinc deficiency on placental function.

overall_design: RNA samples were extracted placentas collected from 7 female mice fed a zinc deficient diet (10 mg/kg zinc) and 10 female mice fed a zinc replete diet (40 mg/kg zinc). For each female mouse, except for 3 in which only one placenta was available, 2 placentas, one from a male offspring and one from a female offspring were selected. Overall, gene expression in 31 placentas were analysed.

first: Sam

last: Buckberry

first: Stephen

last: Pederson

first: Claire

last: Roberts


title: Analysis of microRNA expression profiles in exosomes of proximal renal tubular cells in response to oxalate crystal

city: Nanning

first: Xiaofeng

last: Guan

state: Guangxi

address: No 6 SHUANGYONG ROAD

institute: First Affiliated Hospital of Guangxi Medical University

summary: The present study aims to compare the miRNA expression profiles in exosomes derived from HK-2 cells treated with 0, 1, 2 mM sodium oxalate, and to explore the roles of different exosomal-miRNAs in the regulation of calcium oxalate (CaOx) stones formation.

overall_design: microRNA microarray was applied to evaluate the expression of exosomes derived from HK-2 cells exposed to 0, 1, 2 mM sodium oxalate for 48 hours.


title: Gene expression in granulosa cells from heifers rated as poor donors of competent oocytes

city: Quebec

first: David

middle: André

last: Landry

state: Quebec

address: 2440 boul. Hochelaga

department: Animal Science

country: Canada

institute: University Laval

summary: The objective of this study was to gain better understanding of the follicular conditions associated with low oocyte developmental competence in younger donors. In summary, we demonstrated that differences in follicle maturity at collection could explain differences in oocyte competence associated with individual animals.

overall_design: Granulosa cells from 94 Holstein heifers and cows in a commercial embryo production facility were collected following ovarian stimulation and coasting, to compared gene expression from donors of mostly competent oocyte from cows versus incompetent oocyte from heifers

first: Simon

last: Lafontaine

first: Lia

last: Rossi-Perazza

first: François-Xavier

last: Grand

first: Christian

last: Vigneault

first: Patrick

last: Blondin

first: Marc-André

last: Sirard


title: Gene expression in WT and Camkk2 KO murine hematopoietic stem cells

city: Durham

first: LUIGI

last: RACIOPPI

state: North Carolina

address: La Salle, GSRB1 2006

department: Medicine

institute: Duke University

summary: To determine the function of Camkk2 in HSC we performed a microarray analysis on isolated KSL from WT and Camkk2 null mice. Using a threshold of 0.05 for statistical significance (p-value) and a log fold change of expression with absolute value of at least 0.6, 1831 differentially expressed genes (DEGs) were identified out of a total of 29352 genes with measured expression. When compared to WT KSL, 1289 genes were significantly downregulated and 533 genes were upregulated in Camkk2 null HSC. The genes downregulated in Camkk2 null KSL were strongly enriched in HSC, early progenitors and lymphoid-myeloid-affiliated genes (s-myly) primed in HSC. Of note, HSC-affiliated genes found downregulated in Camkk2 KSL included Hlf, Meis1, Pbx-1 and Prdm5 which are 4 of the 8 genes capable to reprogram committed murine blood cells into HSC. The GSEA analysis also showed that genes affiliated with the late progenitor signature and erythroid genes primed in HSC and GMP specific genes (d-my) were significantly upregulated in Camkk2 null KSL. These findings indicate Camkk2 controls crucial transcriptional programs involved in the mechanism of HSC differentiation and lineage commitment.

overall_design: Bone marrow was removed from bones of WT and Camkk2 null mice (16 mice/genotypes), and four biological replicates for each genotype were generated. Hematopoietic stem and progenitor cells were isolated based on the expression of Lineage (Lin) markers, c-Kit and Sca-1 expression. Lin-Kit+ Sca1- and Lin-Kit+ Sca1+ (KL and KLS cells) were sorted from mice directly into Buffer RLT (Qiagen). RNA isolation, quality control and all the procedures required for microarray analysis were performed at Sequencing and Genome Technologies Shared Resource (Duke University) according to standard operative procedures.

