title: Identification of Gram-positive bacteria using BC-GP assay

status: Public on May 30 2014

city: Seoul

first: Seon Young

last: Kim

address: 101 Daehak-ro, Jongno-gu,

country: South Korea

institute: Seoul National University College of Medicine

summary:
Signal intensities of BC-GP array for 105 speimens
The Verigene Gram-Positive Blood Culture (BC-GP) nucleic acid assay is an automated microarray-based test, which can detect 12 Gram-positive bacterial genes and 3 resistance determinants using blood culture broths. We investigated signal intensities of microarray spots, and reclassified undetermined results where the automated system failed and various errors were called in blood culture specimens and spiked samples.

sample_organism:
Escherichia coli
Klebsiella pneumoniae
Leuconostoc lactis
Micrococcus luteus
Staphylococcus aureus
Staphylococcus epidermidis
Staphylococcus haemolyticus
Staphylococcus simulans
Staphylococcus hominis
Streptococcus gordonii
Streptococcus salivarius
Streptococcus thermophilus
Streptococcus agalactiae
Streptococcus pneumoniae
Streptococcus pyogenes
Streptococcus parasanguinis
Streptococcus anginosus
Streptococcus dysgalactiae
Enterococcus faecalis
Enterococcus faecium
Enterococcus gallinarum
Bacillus licheniformis
Listeria monocytogenes
Staphylococcus lugdunensis
Streptococcus mitis
Staphylococcus caprae
Staphylococcus saprophyticus
Staphylococcus capitis
Corynebacterium afermentans
Corynebacterium striatum
Streptococcus constellatus
Streptococcus australis
Streptococcus gallolyticus

platform_organism:
Micrococcus
Staphylococcus
Staphylococcus aureus
Staphylococcus epidermidis
Streptococcus
Streptococcus agalactiae
Streptococcus pneumoniae
Streptococcus pyogenes
Enterococcus faecalis
Enterococcus faecium
Listeria
Staphylococcus lugdunensis
Streptococcus anginosus group

overall_design:
Signal intensity analysis of BC-GP assay.
SAMPLE_077 [Blood culture, Escherichia coli, Gram-negative, BacTALERT, Supernatant, Peripheral blood] had no signal data in the array raw data.  Thus, SAMPLE_077 is not represented in this Series.

first: Seon-Young

first: Kyoung-Un

last: Park


title: Changes in gene expression in BAZ1B knockout and heterozygous targeted clones

status: Public on May 21 2014

city: Tallahassee

first: Brian

middle: P

last: Chadwick

state: FL

address: 319 Stadium Drive, King 3076

department: Biological Science

country: USA

institute: Florida State University

summary:
Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the maintenance of heterochromatin, including at the human inactive X chromosome (Xi). WSTF is encoded by BAZ1B, and is one of twenty-eight genes that are hemizygously deleted in the genetic disorder Williams-Beuren syndrome (WBS).
To explore the function of WSTF, we performed zinc finger nuclease-assisted targeting of the BAZ1B gene and isolated several independent knockout clones in human cells. Our results show that, while heterochromatin at the Xi is unaltered, new inappropriate areas of heterochromatin spontaneously form and resolve throughout the nucleus. In three independent mutants, the expression of a large number of genes were impacted, both up and down, by WSTF loss. In addition, we found that cells lacking WSTF responded appropriately to vitamin D treatment, a process we expected to be disrupted.
Given the inappropriate appearance of regions of heterochromatin in BAZ1B knockout cells, it is evident that WSTF performs a critical role in maintaining chromatin and transcriptional states. Clearly, further exploration is necessary to fully understand the role of WSTF in maintenance of the epigenome and how WSTF haploinsufficiency contributes to the wide array of symptoms exhibited in WBS patients.

overall_design: Samples include three replicate miroarray hybridizations of the parental cells (hTERT-RPE1), three replicates from three independent knock-out clones (D5, F3 and M1), and one set of replicates for a heterozygous mutant clone (A6).

first: Ashley

middle: E

last: Culver-Cochran


title: Mutation Mapping of 40 Streptococcus suis strains

status: Public on May 20 2014

city: Beijing

first: Xiao

last: Zheng

address: Liuzi five hao

country: China

institute: China CDC

type: Genome variation profiling by genome tiling array

summary:
Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. In this study,we evaluated the genetic difference of 40 Streptococcus suis strains belonging to various sequence types by comparative genomic hybridization to identify genes associated with the variation in pathogenicity using NimbleGen’s tilling microarray platform.
Application of Comparative Phylogenomics to Identify Genetic Differences Relating to Pathogenicity of Streptococcus suis

overall_design: Comparative genomic analysis on the 40 S.suis strains of different serotypes and ST types through tilling arrays

first: Han

first: Changyun

last: Ye

first: Jianguo

last: Xu


title: Mammalian fetal ovary development

city: Adelaide

first: Nicholas

last: Hatzirodos

state: SA

address: Medical School Nth Frome Rd

department: Obstetrics and Gynaecology

country: Australia

institute: Adelaide University

summary: Ovarian follicular granulosa cells surround and nurture oocytes, and produce sex steroid hormones.  It is believed that during development the ovarian surface epithelial cells invaginate into the ovary and develop into granulosa cells when associating with oogonia to form follicles.  Using bovine fetal ovaries (n = 53) we identified a novel cell type, termed GREL for Gonadal Ridge Epithelial-Like.  Using 25 markers for GREL and other cells we conducted immunohistochemistry and electron microscopy and chronologically tracked all somatic cell types during development.  Before 70 days of gestation the gonadal ridge/ovarian primordium is formed by proliferation of GREL cells at the surface epithelium of the mesonephros.  Primordial germ cells (PGCs) migrate into the ovarian primordium.  After 70 days, stroma from the underlying mesonephros begins to penetrate the primordium, partitioning the developing ovary into irregularly-shaped ovigerous cords composed of GREL cells and PGCs/oogonia.  Importantly we identified that the cords are separated from the stroma by a basal lamina.  Around 130 days of gestation as the stroma expands laterally below the GREL cells on the surface thus establishing a sub-epithelial basal lamina and an epithelial-stromal interface, and it is at this stage that a mature surface epithelium develops from the GREL cells.  The stroma continues to partition the ovigerous cords into smaller groups of cells eventually forming follicles containing an oogonium/oocyte surrounded by GREL cells, which become granulosa cells.  Thus in contrast to the prevailing theory, the ovarian surface epithelial cells do not invaginate into the ovary to form the granulosa cells of follicles.

overall_design:
Microarray analysis of gene expression was conducted on different cell types cultured from fetal ovaries to identify possible markers of somatic cells during development.
Two different cell types: Gonadal Ridge Epithelial-Like cells (n=2, 130 days gestation) and adult fibroblasts (n=1) were cultured from digested bovine fetal ovaries and gene expression compared with each other by Bovine Genome Affy array analysis in Partek Genomics Suite software, to identify possible markers of somatic cells during development.

first: Katja

last: Hummitzsch

first: Helen

middle: F

last: Irving-Rodgers

first: Wendy

middle: M

last: Bonner

first: Laetitia

last: Sabatier

first: Dieter

last: Reinhardt

first: Yoshikazu

last: Sado

first: Yoshifumi

last: Ninomiya

first: Dagmar

last: Wilhelm

first: Raymond

middle: J

last: Rodgers


title: A novel aCGH method for non-model organisms for assessing genomes and de-novo transcriptome sequencing reads

status: Public on May 19 2014

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

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

sample_organism:
Staphylococcus aureus
Danio rerio

platform_organism:
Staphylococcus aureus
Danio rerio

overall_design: Refer to individual Series


title: Gene expression in bovine ovarian follicle theca interna

summary:
Thecal tissue forms a layer around the follicle just prior to antral stage and grows with the follicle (containing an oocyte) as it matures. The innermost component (theca interna) supplies hormones and other factors necessary to the growth and development of the granulosa and oocyte. Most follicles regress and die (become atretic) at the antral stage, and this process as well as development of the follicle are undoubtedly influenced by the theca.
Transcriptional changes in ovarian theca interna at the global level were examined by microarray during atresia and development to improve our understanding of the mechanisms involved.

overall_design: Four groups of bovine ovarian follicles were selected for analysis . Follicle size, type and array number for each group are, small (3-5 mm) healthy rounded (n=5), healthy columnar (n=5), atretic(n=5) and large healthy (>9mm), (n=4). For each group, the RNA from the theca interna of a single follicle was used to hybridise an array.


title: Endometrial gene expression profiling in pregnant Meishan and Yorkshire pigs on day 12 of gestation

city: Wuhan

first: Ting

last: Gu

state: Hubei

address: Shizi shan road

department: Animal Science

institute: Huazhong Agricultrural University

summary:
BACKGROUND:
Litter size in pigs is a major factor affecting the profitability in the pig industry. The peri-implantation window in pigs is characterized by the coordinated interactions between the maternal uterine endometrium and the rapidly elongating conceptuses and represents a period of time during which a large percentage of the developing conceptuses are lost. However, the gene expression and regulatory networks in the endometrium contributing to the establishment of the maternal: placental interface remain poorly understood.
RESULTS:
We characterized the endometrial gene expression profile during the peri-implantation stage of development by comparing two breeds that demonstrate very different reproductive efficiencies. We employed the porcine Affymetrix GeneChip® to assay the transcriptomic profiles of genes expressed in the uterine endometrium obtained from Meishan and Yorkshire gilts (n = 4 for each breed) on day 12 of gestation (M12 and Y12, respectively). Total of 17,076 probesets were identified as "present" in at least two arrays. A mixed model-based statistical analysis predicted a total of 2,656 (q < 0.1) transcripts as differentially expressed between Meishan and Yorkshire pigs. Eighteen differentially expressed transcripts of interest were validated by quantitative real-time PCR. Gene ontology (GO) annotation revealed that the known functions of the differentially expressed genes were involved in a series of important biological processes relevant to early pregnancy establishment in the pig.
CONCLUSIONS:
The results identified endometrial gene expression profiles of two breeds differing in litter size and identified candidate genes that are related to known physiological pathways related to reproductive prolificacy. These findings provide a deeper understanding of molecular pathways differing between two breeds at the critical peri-implantation stage of pregnancy, which can be utilized to better understand the events contributing to pregnancy establishment in the pig.

overall_design: Meishan and Yorkshire breeds endometirum were selected and RNA been extracted and  hybridized to the Affymetrix microarray. A number of genes have been shown differently expressed on two breeds.

first: Meng

last: Zhu

first: Long

last: Qu

middle: H

last: Huang

first: Dan

last: Nettleton

first: Joan

middle: K

last: Lunney

first: Shu

last: Zhao

first: Christopher

last: Tuggle

first: Martine

last: Schroyen

first: Jason

last: Rose


title: Quantitative trait loci (QTL) study identifies novel genomic regions associated to Chiari-Like Malformation in Griffon Bruxellois dogs

city: Montreal

first: Philippe

last: Lemay

state: Quebec

address: 3175 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: Université de Montréal

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

summary: Chiari-like malformation (CM) is a developmental abnormality of the craniocervical junction that is common in the Griffon Bruxellois (GB) breed with an estimated prevalence of 65%. This disease is characterized by overcrowding of the neural parenchyma at the craniocervical junction and disturbance of cerebrospinal fluid (CSF) flow. The most common clinical sign is pain either as a direct consequence of CM or neuropathic pain as a consequence of secondary syringomyelia. The etiology of CM remains unknown but genetic factors play an important role. To investigate the genetic complexity of the disease, a quantitative trait locus (QTL) approach was adopted. A total of 14 quantitative skull and atlas measurements were taken and were tested for association to CM. Six traits were found to be associated to CM and were subjected to a whole-genome association study using the Illumina canine high density bead chip in 74 GB dogs (50 affected and 24 controls). Linear and mixed regression analyses were used to identify quantitative trait loci.

overall_design:
To identify the presence of causative haplotype for Chiari-Like Malformation 80 Griffon Bruxellois dogs were genotyped using Illumina CanineHD Beadchip. This cohort consisted of 53 cases and 27 controls. Ten samples were whole genome amplified using the Qiagen Repli-g kit following the protocol. Linear and mixed regression model were used to define association between morphologic traits and genetic data.

The sample traits (provided in the sample characteristics field) are described in the 'README_Traits_description.pdf'
Processed data were obtained in 3 different normalization batches. The normalization batch/raw data file information is provided in the sample description field.

first: Susan

last: Knowler

first: Clare

last: Rusbridge

first: Zoha

last: Kibar


title: Transcriptome analysis of the phytopathogen Xylella fastidiosa in response to salt and osmotic stress

status: Public on May 25 2014

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

institute: Institute for Systems Biology

summary:
The global transcriptional response of the phytopathogenic bacterium X. fastidiosa to a sudden increase in salinity and osmolarity of the medium was investigated using DNA microarrays. Time-course experiments were carried out by exposing bacterial cells to high salinity (250 mM NaCl) and high osmolarity (300 mM sucrose) conditions revealing 142 upregulated genes under both stresses, including pathogenicity related genes, genes encoding transcriptional regulators, as well as genes related to DNA metabolism and mobile genetic elements. In addition, 38 genes were downregulated under both conditions, most of them related to ribosomal and heat shock proteins. A total of 192 genes were upregulated exclusively in the presence of NaCl, including genes encoding transporters, genes involved in oxidative-stress response and genes related to cell structure. A smaller number of genes (44 genes) were induced only in the presence of sucrose, most of them encoding hypothetical and conserved hypothetical proteins. Interestingly, 57% of the genes differentially expressed under both stress conditions have no putative function assigned, emphasizing the importance of high-throughput experiments to start the characterization of these genes in X. fastidiosa.
Keywords: stress response, osmotic and salt stress

overall_design: Direct comparison between osmotic or salt stress condition and control (29oC) condition. Some hybridizations are dye-swaped. There are at least 3 biological replicates (independent harvest) and 2 technical replicates of each array (L - left and R - right).

first: Suely

middle: L

last: Gomes


title: A novel aCGH method for non-model organisms for assessing genomes and de-novo transcriptome sequencing reads (Danio rerio)

last: Jonker

summary: Genomes and transcriptomes of non-model organisms can be analyzed using next-generation sequencing technologies, but de-novo sequencing and annotating a full eukaryotic genome is still challenging. So, -omics experimentation with non-model organisms requires a suite of technologies to obtain reliable results in a cost-effective manner. Here, a novel method for microarray-based genome analysis is presented which is especially suitable for non-model organisms. We show that it is useful for complementing regular aCGH analyses and for evaluating transcriptome next-generation sequencing reads. The principle of the method is straightforward: feature intensities obtained after hybridizing the test genome are compared with the feature intensities of a control hybridization. The control hybridization is performed with negative control probes (no targets in the control sample), and with positive control probes (with targets in the control sample). The method has in principle a resolution of a single probe and it does not depend on the structural information of a reference genome: the genomic ordering of probe targets is irrelevant. In a test, analyzing the genome content of a sequenced bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful demonstrated by receiver operating characteristic area under the curve values larger than 0.9995.

overall_design: DNA from twelve Danio rerio individuals was extracted, fragmented, and hybridized onto the D. rerio microarray. DNA from the pool was used as common reference, but this channel was omitted in further analyses.

first: Wim

last: de Leeuw

first: Marino

last: Marinković

first: Floyd

middle: R

last: Wittink

first: Han

last: Rauwerda

first: Oskar

last: Bruning

middle: A

last: Ensink

first: Ad

middle: C

last: Fluit

first: C

last: Boel

first: Mark

last: de Jong

first: Timo

last: Breit


title: Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart: genotyping

first: Michiel

middle: Emanuel

last: Adriaens

address: Meibergdreef 15

department: Experimental Cardiology

institute: AMC

summary: In recent years genome-wide association studies (GWAS) have uncovered numerous chromosomal loci associated with various electrocardiographic traits and cardiac arrhythmia predisposition. A considerable fraction of these loci lie within inter-genic regions. Trait-associated SNPs located in putative regulatory regions likely exert their effect by modulating gene expression. Hence, the key to unraveling the molecular mechanisms underlying cardiac traits is to interrogate variants for association with differential transcript abundance by expression quantitative trait locus (eQTL) analysis. In this study we conducted an eQTL analysis of human heart. To this end, left ventricular mycardium samples from non-diseased human donor hearts were hybridized to Illumina HumanOmniExpress BeadChips for genotyping (n = 129) and Illumina Human HT12 Version 4 BeadChips (n = 129) for transcription profiling.

overall_design: To assess the genotypes of 129 human donor hearts from the study, genome-wide SNP genotyping was carried out using Illumina HumanOmniExpress Beadchips interrogating 733,202 genetic markers.

first: Tamara

last: Koopmann

first: Connie

last: Bezzina


title: Gene expression changes in the fetal rhesus monkey uterus from early to late gestation and the effects of in utero exposure to BPA

status: Public on May 22 2014

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: We used the rhesus monkey (Macaca mulatta) as our animal model for the current study with two goals: to characterize the changes in histology and gene expression from early to late gestation (prenatal uterine organogenesis) and to determine if there are effects of prenatal exposure to bisphenol A (BPA) on the developing female uterus.

overall_design:
Pregnant rhesus monkeys carrying a female fetus (N=22) were divided into two experimental groups, based on gestational timing: 'early' (N=10) and 'late' (N=12). These groups were then equally sub-divided into control (unexposed) and BPA (exposed) groups (5 Early Control, 5 Early BPA-exposed, 6 Late Control and 6 Late BPA-exposed.) The BPA-exposed monkeys received a deuterated BPA (dBPA, CDN Isotopes, Quebec, Canada) fruit treat on a daily basis, at a dose of 400ug/kg/day). The dosing was aimed at achieving serum levels of BPA detected in adult human biomonitoring studies. The control animals received a vehicle control on a daily basis.
The 'early' time period (mid-gestation) referred to gestational days 50-100, approximating the second trimester of human gestation. The fetal monkeys in the 'early' group were delivered via cesarean section on gestation day 100 and euthanized. Samples of maternal and fetal blood and amniotic fluid were obtained. Maternal and fetal weights were also recorded.
The 'late' time period referred to gestational days 100-165, approximating the third trimester of human gestation. The fetal monkeys in the 'late' group were delivered vaginally and euthanized. There were five idiopathic stillbirths (2 Control, 3 BPA-exposed) in the late group. Samples of maternal and fetal blood and amniotic fluid were obtained. Maternal and fetal weights were also recorded.
After delivery, the fetal uterus was excised and cut sagitally from fundus to cervix; one side was fixed for histological evaluation and the other half was frozen for analysis of gene expression by microarray. The stillbirths were excluded from the microarray.

first: Kathryn

last: Calhoun

first: Elizabeth

last: Padilla-Banks

first: Kevin

last: Gerrish

first: S

last: Young

first: P

last: Hunt

last: VandeVoort

first: Carmen

last: Williams


title: Combining Next-Generation Sequencing and Microarray Technology into a Transcriptomics Approach for the Non-Model Organism Chironomus riparius

first: Martijs

last: Jonker

summary: Whole-transcriptome gene-expression analyses are commonly performed in species that have a sequenced genome and for which microarrays are commercially available. To do such analyses in species with no or limited genome data, i.e. non-model organisms, necessary transcriptomics resources, i.e. an annotated transcriptome and a validated gene-expression microarray, must first be developed. The aim of the present study was to establish an advanced approach for developing transcriptomics resources for non-model organisms by combining next-generation sequencing (NGS) and microarray technology. We applied our approach to the non-biting midge Chironomus riparius, an ecologically relevant species that is widely used in sediment ecotoxicity testing. We sampled extensively covering all C. riparius developmental stages as well as toxicant exposed larvae and obtained from a normalized cDNA library 1.5 M NGS reads totalling 501 Mbp. Using the NGS data we developed transcriptomics resources in several steps. First, we designed 844 k probes directly on the NGS reads, as well as 76 k probes targeting expressed sequence tags of related species. These probes were tested for their affinity to C. riparius DNA and mRNA, by performing two biological experiments with a 1 M probe-selection microarray that contained the entire probe-library. Subsequently, the 1.5 M NGS reads were assembled into 23,709 isotigs and 135,082 singletons, which were associated to ~55 k, respectively, ~61 k gene ontology terms and which corresponded together to 22,593 unique protein accessions. An algorithm was developed that took the assembly and the probe affinities to DNA and mRNA into account, what resulted in 59 k highly-reliable probes that targeted uniquely 95% of the isotigs and 18% of the singletons. Concluding, our approach allowed the development of high-quality transcriptomics resources for C. riparius, and is applicable to any non-model organism. It is expected, that these resources will advance ecotoxicity testing with C. riparius as whole-transcriptome gene-expression analysis are now possible with this species.