first: Luigi

last: Racioppi


title: Loss of Cic leads to aberrant neural stem cell proliferation and differentiation and promotes gliomagenesis

first: Hai

last: Yan

state: NC

address: 199B-MSRB, Research Drive

department: Pathology

summary: Mouse neural stem cells were generated from conditional knockout mice (Cicflox/flox) or the wild trype control mice (Cic+/+). Cic is conditionally knocked out following expression of Cre-recombinase. Cre-recombinase was incorporated in vitro via adenoviral-Cre transduction.

overall_design: Four Cic+/+ and three Cic-/- NSCs were established from individual animals followed by adenoviral-Cre transduction. Ablation of Cic was confirmed by PCR.

first: Rui

last: Yang

first: Lee

last: Chen

first: Landon

last: Hansen

first: Austin

middle: B

last: Carpenter

first: Casey

last: Moure

first: Heng

last: Liu

first: Christopher

last: Pirozzi

first: Bill

last: Diplas

first: Matthew

middle: S

last: Waitkus

first: Paula

last: Greer

first: Huishan

last: Zhu

first: Roger

middle: E

last: Mclendon

first: Darell

last: Bigner

first: Yiping

last: He


title: Development of gene expression signatures for lung cancer cells interaction with human monocyte-derived macrophages

city: New Taipei City

first: Sheng-Ming

last: Wu

address: No.291, Zhongzheng Rd., Zhonghe District

country: Taiwan

institute: Taipei Medical University Shuang-Ho Hospital

summary: To further investigate the lung cenr progression, we have employed gene expression profiling as a discovery platform to identify genes with the potential involved in MDM interaction .

overall_design: Human peripheral monoctyte cells (PBMCs) from lung cancer patients were collected. PBMCs were treated with GM-CSF and differentiated to MDM. MDM cells were cocultured with or without lung cancer cells for 24h. Total RNAs were extracted from H827 cancer cells.

first: Kang-Yun

last: Lee

first: Po-Hao

last: Feng


title: Novel Pulmonary Imaging Biomarkers and Cutaneous Gene Expression Subsetting for Patient Selection and Outcome Assessment in the Dasatinib Treatment of Systemic Sclerosis-associated Interstitial Lung Disease

city: Hanover

first: Viktor

last: Martyanov

state: NH

address: 7400 Remsen

department: Genetics

institute: Geisel School of Medicine at Dartmouth

summary: There are no effective treatments or clinical response markers for systemic sclerosis (SSc). We sought to assess the potential of novel imaging biomarkers and gene expression profiling approaches in a clinical trial of the tyrosine kinase inhibitor dasatinib in SSc patients with interstitial lung disease (SSc-ILD).

overall_design: Patients were enrolled in a single-arm open-label trial of dasatinib. Primary objective was to assess safety and pharmacokinetics. Secondary and exploratory outcomes included clinical assessments, quantitative high-resolution computed tomography (HRCT) of the chest, serum biomarkers, and intrinsic gene expression subset assignments in skin.

first: Grace-Hyun

last: Kim

first: Wendy

last: Hayes

first: Shuyan

last: Du

first: Bishu

last: Ganguly

first: Oumar

last: Sy

first: Sun

first: Galina

last: Bogatkevich

first: Gary

last: Schieven

first: Elena

last: Schiopu

first: Roberta

last: Marangoni

first: Jonathan

last: Goldin

first: Michael

last: Whitfield

first: John

last: Varga


title: Effect of benzimidazole derivative C162 on Staphylococcus aureus virulence

city: UKM Bangi

first: Cin

last: Kong

state: Selangor

address: Faculty of Science and Technology

department: School of Bioscience and Biotechnology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

summary: From a Caenorhabditis elegans - S. aureus anti-infective screen, we identified benzimidazole derivative C162 as one of the potential anti-infective candidate that rescued the infected-nematodes from infection. This compound was found to exhibit anti-biofilm activity against S. aureus. To investigate the transcriptome profile of S. aureus in response to benzimidazole derivative C162, a genome-wide transcriptome analysis was performed on C162-treated S. aureus using the Affymetrix GeneChip S. aureus Genome Arrays. Our main interest is to look at the expression profiles of the biofilm-associated and virulence genes.