sample_organism:
Anopheles gambiae
Chironomus riparius

overall_design: 1x 1M CGH array with Cy3 labeled C. riparius gDNA and Cy5 labeled A. gambiae gDNA. The microarray was designed against C. riparius mRNA sequencing reads, and has been used to identify trustworthy sequencing reads to design an expression array. This 1M array is therefore not functionally annotated.

first: Marino

last: Marinkovic'

first: Wim

last: de Leeuw

last: Kraak

last: Admiraal


title: Getting inside of the molecular pathways associated with intersex in the rainbow darter (Etheostoma caeruleum)

city: Saint John

first: Paulina

middle: Andrea

last: Bahamonde

state: New Brunswick

address: 100 Tucker Park Road

department: Biology Department

institute: University of New Brunswick

summary: Rainbow darter (Etheostoma caeruleum) are a small benthic fish found in North America.  This species is sensitive to sewage effluent in the environment, showing the presence of intersex in up to 80% of males in near-field areas in the Grand River, ON.  To learn more about the molecular events associated with intersex, we developed a customized oligonucleotide microarray (4x180K) with next generation sequencing (454 Roche) to characterize molecular responses in the gonad.  Transcriptomics was performed on both males and females from both a reference site and a polluted site.  Males with and without intersex from the polluted site were compared to the control males.

overall_design: Rainbow darter were sampled from from the Grand River in May 2011.  Fish were selected according to the location, gonad maturity, and intersex index.  Reference fish were taken from the upstream to the urban area; exposed fish were taken from downstream of from Kitchener MWWE treatment plant.

last: McMaster

last: Servos

first: Chris

last: Martyniuk

first: Kelly

last: Munkittrick


title: Expression analysis of the effects of methyl-donor deficient diet on male mice (part 2)

status: Public on May 29 2014

city: Leicester

first: Yuri

last: Dubrova

address: University Road

department: Genetics

country: United Kingdom

institute: University of Leicester

summary:
BALB/c male mice were maintained for 8 weeks on a synthetic diet lacking in choline and folic acid and mated with control females. Tissue samples were taken from eigth-week old male offspring of control and treated males. The design of this study is further described in Voutounou, M., C .D. Glen, and Y. E. 2012. The effects of methyl-donor deficiency on mutation induction and transgenerational instability in mice. Mutat. Res. 734(1):1-4 (PMID: 22569175)
The pattern of gene expression in liver and kidney of mice sacrificed immediatelly after the end of dietary restrictions is significatly altered.

overall_design: A ten 12x135K chip study using total RNA extracted from kidney and liver of control and treated BALB/c male mice. The expression of 42,575 genes was measured with two-fold technical redundancy.


title: Expression analysis of the effects of methyl-donor deficient diet on male mice (part 3)

summary:
CBA/Ca male mice were maintained for 8 weeks on a synthetic diet lacking in choline and folic acid and sacrificed 0 and 2 weeks after the end of dietary restrictions. The design of this study is further described in Voutounou, M., C .D. Glen, and Y. E. 2012. The effects of methyl-donor deficiency on mutation induction and transgenerational instability in mice. Mutat. Res. 734(1):1-4 (PMID: 22569175)
The pattern of gene expression in liver of mice sacrificed immediatelly after the end of dietary restrictions is significatly altered.


title: Expression analysis of the effects of methyl-donor deficient diet on male mice (part 1)

summary:
BALB/c and CBA/Ca male mice were maintained for 8 weeks on a synthetic diet lacking in choline and folic acid and sacrificed after the end of dietary restrictions. The design of this study is further described in Voutounou, M., C .D. Glen, and Y. E. 2012. The effects of methyl-donor deficiency on mutation induction and transgenerational instability in mice. Mutat. Res. 734(1):1-4 (PMID: 22569175)
The pattern of gene expression in spleen of mice sacrificed immediatelly after the end of dietary restrictions is not significatly altered.

overall_design: A six 12x135K chip study using total RNA extracted from kidney and liver of control and treated BALB/c male mice. The expression of 42,575 genes was measured with two-fold technical redundancy.


title: Transcriptome analysis of gilthead sea bream (Sparus aurata) brain after exposure to environmental concentrations of human pharmaceuticals

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

summary: A gilthead sea bream (Sparus aurata) microarray platform was developed to identify brain gene expression profiles in response to environmental concentrations of human pharmaceuticals.

overall_design: Comparative analysis of gene expression profiles was conducted among brain of gilthead seabream exposed to Acetaminophen (APAP; analgesic), Carbamazepine (CBZ; anti-epileptic) and Atenolol (AT; β-blocker). All groups of samples were also compared with brain of control individuals.

first: Miriam

last: Hampel

first: Massimo

last: Milan


title: Profiling of Cell cycle genes dysregulated by knockdown of lncRNAs at 8q24.21 using Nanostring Gene Expression Assay

city: Columbus

first: Taewan

last: Kim

state: OH

institute: The Ohio State University

summary:
Idetification of cell cycle-related genes dysregulated by knockdown of CARLos (lncRNAs) in colorectal cancer-derived HCT116
Idetification of cell cycle-related genes dysregulated by knockdown of CARLos (lncRNAs) in prostate cancer-derived PC3

overall_design: Using siRNAs targeting CARLos, the cells were transfected and RNA samples from the treated cells were subjected to Nanostring Gene Expression Assay

first: Hansjuerg

last: Alder


title: Gene expression in cultured bovine ovarian granulosa

first: Nicholas

last: Hatzirodos

summary:
The growth of the mammalian ovarian follicle requires the formation of a fluid filled antrum, and maturation and differentiation of the ovarian granulosa cells, largely under the control of Follicle Stimulating Hormone (FSH).  Many follicles will regress and die by a process called atresia at this early antral stage. We therefore decided to analyse the gene expression profiles of granulosa cells cultured in the presence or absence of FSH and Tumour Necrosis Factor-alpha (TNFα), an apoptotic factor, to simulate the key influences. Different concentratons of FSH and TNFa  in granulosa culture were used to determine effective conditions via estradiol and progesterone production, and cell number.
RNA for the array experiments and quantitative real time PCR was extracted from cells cultured  with FSH added at 0.33 and TNFα at 50 ng/ml.

overall_design: Four treatments of :  (1) FSH alone, (2) TNFα alone, (3) FSH + TNFα and  (4) control = neither drug, with replicates (n=4, except controls n=3 ) were used to generate RNA for the gene expression arrays (n=15)

first: Claire

last: Glister

first: Hummitzsch

last: Katja

first: Raymond

last: Rodgers

first: Phillip

middle: G

last: Knight


title: Gene expression rhythms in rainbow darter male (Etheostoma caeruleum) across an annual reproductive cycle

summary: We have been studying intersex in male rainbow darter (Etheostoma caeruleum) associated with exposure to sewage effluents.  To understand changes in the gene transcriptome associated with intersex it was necessary to have a better understanding of normal annual changes in the transcriptome. The goal of this research is to identify patterns of gene expression associated with the different stages of gonad development during the annual cycle. The studies of molecular pathways involve in ovarian or testis development has been poorly studied. While most studies focus on female ovarian changes, there is a gap in understanding testis development. A customized second generation microarray for rainbow darter (8x15k) was used to identify patterns of gene expression -in terms of mRNA abundance- in male rainbow darter gonads during an annual cycle.

overall_design: Rainbow darter males were collected on field work surveys in May (spawning), August (post-spawning), and October (recrudescence) 2011, and January (developing) and March (pre-spawning) 2012, using a back pack electrofisher from a clean area at the Grand River, ON, Canada.

first: Mark


title: The Streptomyces lividans lsp mutant

city: Campus de Cantoblanco

first: Sonia

last: Gullón

state: Madrid

address: Darwin 3

country: Spain

institute: CNB-CSIC

summary: The Streptomyces lividans lsp gene encodes a type II signal peptidase (Lsp) that cleaves the type II leader peptides of lipoproteins. Transcriptional profiling of the bacterium depleted of the lsp gene mainly resulted in deactivation of the sigma U regulon, as well as in downregulation of genes involved in the biogenesis and function of ribosomes and genes encoding some major secretory proteins as determined by hybridisation of commercially available S. lividans genome-wide microarrays. Almost 50% of the dowregulated genes have been described as forming part of the stringent response in streptomycetes. The gene encoding the S. lividans extracellular foldase, the lipoprotein FkpA, is equally downregulated. Therefore, the deletion of lsp from the S. livdans genome temporarily triggers a cellular stress where the stringent response is, at least, partially induced.

overall_design: All microarray analyses were performed with RNA samples obtained from three independent cultures grown under identical conditions. The cDNA obtained from each RNA preparation of the Lsp-deficient strain was hybridised with the cDNA obtained from the equivalent RNA preparation of the wild type strain (S. lividans TK21).

first: Esther

middle: I

last: García

first: Rafael

last: Mellado


title: The immediate global responses of Aliivibrio salmonicida to iron limitations

status: Public on May 27 2014

city: Tromsoe

first: Espen

middle: Mikal

last: Robertsen

address: Breivika

department: Chemistry

country: Norway

institute: University of Tromsoe

summary: Iron is an essential micronutrient for all living organisms, and sequestering of iron and the virulence of pathogenic bacteria are believed to be correlated. As the defense mechanisms, potential hosts therefore keep the level of free iron inside the body to a minimum. The iron metabolism is well studied in general for several pathogens of humans and animals, but it is still mostly unclear how gene expression levels change in pathogens during the initial stages of infections. In this work, using Aliivibrio salmonicida we studied the immediate changes in transcription levels in response to a sudden decrease in iron levels. Microarray technology was used to monitor global changes in transcriptional levels. Cultures of A. salmonicida were grown to mid log phase before the iron chelator 2,2’-dipyridyl was added and samples were collected after 15 minutes of growth. Using our statistical cut-off values, we retrieved thirty-two differentially expressed genes where the most up-regulated genes belong to an operon encoding proteins responsible for producing the siderophore bisucaberin.