overall_design: We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (treated) of 6.25 µM benzimidazole derivative C162. We calculated the fold change as the ratio between the signal averages of three untreated and three C162-treated cultures at a single time-point (overnight incubation for 16-18 hours).

first: Sheila

last: Nathan


title: Efficient derivation of stable primed pluripotent embryonic stem cells from bovine blastocysts [ChIP-seq]

status: Public on Feb 11 2018

city: Davis

first: Pablo

last: Ross

address: 1 Shields Ave

country: USA

institute: University of California, Davis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Embryonic stem cells (ESCs) are derived from the inner cell mass of preimplantation blastocysts. From agricultural and biomedical perspectives, the derivation of stable ESCs from domestic ungulates is important for genomic testing and selection, genome engineering, and modeling human diseases. Cattle are one of the most important domestic ungulates that are commonly used for food and bioreactors. To date, however, it remains a challenge to produce stable pluripotent bovine ESC lines. Employing a culture system containing fibroblast growth factor 2 and an inhibitor of the canonical Wnt-signaling pathway, we derived pluripotent bovine ESCs (bESCs) with stable morphology, transcriptome, karyotype, population-doubling time, pluripotency marker gene expression, and epigenetic features. Under this condition bESC lines were efficiently derived (100% in optimal conditions), were established quickly (3–4 wk), and were simple to propagate (by trypsin treatment). When used as donors for nuclear transfer, bESCs produced normal blastocyst rates, thereby opening the possibility for genomic selection, genome editing, and production of cattle with high genetic value.

overall_design: Examination of H3K4me3 and H3K27me3 in 2 independent lines of bESCs

first: Yanina

last: Bogliotti


title: Specific metabolic activation of adipose tissue macrophages during obesity promotes inflammatory responses

status: Public on Feb 02 2018

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Recent studies have identified intracellular metabolism as a fundamental determinant of macrophage function. In obesity, proinflammatory macrophages accumulate in adipose tissue and trigger chronic low-grade inflammation, that promotes the development of systemic insulin resistance, yet changes in their intracellular energy metabolism are currently unknown. We therefore set out to study metabolic signatures of adipose tissue macrophages (ATMs) in lean and obese conditions. F4/80-positive ATMs were isolated from obese vs lean mice. High-fat feeding of wild-type mice and myeloid-specific Hif1α-/- mice was used to examine the role of hypoxia-inducible factor-1α (HIF-1α) in ATMs part of obese adipose tissue. In vitro, bone marrow-derived macrophages were co-cultured with adipose tissue explants to examine adipose tissue-induced changes in macrophage phenotypes. Transcriptome analysis, real-time flux measurements, ELISA and several other approaches were used to determine the metabolic signatures and inflammatory status of macrophages. In addition, various metabolic routes were inhibited to determine their relevance for cytokine production. Transcriptome analysis and extracellular flux measurements of mouse ATMs revealed unique metabolic rewiring in obesity characterised by both increased glycolysis and oxidative phosphorylation. Similar metabolic activation of CD14+ cells in obese individuals was associated with diabetes outcome. These changes were not observed in peritoneal macrophages from obese vs lean mice and did not resemble metabolic rewiring in M1-primed macrophages. Instead, metabolic activation of macrophages was dose-dependently induced by a set of adipose tissue-derived factors that could not be reduced to leptin or lactate. Using metabolic inhibitors, we identified various metabolic routes, including fatty acid oxidation, glycolysis and glutaminolysis, that contributed to cytokine release by ATMs in lean adipose tissue. Glycolysis appeared to be the main contributor to the proinflammatory trait of macrophages in obese adipose tissue. HIF-1α, a key regulator of glycolysis, nonetheless appeared to play no critical role in proinflammatory activation of ATMs during early stages of obesity. Our results reveal unique metabolic activation of ATMs in obesity that promotes inflammatory cytokine release. Further understanding of metabolic programming in ATMs will most likely lead to novel therapeutic targets to curtail inflammatory responses in obesity.