overall_design: Six biological replicates of A. salmonicida wild type strain LFI1238 were grown in suspension in LB medium, at 8 °C ,  200 rpm and split in two halves at OD600nm 0.5, keeping one half of each replicate as control (still growing while the treated samples were growing with 2,2-dipyridyl treatment) while the other half were treated with 50µM 2,2-dipyridyl for 15 minutes.

first: Sunniva

last: Thode

first: Tim

last: Kahlke

first: Hilde

last: Hansen

first: Peik

last: Haugen


title: Expression analysis of strains Lactococcus lactis KCTC 3769T, L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T

status: Public on May 28 2014

first: Maytiya

last: Konkit

address: 84, Heukseok-ro, Dongjak-ku

department: Microbiology

institute: Chung-Ang University

summary: Investigation of whole genome gene expression level changes in Lactococcus lactis KCTC 3769T,L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T  .  This proves that transcriptional profiling can facilitate in elucidating the genetic distance between closely related strains.

sample_organism:
Lactococcus lactis
Lactococcus garvieae
Pseudolactococcus piscium
Pseudolactococcus plantarum
Pseudolactococcus raffinolactis
Pseudolactococcus chungangensis
Lactococcus fujiensis

overall_design: A one chip study using total RNA recovered from of L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T . For the the transcriptome of of L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T was analyzed using the Lactococcus lactis KCTC 3769T microarray platform

first: JongHwa

first: Wonyong


title: Gene expression in bovine ovarian follicle granulosa

first: Nicholas

summary:
Granulosa cells mature and die as ovarian follicles enlarge and die (undergo atresia) under the influence of hormones and intrafollicular factors. Later in follicular development, a fluid-filled antrum is formed, a process which is accompanied by a high rate of atresia. These small antral follicles (5 mm or less in diameter in the cow) contain granulosa of 2 different phenotypes, rounded or columnar, whereas follicles larger than 5 mm have the rounded phenotype only. Prior to ovulation, in larger follicles greater than 10 mm in size, the granulosa begin to migrate and differentiate in preparation for oocyte release and formation of the corpus luteum.
These two key phases of follicular development were studied by gene expression microarray analysis using a bovine model to dissect the molecular mechanisms underlying these processes.

overall_design: Four groups of bovine ovarian follicles were selected for analysis. Follicle size, type and array number for each group are as follows: small (3-5 mm) healthy rounded (n=5), small healthy columnar (n=5), atretic (n=5) and large healthy (>10 mm; n=4). For each group, the RNA from a single follicle was used to hybridise an array, except for 3 small healthy samples which were pooled from 2 follicles each due to low RNA.

first: Katja

last: Hummitzsch

first: Helen

last: Irving-Rodgers

first: Lyn

last: Harland

first: Stephanie

last: Morris


title: The transcriptomic changes affected by BDF2 and SIR2 under salt stress

status: Public on May 26 2014

city: Jinan

first: Xiaoming

last: Bao

state: Shandong

address: Shanda Nan Road 27

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: The strain bdf1∆bdf2∆[BDF2 L][SIR2 H] improved salt resistance of bdf1∆. To gain further insight into the mechanism of BDF1 in suppressing bdf1∆ salt sensitivity, DNA microarray analysis was performed to determine the reason for the salt sensitivity of bdf1∆ cells and the process of how coexpression of SIR2 and BDF2 improves salt resistance. Transcriptomic analysis under salt treatment (0.6 mol.L-1 NaCl for 45 min) was performed using three different strains: bdf1∆bdf2∆[BDF2 L][SIR2 H],  bdf1∆bdf2∆[BDF2 L][pYX242] and bdf1∆[pRS316][pYX242]. The transcription of 3244 genes were significantly changed( > 2-fold) in bdf1∆bdf2∆[BDF2 L][SIR2 H] compared with bdf1∆[pRS316][pYX242] upon NaCl stress (0.6 mol.L-1 NaCl for 45 min). Only 281 genes were significantly changed ( > 2-fold) in bdf1∆bdf2∆[BDF2 L][pYX242]  compared with bdf1∆[pRS316][pYX242] upon NaCl stress (0.6 mol∙L-1 NaCl for 45 min). BF2:bdf1∆[pRS316][pYX242]. BF2B: bdf1∆bdf2∆[BDF2 L][pYX242]. BF2S:bdf1∆bdf2∆[BDF2 L][SIR2 H].

overall_design: BF2B vs BF2 under salt treatment (0.6 mol.L-1 NaCl for 45 min); BF2S vs BF2 under salt treatment (0.6 mol.L-1 NaCl for 45 min).

first: Jiafang

last: Fu

first: Jin

last: Hou

first: Lei

last: Chen

first: Mingpeng

last: Wang

first: Yu

last: Shen

first: Zhaojie

last: Zhang


title: Expression analysis of the effects of methyl-donor deficient diet on male mice (parts 1 to 3)

first: Yuri

last: Dubrova

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

overall_design: Refer to individual Series


title: Resistance to aerobic exercise training causes metabolic dysfunction and reveals novel exercise-regulated signaling networks

status: Public on May 23 2014

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

summary: Low aerobic exercise capacity is a risk factor for diabetes and strong predictor of mortality; yet some individuals are exercise resistant, and unable to improve exercise capacity through exercise training. To test the hypothesis that resistance to aerobic exercise training underlies metabolic disease-risk, we used selective breeding for 15 generation to develop rat models of low- and high-aerobic response to training. Before exercise training, rats selected as low- and high-responders had similar exercise capacities. However, after 8-wks of treadmill training low-responders failed to improve their exercise capacity, while high-responders improved by 54%. Remarkably, low-responders to aerobic training exhibited pronounced metabolic dysfunction characterized by insulin resistance and increased adiposity, demonstrating that the exercise resistant phenotype segregates with disease risk. Low-responders had impaired exercise-induced angiogenes0is in muscle; however, mitochondrial capacity was intact and increased normally with exercise training, demonstrating that mitochondria are not limiting for aerobic adaptation or responsible for metabolic dysfunction in low-responders. Low-responders had increased stress/inflammatory signaling and altered TGFβ signaling, characterized by hyperphosphorylation of a novel exercise-regulated phosphorylation site on SMAD2. Using this powerful biological model system we have discovered key pathways for low exercise training response that may represent novel targets for the treatment of metabolic disease.

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

overall_design: Cardiac and skeletal muscle from 3 high and 3 low responder rats were examined for differential miRNA expression using Exiqon microarrays


title: Differential expression of miRNAs in colons of STC patients

first: Congqing

last: Jiang

address: 169 Donghu Road, Wuchang District

department: Department of Colorectal Surgery

institute: Zhongnan Hospital of Wuhan University

summary: To investigate the pathogenesis of slow transit constipation (STC), we have employed  microarray-based miRNA analysis as a discovery platform to identify miRNAs  potentially related with STC pathogenesis.Full-thickness specimens were obtained from colons of  STC patients undergoing total colectomy and ileorectal anastomosis or subtotal colectomy with antiperistaltic cecoproctostomy. And patients undergoing radical surgery for non-obstructing colon cancer (left colon cancer) as control. These patients were not constipated and had no colonic dilatation. The control specimens were obtained at least 5 cm from the resection margin in tumor free areas. Expression of five miRNAs (miRNA-128, miRNA-129-3p, miRNA-20b,miRNA-27b and miRNA-30b) from this signature was   identified by arbitrarily setting the threshold at a fold change of 1.3 or above combined with p < 0.05 in the same RNA samples. Expression of miRNAs in the colon may be involved in STC pathogenesis.

overall_design: The samples were obtained and washed with cold PBS, transported in liquid nitrogen and immediately stored in liquid nitrogen after removal. Total RNA was isolated from frozen histologic specimens using a mirVana™ RNA isolation Kit.

first: Weicheng

last: Liu


title: Gene expression analysis of tumorigenic versus non-tumorigenic canine osteosarcoma cell lines

city: Madison

first: Timothy

last: Stein

state: WI

address: 2015 Linden Drive

department: Medical Sciences

institute: University of Wisconsin-Madison

summary: An increased serum alkaline phosphatase concentration is known to be associated with a negative prognosis in canine and human osteosarcoma.  To expand upon previous studies regarding the biological relevance of increased serum alkaline phosphatase as a negative prognostic factor, xenogeneic heterotopic transplants were performed using six canine primary osteosarcoma cell lines generated from patients with differing serum alkaline phosphatase concentrations (3 normal and 3 increased).  Three of the six cell lines were capable of generating tumors and tumor formation was independent of the serum alkaline phosphatase status of the cell line.  Microarray analysis identified 379 genes as being differentially-expressed between the tumorigenic and non-tumorigenic cell lines.  Frizzled-6 was up-regulated to the greatest extent (7.78 fold) in tumorigenic cell lines compared to non-tumorigenic cell lines. Frizzled-6, a co-receptor for Wnt ligands has been associated with enhanced tumor-initiating cells and poor prognosis for other tumors. The increased expression of frizzled-6 was confirmed by QPCR and Western blot analysis. Additionally, the tumorigenic cell lines also had an increase in the percentage of side population cells compared to non-tumorigenic cell lines (5.89% versus 1.58%, respectively).  There were no differences in tumorigenicity, frizzled-6, or percentage of side population cells noted between osteosarcoma cell lines generated from patients of differing serum alkaline phosphatase concentration.  However, to our knowledge this is the first study to identified frizzled-6 as a possible marker of osteosarcoma cell populations with enhanced tumorigenicity and side population cells.  Future work will focus on defining the role of frizzled-6 in osteosarcoma tumorigenesis and tumor-initiating cells.

overall_design: A total of six canine primary osteosarcoma cell lines were used in this study.  Three cell lines were capable of forming tumors when transplanted into mice (tumorigenic) and three cell lines were not capable of forming tumors upon transplant into mice (non-tumorigenic).  The gene expression data is from the primary cell lines, not the transplanted cells.  There were no reference cell lines or controls used in this study.