overall_design: Adipose tissue macrophages were isolated by F4/80+ positive selection from epididymal adipose tissue of male C57Bl/6 mice fed a low fat or high fat diet

first: Lily

last: Boutens

first: Rinke

last: Stienstra


title: Effect of TUC338 knockdown on gene expression

status: Public on Feb 09 2018

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

summary:
The ultraconserved RNA TUC338 is expressed in hepatocellular cancer and can modulate cell proliferation. Details are provided in Braconi et al,Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):786-91.
In this analysis, we knocked down TUC338 in HepG2 cells and analyzed gene expression.

overall_design: 2 conditions were analyzed, cells with control LNA, and cells with LNA to TUC338, with experimentally validated knockdown

first: Chiara

last: Braconi


title: Gene expression of zebrafish testes after MCLR exposure

city: Hefei

first: Zhao

last: Sujuan

address: Meishan road 81

country: China

institute: Anhui Medical University

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify the change of gene in zebrafish testes between the control and MCLR groups. zebraﬁsh were exposed to 20 μg/L MCLR for 6 weeks. Fresh testes tissue samples from 5 individuals were collected as one sample. Expression of three genes (hsp70, fgf1a and tgfβ1) from this signature was quantified in the same RNA samples by real-time PCR, confirming the reliability of microarray analysis.

overall_design: MCLR-induced gene expression in zebrafish testes was measured after exposure to doses of 20μg/L. for 6 weeks. Two independent experiments were performed at two groups (control and 20μg/L MCLR) for each experiment.

first: Sujuan

last: Zhao

first: Guangyu

last: Li


title: Expression data from mouse prostates

status: Public on Feb 06 2018

city: Nanjing

first: Ruitong

last: Han

address: No. 22, Hankou Road, Gulou District

institute: Nanjing University

summary:
Pregnant females were distributed into two experimental groups: control group and MC-LR group which were exposed to 0 and 10 μg/L of MC-LR through drinking water separately during fetal and lactational periods. In 30 days old, the animals were euthanized.
Testes were determined to investigate the different expressions of piRNAs using a piRNA microarray.

overall_design: Pregnant mice were randomly divided into 2 groups: control group and MC-LR group, with each mouse kept separately. From gestation day 12 to postnatal day 21, 2 groups of pregnant mice were exposed to 0 and 10 μg/L of MC-LR through drinking water. The male offspring were breastfed after natural birth. 30 days after birth, the organs were promptly frozen in liquid nitrogen until further analysis.empty-2P, empty-4P, empty-5P were the three samples from 3 offsprings of different pregnant mice in control group. 10-3P, 10-4P, 10-7P were the three samples from 3 offsprings of different pregnant mice in MC-LR group.

first: Dongmei

first: Han

last: Ruitong


title: Free SepF blocks recruitment of late cell division proteins

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

summary: The cell division protein SepF aligns polymers formed by the key cell division protein FtsZ during synthesis of the (Fts)Z-ring at midcell, the first stage in cytokinesis. In addition, SepF acts as a membrane anchor for the Z-ring. SepF is conserved in Gram-positive and cyanobacteria. Recently, it was shown that SepF overproduction in Mycobacterium smegmatis blocks cell division. Here we investigated this in more detail using the Gram-positive model system Bacillus subtilis. Surprisingly, overproduction of SepF does not interfere with assembly of the Z-ring, but blocks assembly of the late cell division proteins responsible for septum synthesis. Transposon mutagenesis suggested that SepF overproduction inactivates the WalKR two-component system involved in cell division. Indeed, SepF overproduction impairs WalK localization, possibly because septal WalK localization requires late cell division proteins. Unexpectedly, transcriptome analysis showed that WalKR activity was not affected. Another surprise was that the cell division phenotype occurs when SepF does not bind to FtsZ. Further analyses provided an explanation for the contradictory transposon and transcriptome results, and suggested that SepF competes with other cell division proteins for binding to FtsZ. Our data show that an imbalance in early cell division proteins can interfere with recruitment of late cell division proteins.

overall_design: Comparing wild type Bacillus subtilis strain 168 (n=2) with Bacillus subtilis YK240 (Pxyl-sepF, n = 3)

first: Yongqiang

last: Gao

first: Leendert

middle: W

last: Hamoen