first: Lucas

last: Rodrigues

first: Michael

last: Newton


title: Gene Expression in the Human Mammary Epithelium in response to consumption of high fat (H-FAT) and high carbohdyrate (H-CHO) diets.

city: Houston

first: Mahmoud

middle: Ali

last: Mohammad

state: Texas

address: 1100 Bates St.

department: Pediatrics-Nutrition

institute: Baylor College of Medicine

summary: Mammary gland (MG) de novo lipogenesis contributes significantly to milk fat in animals but little is known in humans.  We hypothesized that de novo lipogenesis, as reflected by incorporation of 13C carbons from [U-13C]glucose into fatty acids (FAs) and glycerol in triglycerides (TG), will be greater: a. in milk than plasma TG,  b. during  a high carbohydrate (H-CHO) diet than high fat (H-FAT) diet and  c. during feeding than fasting. Healthy lactating women were studied on two isocaloric, isonitrogenous diets. On one occasion subjects received diets containing H-FAT or H-CHO diet for 1 week.  Incorporation of 13C from infused [U-13C]glucose into FAs and glycerol was measured using GC/MS methodology and gene expression using RNA isolated from breast milk fat globule (MFG). Incorporation of 13C2 into milk FAs, increased with increased chain length of the FAs from C2:0 to C12:0 but progressively declined in C14:0 and C16:0 and was not detected in FAs >C16. During feeding, regardless of diets, enrichment of 13C2 in milk FA and 13C3 in milk glycerol were ~3 and ~7 fold higher compared to plasma FA and glycerol, respectively. Following an overnight fast during H-CHO and H-FAT diets study periods, 25% and 6%, respectively, of medium chain FAs (MCFAs, C6-C12) were derived from glucose but increased to 75% and 25% with feeding. The expression of genes involved in FA or glycerol synthesis pathways was unchanged regardless of diet or fast-fed conditions. Conclusions: The human MG is capable of de novo lipogenesis, of primarily MCFAs and glycerol, which is influenced by the macro-nutrient composition of the maternal diet.

overall_design: On day 7 of consumption of each of the two diets milk samples collected from 7 healthy, lean, exclusively breastfeeding women following an overnight fast and feeding conditions [7 x 2 x 2 = 28 samples] were processed for isotope enrichments and RNA isolation from the milk fat globules. The total RNA was utilized for microarray analyses.

first: Agneta

last: Sunehag

first: Morey

middle: W

last: Haymond


title: Root gene expression profiles of two maize inbred lines (Lo5 and T250) in response to nitrate treatment

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

institute: University of Verona

summary: Among the mineral elements necessary for plant growth, nitrogen (N) is the macronutrient required in larger amounts. The optimization of N use efficiency (NUE) in maize could be obtained through both genetic improvement and agronomic practices in order to enhance production and reduce the negative impact of the N fertilizer use on the environment. Physiological characterizations of inbred lines with different NUE are available in maize.

overall_design: Maize (Zea mays L.) seeds of two inbred lines (T250,  Lo5) previously soaked in running water for 24 h, were allowed to germinate in the dark at 28°C for 72 h over an aerated solution of 0.5 mM CaSO4. Half part of two-d-old seedlings was grown in a nutrient solution with 200 μM of KNO3 (treated samples, +NO3-) and the other half with appropriate amounts of the corresponding chloride salt (KCl) (control samples, -NO3-). Three biological replicates were obtained by three independent experiments and collecting roots of treated (200 μM NO3-) and not treated plants after 0, 1, 2 e 4 h for Lo5 inbred line and after 0, 5, 11 and 12 h for T250.

first: Stefania

last: Astolfi

first: Sabrina

last: Zuchi

first: Youry

last: Pii

first: Paola

last: Tononi

first: Katia

last: Guardini

first: Zeno

last: Varanini


title: Polyubiquitination analysis upon GSK3 inhibition in HeLa cell extracts

status: Public on May 15 2014

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

summary: HeLa cell extracts with or without GSK3 enzyme inhibition were assayed using protein microarrays in order to detect GSK3-dependent changes in protein polyubiquitination.

overall_design: HeLa lysates in triplicates were supplemented with ubiquitin and incubated on protein microarrays (ProtoArray 5.0; Invitrogen) in the presence or absence of the GSK3 inhibitor SB-216763. Polyubiquitination of the arrayed proteins was detected using specific antibodies. ProtoArray 5.0 contains over 9,000 full-length human proteins purified and arrayed in duplicate under native conditions to maximize functionality.

first: Sergio

middle: P

last: Acebron

first: Christof

last: Niehrs


title: Intrahepatic miRNA/mRNA expression in non-responders to pegylated interferon plus ribavirin combination therapy for chronic hepatitis C (miRNA microarray data)

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

summary: Despite advance in interferon-based treatment for chronic hepatitis C, difficult-to-treat patients remain in existence yet. To identify key genes involved in difficult-to-treat characteristics, gene expression patterns of miRNA and RNA were analyzed by profiling pretreatment liver tissues from five sustained virological responders (SVR), three relapsers (R) and four non-responders (NR). Expression levels of miRNA and mRNA were compared between SVR/R and NR groups by using microarray, respectively. Quantitative real-time reverse-transcriptase polymerase chain reaction and statistical analyses validated genes with significantly differential expression levels in 50 liver tissues: proliferation-, inflammation- and anti-apoptosis-related mRNA expression levels increased significantly in NR, compared to SVR/R. Of miRNA with significantly differential expression levels on microarray, several miRNA were correlated inversely with those significant mRNA. In vitro studies by using miRNA inhibitors and mimics verified the inverse correlation between the miRNA and mRNA. These findings enhance our understanding of the difficult-to-treat molecular mechanism and identification of target molecules for novel treatments.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Moderated t-statistics based on the empirical Bayes approach were performed to identify miRNA differentially expressed between SVRs/relapses and NVRs using the “limma” package from BioConductor software (http://www.bioconductor.org/) under R statistical software version 2.12.1 (http://www.r-project.org/). Because of multiple hypothesis testing, p values were adjusted by the Benjamini-Hochberg false discovery rate (FDR) method. Related mRNA expression data are in GSE42697.

first: Akihito

last: Tsubota

first: Ken

last: Miyaguchi

first: Rie

last: Agata

first: Yoko

last: Yumoto

first: Yoshihisa

last: Namiki

first: Keisuke

last: Nagatsuma

first: Hiroshi

last: Tanaka

first: Norio

last: Tada


title: Transcriptomic profile of Clostridium thermocellum ATCC27405 using switchgrass as carbon source

status: Public on May 08 2014

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

type: Expression profiling by genome tiling array

summary: Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium that ferments cellulose into ethanol. It is a candidate industrial consolidated bioprocess (CBP) biocatalyst for lignocellulosic bioethanol production to produce bioethanol directly from cellulosic biomass. However, few transcriptomic studies have been reported so far for C. thermocellum using biomass as carbon source. In this study, samples were taken from exponential and stationary phases of C. thermocellum cells growing in MTC media with pretreated switchgrass as carbon source, and transcriptomic profiling change of C. thermocellum during different growth phase was investigated using both expression array and tiling array. This study will help the understanding of gene expression of C. thermocellum using cellulosic biomass as carbon source and the knowledge will facilitate future metabolic engineering effort for strain improvement.

overall_design:
[HX12 expression array]: A eleven array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different growth phase of  T2 and T3 with switchgrass as carbon source. Two biological replicates used for each phase.
[3Plex tiling array]: A six array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different growth phase of  T2 and T3 with switchgrass as carbon source. Two biological replicates used for each phase.

last: Yang

first: Steven

middle: D

last: Brown

first: Lezlee

last: Dice


title: KC002-EH005:  Genetic and epigenetic features of induced pluripotent stem cell-derived dopaminergic neurons

status: Public on May 13 2014

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: Induced pluripotent stem cells (iPSCs) hold great promise for in vitro disease modeling and cell replacement therapy for Parkinson’s disease (PD). Both applications crucially require an in-depth profiling of the disease-relevant, iPSC-derived cell type. Midbrain dopaminergic (mDA) neurons derived from pluripotent stem cells are of substantial interest because of their instrumental value for PD therapy. IPSC-derived mDA neuron-like cells have been generated, however, detailed genetic and epigenetic characterization of strictly purified in vitro generated DA neurons has so far lagged behind.      We generated mouse Pitx3gfp/+ iPSC-derived DA neurons that, after fluorescent activated cell sorting (FACS) allowed comprehensive comparison to mesodiencephalic dopaminergic (mdDA) neurons from Fac-sorted Pitx3gfp/+ ventral midbrains. We performed detailed analysis of global gene expression and genome-scale DNA methylation of CpG islands (CGIs) by reduced representation bisulfite sequencing. The reprogramming pathway from fibroblasts to iPSCs left parental cell footprints for both gene expression and DNA methylation. However, most gene expression patterns of iPSC-derived DA neurons closely resembled that of primary mdDA neurons with the strongest correlations for mdDA specific genes. Also, for DNA methylation patterns, high similarities were found for the vast majority of CGIs when comparing primary mdDA neurons with iPSC-derived DA neurons. Additionally, we found de novo DNA methylation during in vitro differentiation for hundreds of genes specifically in lineage-committed neural precursors that persisted in iPSC-derived DA neurons.       Our study provides novel detailed characteristics of iPSC-derived DA neurons in comparison to the primary cell type. These findings add important information to our knowledge about these biomedically highly valuable, in vitro generated neurons.

overall_design: Microarray expression study comparing 3 samples of facs-sorted, Pitx3-gfp positive cells from each experimental group to a common reference consisting of adult mouse midbrain RNA. Each sample was analysed in normal and opposite dye orientation.

first: Reinhard

last: Roessler

first: Sebastien

last: Smallwood

first: Jesse

last: Veenfliet

first: Koushik

last: Chakrabarty

first: Petros

last: Pechlivanoglou

first: R

last: Pasterkamp

first: Gavin

last: Kelsey

first: Erik

last: Boddeke

first: Marten

last: Smidt

first: Sjef

last: Copray


title: Effects on gene expression in rat liver after administration of RXR agonists: UAB30, 4-methyl-UAB30, and Targretin

status: Public on May 14 2014

city: Bar Harbor

first: Peter

middle: Thomas

last: Vedell

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Examination of three retinoid X receptor (RXR) agonists [Targretin (TRG), UAB30, and 4-methyl-UAB30 (4-Me-UAB30)] showed that all inhibited mammary cancer in rodents and two (TRG and 4-Me-UAB30) strikingly increased serum triglyceride levels. Agents were administered in diets to female Sprague-Dawley rats. Liver RNA was isolated and microarrayed on the Affymetrix GeneChip Rat Exon 1.0 ST array. Statistical tests identified genes that exhibited differential expression and fell into groups, or modules, with differential expression among agonists. Genes in specific modules were changed by one, two, or all three agonists. An interactome analysis assessed the effects on genes that heterodimerize with known nuclear receptors. For proliferator-activated receptor α/RXR-activated genes, the strongest response was TRG > 4-Me-UAB30 > UAB30. Many liver X receptor/RXR-related genes (e.g., Scd-1 and Srebf1, which are associated with increased triglycerides) were highly expressed in TRG and 4-Me-UAB30- but not UAB30-treated livers. Minimal expression changes were associated with retinoic acid receptor or vitamin D receptor heterodimers by any of the agonists. UAB30 unexpectedly and uniquely activated genes associated with the aryl hydrocarbon hydroxylase (Ah) receptor (Cyp1a1, Cyp1a2, Cyp1b1, and Nqo1). Based on the Ah receptor activation, UAB30 was tested for its ability to prevent dimethylbenzanthracene (DMBA)-induced mammary cancers, presumably by inhibiting DMBA activation, and was highly effective. Gene expression changes were determined by reverse transcriptase-polymerase chain reaction in rat livers treated with Targretin for 2.3, 7, and 21 days. These showed similar gene expression changes at all three time points, arguing some steady-state effect. Different patterns of gene expression among the agonists provided insight into molecular differences and allowed one to predict certain physiologic consequences of agonist treatment.

overall_design: Three treatments were administered. Four samples were obtained for each of the 3 treatment groups for a total of 12 treatment samples. Four control samples were analyzed.

middle: T


title: Transcriptome Profiles in Normal Human Bronchial Epithelial Cells after Exposure to γ-rays and different HZE particles

status: Public on May 07 2014

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Distinct transcriptome profiles in response to low-LET and high-LET, and different radiation qualities of HZE particles.

overall_design: Total RNA obtained from HBEC3KT cells after 1, 4, 12 and 24 hours of radiation. Mock-irradiated samples at each time point and control samples before radiation (0 hour) were also collected.

first: Liang-Hao

first: Michael

last: Story


title: Global gene expression analysis of canine cutaneous mast cell tumor

status: Public on May 06 2014

city: Agripolis - Legnaro (PD)

first: Mery

last: Giantin

address: Viale Università, 16

department: Dip. Biomedicina Comparata e Alimentazione

institute: University of Padova

summary: In the present study, canine mast cell tumor (MCT) transcriptome was characterized in order to identify a set of candidate genes potentially useful for MCT classification and prognosis prediction. Fifty-one canine MCT biopsies were enrolled in the study. Isolated and purified total RNAs were individually hybridized to the Agilent Canine V2 4x44k DNA microarray. The comparison of reference differentiated and undifferentiated MCT transcriptome revealed a total of 597 differentially expressed genes (450 up-regulated and 147 down-regulated). The functional analysis of this set of genes provided evidence that they were mainly involved in cell cycle, DNA replication, p53 signaling pathway, nucleotide excision repair and pyrimidine metabolism. Class prediction analysis identified 13 transcripts providing the greatest accuracy of class prediction and divided samples into two categories (differentiated and undifferentiated MCTs). The molecular classification here used was prognostically significant, as the groups were directly correlated with survival time (p = 0.0026).

overall_design: In this study, we analyzed the gene expression profiles of 51 mast cell tumour samples using Agilent Canine V2 4x44k (G2519F, Design ID 021193) DNA microarray platform (60 arrays, 8 replicates) based on single-colour detection (Cyanine-3 only). Microarrays are scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides are scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal left, after all the FE processing steps have been completed, is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Anna

last: Granato

first: Mauro

last: Dacasto


title: R.palustris: cbbT1 overexpression and  cbbT2 overexpression

city: Taipei

first: Chia-Wei

last: Hu

address: No. 1, Sec. 4, Roosevelt Road

department: Institute of molecular and cellular biology

country: Taiwan

institute: National Taiwan university

summary: Transcriptional profiling of Rhodopseudomonas palustris (R. palustris) comparing cbbT1 over-expressing strain with cbbT2 over-expressing strain. Goal was to discriminate the molecular mechanisms between transketolase I (cbbT1) and transketolase II (cbbT2). R.palustris is a purple non-sulfur anoxygenic phototrophic bacterium and transketolase (cbbT1 and cbbT2) is a key enzyme involved in the CBB cycle. Here, we investogated the functions of transketolase isoforms I (cbbT1) and II (cbbT2) in R. palustris through transcriptional profiling and other functional assays.

overall_design: Four-condition experiment, cbbT1 over-expressing cells, cbbT2 over-expressing cells, Negative control strain with empty plasmid, Wild type strain.

first: Ya-Ling

last: Chang


title: miRNAs expression profiling in circulating lymphocytes of CML patients after imatinib discontinuation

city: tokyo

first: ohtsuki

last: kazushige

institute: tokyo medical university

summary: Some chronic myeloid leukemia (CML) patients with complete molecular response (CMR) are considered able to sustain the CMR after imatinib discontinuation (STOP-IM). Mahon et al. reported that among patients with a CMR lasting at least 2 consecutive years, the CMR was sustained in 41% after imatinib discontinuation. To more appropriately identify patients who can safely discontinue imatinib, we assessed the miRNA profiles of CML patients. We compared CML patients who sustained CMR for more than 6 months after discontinuation of imatinib (STOP-IM group) with those who were receiving imatinib with CMR (currently called as UMD: undetermined minimal disease), and with healthy volunteers (controls).

overall_design: Peripheral blood mononuclear cells (PBMCs) were harvested form 10ml of whole blood. Isolation of total RNA was performed using the mirVana PARIS kit (Ambion, Austin, TX, USA). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B were used as acontrol. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).


title: Escherichia coli K-12: luxS mutant LW12 vs. wild type W3110 under H2O2 stress

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

summary: Transcriptional profiling of Escherichia coli K-12 comparing luxS mutant LW12 with wild type W3110 exposure to 10mM or 30mM hydrogen peroxide.

overall_design: Two-condition experiment, luxS mutant LW12 vs. wild type W3110, treatment with 10mM hydrogen peroxide for 30min or treatment with 30mM hydrogen peroxide for 30min. Two biological replicates.

first: A

last: Kang

first: Matthew

last: Chang Wook


title: Cell-specific and spatio-temporal controls of the estrogen-responsive trefoil factor (TFF) locus activity.II.

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

summary: Cell-specific transcriptional regulations exerted by the estrogen (E2) receptor alpha (ER) heavily rely upon timely and spatially coordinated processes. We engaged a comparative analysis of such dynamic molecular events at the TFF locus harbouring a cluster of genes co-regulated by E2, in two distinct breast cancer cell lines. Using a combination of methods, we show that the recruitment of ER on cell-specific sites triggers dynamic local modifications of chromatin, which are coordinated in time all along the locus. DNA-FISH experiments further demonstrate that these changes are associated with an E2-dependent reduction in plasticity of this genomic region and are dependent upon cohesin. Importantly, 3C/4C experiments and the use of triplex forming oligonucleotides (TFOs) allowed us to precisely map the three-dimensional network of regulatory events that permits the estrogenic response of this genomic region. These data also evidenced an unexpected functional redundancy of enhancers.

overall_design: Samples (GSM587996-GSM588013): A 18 chip study aiming to characterize Estradiol (E2)-sensitive genes in MCF-7 and MDA::ER cells following 4h or 16h treatment with E2. RNAs were prepared from three independent triplicate experiments. Each of the three technical replicate correspond to pooled RNAs from 1 experiment. Controls for these experiments are 6 arrays corresponding to vehicle-treated MCF-7 and MDA::ER cells.

first: Justine

last: Quintin

first: Christine

last: LePéron

first: Gaelle

last: Palierne

first: Maud

last: Bizot

first: Stephanie

last: Cunha

first: Aurélien

last: Sérandour

first: Stéphane

last: Avner

first: Frédéric

last: Percevault

first: Sébastien

last: Huet

first: Erwan

last: Watrin

first: Jérome

last: Eeckhoute

first: Vincent

last: Legagneux

first: Gilles

last: Salbert


title: Identification of genomic loci associated with Rhodococcus equi susceptibility in foals

status: Public on May 10 2014

city: College Station

first: Cole

middle: M

last: McQueeen

address: 4467 VMRB

institute: Texas A&M University

summary: aCGH performed to identify copy number variants in Quarter Horses and perform casec-control GWAS

overall_design: Two-condition experiment, All samples were compared to a single Quarter Horse reference to identify copy number variants to be used in the CNV GWAS

last: McQueen

first: Ryan

last: Doan

first: Scott

middle: V

last: Dindot

first: Jessica

last: Bourquin

first: Zlatomir

middle: Z

last: Zlatev

first: M

last: Chaffin

first: Glenn

last: Blodgett

first: Ivan

last: Ivanov

first: Noah

last: Cohen


title: Cell-specific and spatio-temporal controls of the estrogen-responsive trefoil factor (TFF) locus activity

first: Raphaël

last: Métivier

type: Genome binding/occupancy profiling by genome tiling array

overall_design: Independent duplicate array series, using on one array pooled ChIP triplicates prepared from separate MDA::ER or MCF-7 cell cultures treated with estradiol for 50 minutes.

first: Justine

last: Quintin

first: Christine

last: Le Péron

first: Gaelle

last: Palierne

first: Maud

last: Bizot

first: Stephanie

last: Cunha

first: Aurelien

last: Serandour

last: Avner

first: Frederic

first: Sebastien


title: Evidence that variation in adult body size among mammalian species is achieved by modulating the pace of a growth-regulating genetic program

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Body size varies enormously among mammalian species. In small mammals, body growth is typically suppressed rapidly, within weeks, whereas in large mammals, growth is suppressed slowly, over years, allowing for a greater adult size. We recently reported evidence that body growth suppression in rodents is caused in part by a juvenile genetic program that occurs in multiple tissues simultaneously and involves the downregulation of a large set of growth-promoting genes. We hypothesized that this genetic program is conserved in large mammals but that its time course is evolutionarily modulated such that it plays out more slowly, allowing for more prolonged growth. Consistent with this hypothesis, using expression microarray analysis, we identified a set of genes that are downregulated with age in both juvenile sheep kidney and lung. This overlapping gene set was enriched for genes involved in cell proliferation and growth and showed striking similarity to a set of genes downregulated with age in multiple organs of the juvenile mouse and rat, indicating that the multiorgan juvenile genetic program previously described in rodents has been conserved in the 80 million years since sheep and rodents diverged in evolution. Using microarray and real-time PCR, we found that the pace of this program was most rapid in mice, more gradual in rats, and most gradual in sheep. The findings support the hypothesis that a growth-regulating genetic program is conserved among mammalian species but that its pace is modulated to allow more prolonged growth and therefore greater adult body size in larger mammals.

overall_design: Tissues samples were collect from Lung and Kindey respectively with five biological replications of sheep (Ovis aries) that were collected, frozen in liquid nitrogen, and stored at -70 °C and tested on bovine array.

first: Angela

last: Delaney

first: Julian

middle: K

last: Lui

first: Geoffrey

last: Rezvani

first: Weiping

first: Patricia

last: Forcinito

first: Crystal

middle: F

last: Cheung

first: Vasantha

last: Padmanabhan

first: Jeffrey

last: Baron


title: Effects of carbazole-degradative plasmid pCAR1 on biofilm morphology in three Pseudomonas strains.

city: Tokyo

first: Hideaki

last: Nojiri

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

department: Biotechnology Research Center

institute: The University of Tokyo

summary: To elucidate the impact of the carriage of carbazole-degradative plasmid pCAR1 on biofilm formation by host bacteria, we compared biofilm morphology of pCAR1-free and pCAR1-carrying three Pseudomonas hosts: P. putida KT2440, P. aeruginosa PAO1 and P. fluorescens Pf0-1 using confocal laser scanning microscopy. Although pCAR1 carriage had no significant influence on biofilm formed by PAO1 and Pf0-1, pCAR1-carrying KT2440 became filamentous and formed flat biofilm, whereas pCAR1-free KT2440 formed mushroom-like biofilm. pCAR1 carries three genes encoding nucleoid-associated proteins (NAPs); Pmr, Pnd, and Phu. Because intensive filamentous morphology was observed in two double mutants (DpmrDpnd and DpmrDphu), these NAPs cooperatively suppress cell filamentation and flat biofilm formation in KT2440(pCAR1) cells. Based on the results of transcriptome analyses of these double mutants, we could find 32 candidate genes which may be involved in the filamentation of KT2440(pCAR1). Overproduction in KT2440 and KT2440(pCAR1) of three of candidate genes (PP_2193, PP_0308, or PP_0309) induced temporal filamentation of the cells, suggesting that pCAR1 induced the abnormal filamentous morphology of KT2440 cells by overexpression of plural genes including PP_2193, PP_0308, and PP_0309. In addition, pCAR1-borne NAPs suppress the morphological changes probably by decreasing the transcriptome change by pCAR1 carriage.

platform_organism:
Pseudomonas
Pseudomonas putida KT2440

overall_design: The pCAR1 carriage impact of chromosomal RNA maps in biofilm formation.

first: Seunguk

last: Lee

first: Yurika

last: Takahashi

first: Hiromu

last: Oura

first: Kazunori

last: Okada

first: Hisakazu

last: Yamane

first: Nobuhiko

last: Nomura


title: A novel aCGH method for non-model organisms for assessing genomes and de-novo transcriptome sequencing reads (Staphylococcus aureus)

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

summary: Genomes and transcriptomes of non-model organisms can be analyzed using next-generation sequencing technologies, but de-novo sequencing and annotating a full eukaryotic genome is still challenging. So, -omics experimentation with non-model organisms requires a suite of technologies to obtain reliable results in a cost-effective manner. Here, a novel method for microarray-based genome analysis is presented which is especially suitable for non-model organisms. We show that it is useful for complementing regular aCGH analyses and for evaluating transcriptome next-generation sequencing reads. The principle of the method is straightforward: feature intensities obtained after hybridizing the test genome are compared with the feature intensities of a control hybridization. The control hybridization is performed with negative control probes (no targets in the control sample), and with positive control probes (with targets in the control sample). The method has in principle a resolution of a single probe and it does not depend on the structural information of a reference genome: the genomic ordering of probe targets is irrelevant. In a test, analyzing the genome content of a sequenced bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful demonstrated by receiver operating characteristic area under the curve values larger than 0.9995.

overall_design: DNA from eleven Staphylococcus aureus strains was extracted in three replicates, fragmented, and hybridized onto the S. aureus multistrain microarray. DNA from MRSA252 was used as common reference, but this channel was omitted in further analyses.

middle: J

first: Wim

last: de Leeuw

first: Marino

last: Marinković

first: Floyd

middle: R

last: Wittink

first: Han

last: Rauwerda

first: Oskar

last: Bruning

middle: A

last: Ensink

first: Ad

middle: C

last: Fluit

first: C

middle: H

last: Boel

first: Mark

last: de Jong

first: Timo

last: Breit


title: Targeted genetical genomic to identify genetic mechanisms affecting complex traits: example of meat pH in the chicken

status: Public on May 02 2014

city: Saint-Jean-sur-Richelieu

first: Javad

last: Nadaf

address: 84 Richelieu Street

institute: INRA,RI,DNALandmarks

summary:
Abstract:Genetical genomics has been suggested and proven to be a powerful approach to study the genotype-phenotype gap. However, the relatively low power of these experiments (usually related to the high cost) has hindered fulfilment of its promise, especially for loci (QTL) of moderate effects.  One strategy to overcome the issue is to use a targeted approach: to focus the experiment on one QTL of particular interest. It has two clear advantages: (i) It reduces the problem to a simple comparison between different genotypic groups at the QTL and (ii) it is a good starting point to investigate downstream effects of the QTL. In the present study, from 698 F2 birds used for QTL mapping, gene expression profiles of 24 (12 from each homozygote genotypes at the QTL) were investigated. The targeted QTL was located on chromosome 1 and affected initial pH of meat. The biological mechanisms controlling this trait can be similar to those affecting malignant hyperthermia or muscle fatigue in human.
The gene expression study identified ten strong local signals (potentially cis-eQTL) which were markedly more significant compared to the rest of the genome. The differentially expressed genes all mapped to a region < 1 Mb, suggesting a remarkable reduction of the QTL interval compared to the linkage study.  These results combined with analysis of downstream effect of the QTL (using gene network analysis) suggest that the QTL is controlling pH by governing oxidative stress.   The eQTL results were reproducible with using as few as 4 arrays on pooled samples (with lower significance level). The results demonstrate that this cost effective approach is promising not only for characterization of a QTL also for studying its downstream effects.

overall_design: there are 24 samples from to different genotypes. Each group of genotype has 12 samples. The two groups are compared using a dye balanced design.

first: Cecile

last: Berrie

first: Ian

last: Dunn

first: Elisabeth

last: Le Bihan-Duval

first: Dirk-Jan

last: De Koning


title: Genomic responses to arsenic in Synechocystis

city: Sevilla

first: Luis

last: Lopez Maury

address: Av Americo Vespucio 49

institute: IBVF

summary: Arsenic is an ubiquitous contaminant and a toxic metalloid which presents two main redox states in nature: arsenite [AsIII] and arsenate [AsV]. Arsenic resistance in Synechocystis sp. strain PCC 6803 is mediated by the arsBHC operon and two additional arsenate reductases encoded by the arsI1 and arsI2 genes. Here we describe the genome-wide responses in response to the presence of arsenate and arsenite in wild type and in mutants in the arsenic resistance system. Both forms of arsenic produced similar responses in the wild type strain including induction of several stress related genes and repression of energy generation processes. The responses observed in the arsB mutant strain were similar to the wild type in short term but were maintained in time while they were only transient in the wild type strain. In contrast, the responses observed in a strain lacking all arsenate reductases (the SARS12 strain) were somewhat different and included lower induction of genes involved in metal homeostasis and Fe-S cluster biogenesis. These results suggest that these two processes are targeted by arsenite in the wild type strain. Finally, analysis of the arsR mutant strain revealed that ArsR seems to only control 5 genes in the genome. Furthermore, over-expression of ArsB conferred hypersentivity to nickel, copper and cadmium in an arsR mutant strain.

overall_design:
Analysis of genome-wide gene expression patterns in response to arsenic in WT and mutants involved in arsenic detoxification in the cyanobacterium Synechocystis sp PCC 6803.
Cells treated with arsenate or arsenite for 1h.
Details:  WT cells were treated with 1 mM arsenite for 1 h and its expression profile compared to untreated cells (grown in BG11C media). The effects of arsenate were analyzed in the same way but using a modified BG11C media that constains 15% of the normal phosphate concentration (BG11C low phosphate). A reduction in the phosphate concentration in the media is essential to detect grow inhibition after arsenate addition. In the same way that for arsenite cells were treated with 50 mM arsenate for 1 h and their expression profile was compared to untreated cells. Expression profiles of mutant strains lacking arsB gene (SARSB strain; this strain is hypersensitive to arsenite because it lacks the arsenite exporter) or arsR gene (SARSR strain; this strain expresses the arsBHC constitutively) in control conditions and in response to arsenite addition were also analyzed. In addition the expression profiles of a mutant lacking arsenate reductases (SARS12 strain that has interrupted arsC, arsI1 and arsI2 genes; this strain is hypersensitive to arsenate) were analyzed in both control conditions and after addition of 50 mM arsenate.

first: Ana

last: Sanchez-Riego

first: Francisco

last: Florencio

last: Lopez-Maury


title: Control of shoot branching by Light quality in Arabidopsis plants (wt and brc1-2)

status: Public on May 11 2014

city: Campus de Cantoblanco

first: César

last: Poza-Carrión

address: Darwin 3

institute: CNB-CSIC

summary:
Plant architecture greatly depends on its branching patterns. Branches are formed from meristems initiated in the axils of leaves. Axillary meristems may develop immediately giving new shoots or they may become arrested after a short period of growth as dormant axillary buds. This decision is affected by endogenous and environmental factors. We are studying two Arabidopsis genes coding for TCP transcription factors, BRANCHED1 (BRC1) and BRANCHED2 (BRC2) that control this key decision. Several endogenous and environmental stimuli affect this process one of them is the quality of ambient light. Plants have developed sophisticated mechanisms that allow them to detect the presence of nearby plants and trigger responses of development to avoid the shade. This set of responses is known as shade avoidance. One response to this syndrome, with high agronomic relevance, is the suppression of branching. The genetic basis of this response is still largely unknown.
Our goal is to carry out, in Arabidopsis, a systematic study of the genetic control of the removal of branching during the escape response of the shadow. We found that Arabidopsis plants produce fewer branches when grown at high density. We also found that the removal of high-density branch is accompanied by up-regulation of BRC1. On the other hand, short light treatment enriched in far-red (which simulate the shade plant) also cause an accumulation of BRC1 mRNA levels in plants grown at low density. Besides initial data off transcriptomic analysis (wt vs. brc1-2) indicate that BRC1 could be involved in signaling / response to light in the axillary buds. In this study we have identified several potential target genes of BRC1 involved in the response to light. One is PIL2 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 2), a gene that encodes a bHLH transcription factor that interacts with APRR1/TOC1. We are currently characterizing in more detail at the genetic and molecular level the BRC1 relationship with this and other potential target genes and their role in the control of branching patterns.

overall_design: The microarray analysis was performed using RNA samples obtained from three independent plant pools grown under identical conditions. The cDNA synthesized from RNA of wild type or brc1-2 plants grown either in white light  (WT-WL, brc1-2-WL) or red+far red light (WT-FR, brc1-2-FR) was hybridized.

first: Pilar

last: Cubas


title: Trichostatin A does not correct specific errors of somatic cell nuclear transfer on the transcriptomic level; highlighing the non-random nature of oocyte-mediated reprogramming errors.

status: Public on May 03 2014

city: Isfahan

first: Sayyed Morteza

last: Hosseini

address: Royan Street

department: Embryology

country: Iran

institute: Royan Institute

summary: Bovine cloned and IVF blastocysts at day 7  were collected and used for comparative transcriptomics.

overall_design: A potent histone deacetylase inhibitor, Trichostatin A (TSA), was used to understand the effect of assisted epigenetic modification on the transcriptional profile of SCNT blastocysts and to identify specific genes or categories of genes affected in the developing embryos.

first: Sayyed

first: Isabelle

last: Dufort

first: Mehdi

last: Hajian

first: Farnoosh

last: Jafarpour

first: Somayyeh

last: Ostadhosseini

first: Julie

last: Nieminen

first: Mohammad

last: Nasr-Esfahani

first: Marc

last: Sirard


title: Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC28.1]

status: Public on May 01 2014

city: New York

first: Si

last: Li

state: New York

address: 12 Waverly Place

department: Biology

institute: New York University

summary: Dictyostelium discoideum, a microbial model for social evolution, is known to distinguish self from non-self and show genotype-dependent behavior during chimeric development. Aside from a small number of cell-cell recognition genes, however, little is known about the genetic basis of self/non-self recognition in this species. Based on the key hypothesis that there should be differential expression of genes if D. discoideum cells were interacting with non-clone mates, we performed transcriptomic profiling study in this species during clonal vs. chimeric development. Wild strains isolated from North Carolina, which have been shown to form a dominance hierarchy when co-developing in chimeras, were used. The transcriptomic profiles of D. discoideum cells in clones vs. different chimeras were compared at five different developmental stages using a customized microarray. Effects of chimerism on global transcriptional patterns associated with social interactions were observed. The chimera developmental program may also provide insights on behavioral changes associated with social conflicts in this species.

overall_design: two-condition chimera experiments: two conditions (chimeric: NC105.1-RFP + NC28.1 vs. control: NC105.1-RFP + NC105.1), five time points for each condition (4 h, 8 h, 12 h, 16 h, and 20 h), two biological replicates for each condition at each time point, two technical replicates for each biological replicate (Cy5 vs. Cy3)

middle: I

first: Michael

last: Purugganan


title: Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC63.2]

overall_design: two-condition chimera experiments: two conditions (chimeric: NC105.1-RFP + NC63.2 vs. control: NC105.1-RFP + NC105.1), five time points for each condition (4 h, 8 h, 12 h, 16 h, and 20 h), two biological replicates for each condition at each time point, two technical replicates for each biological replicate (Cy5 vs. Cy3)


title: Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC85.2]

overall_design: two-condition chimera experiments: two conditions (chimeric: NC105.1-RFP + NC85.2 vs. control: NC105.1-RFP + NC105.1), five time points for each condition (4 h, 8 h, 12 h, 16 h, and 20 h), two biological replicates for each condition at each time point, two technical replicates for each biological replicate (Cy5 vs. Cy3)


title: Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum

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

overall_design: Refer to individual Series


title: Sex- and population-specific hormetic responses to increasing dietary selenium in zebrafish (Danio rerio)

city: Moscow

first: Maia

last: Benner

state: Idaho

address: 875 Perimeter Drive

department: Biological Sciences

institute: University of Idaho

summary:
We tested the hypothesis that the behavioral response to selenium (Se) follows a hormetic dose response pattern, manifested through the functions of selenoproteins within the brain. We measured anxiety-related behaviors in zebrafish (Danio rerio) at deficient, control and supplemented levels of dietary Se, and measured the transcriptional response of selenoprotein genes important for neuroprotection. We also used a microarray approach to assess the transcriptomic response of the midbrain to Se.
The behavioral response to Se was characterized by hormesis, and the direction, magnitude, and shape of the hormetic responses were dependent on both sex and zebrafish population. Transcription of selenoproteins within the midbrain also responded to Se in a similar hormetic dose-dependent manner, with sex and population influencing the trajectory of the responses. The hormetic behavioral response to Se may therefore be manifested through selenoproteins in the brain, but the influence is not direct.

overall_design: We performed a microarray analysis comparing the midbrain-specific transcriptome between male zebrafish from two populations (Pargana: P and Transgenic Mosaic 1: T) fed either a control, Se deficient, or Se supplemented diet (17 total samples: 9 fish per population, 3 fish per diet: missing 1 P control sample).

first: Matt

middle: L

last: Settles

first: Gordon

last: Murdoch

first: Ron

last: Hardy

first: Barrie

last: Robison


title: Genetic stability in FA cells before and after gene editing and cell reprogramming.

city: Madrid

first: Javier

last: Suela

state: M

address: Faraday 7

institute: NIMGenetics

summary: Fibroblasts from a Fanconi anemia (FA) patient  (FA-52) before and after correction by gene editing and transduction with a lentiviral vector expressing telomerase (geFA-52T fibroblasts). IPCs were generated from fibroblasts corrected by gene editing using STEMCCA LV (geFA-52T IPSCs clone 16) and finally the reprogramming cassette was excised (excised geFA-52T IPSCs clone 16.1)

overall_design: Four groups: Fibroblasts from a FA patient  (FA-52) before and after correction by gene editing and transduction with a lentiviral vector expressing telomerase (geFA-52T) and gene editied IPSCs before and after excision of the reprogramming cassette (geFA-52T IPSCs clone 16 and excised geFA-52T IPSCs clone 16.1)

first: Paula

last: Rio

first: Juan

last: Bueren


title: Neoblast expression in head and tail regeneration

city: Evanston

first: Christian

middle: Paul

last: Petersen

state: IL

address: 2205 Tech Drive, Hogan 2-100

department: Molecular Biosciences

institute: Northwestern University

summary: X1 neoblasts (G2/S/M cells) were isolated by FACS from injury site-proximal tissue in a timeseries during head (anterior) and tail (posterior) regeneration in Schmidtea mediterranea

overall_design: 24 samples: 2 treatments (head versus tail regeneration), 3 timepoints (0,24,48,72 hours post amputation), 3 biological replicates each condition

first: C

last: Vasquez-Doorman


title: Implications of the miR-10 family in chemotherapy response of NPM1 mutated AML

city: Columbus

first: Ramiro

last: Garzon

address: 460 12th street

institute: Ohio State University

summary: Nucleophosmin mutated AML (NPM1mut-AML) patients have a high rate of complete remission (CR) to induction chemotherapy. However, the mechanisms responsible for such effects are unknown. Since miR-10 family members are expressed at high levels in NPM1mut-AML, we evaluated whether these microRNAs could predict chemotherapy response in AML. We found that high baseline miR-10 family expression in 54 untreated cytogenetically heterogeneous AML patients was associated with achieving CR. However, when we included NPM1 mutation status in the multivariable model, there was a significant interaction effect between miR-10a-5p expression and NPM1 mutation status. Similar results were observed when using a second cohort of 183 cytogenetically normal older (age≥60 years) AML patients.  Loss and gain of function experiments using miR-10a-5p in cell lines and primary blasts did not demonstrate any effect in apoptosis or cell proliferation at baseline or after chemotherapy. These data support a bystander role for the miR-10 family in NPM1mut-AML.

overall_design: Pretreatment miRNA expression was analyzed in 54 de novo adult AML patients obtained from the MD Anderson Cancer Center Leukemia Tissue Bank  (LTB) using the Ohio State University (OSU) miRNA microarray (ver.3).

first: Violaine

last: Havelange

first: Parvathi

last: Ranganathan

first: Susan

last: Geyer

first: Deedra

last: Nicolet

first: Xiaomeng

last: Huang

first: Xueyan

last: Yu

first: Stefano

last: Volinia

first: Steven

last: Kornblau

last: Andreeff

first: Carlo

last: Croce

first: Guido

last: Marcucci

first: Clara

last: Bloomfield


title: Expression analysis of E. coli DH1 after exposure with {C2mim]Cl

city: Emeryville

first: Marijke

last: Frederix

state: CA

address: 5885 Hollis Street

institute: JBEI

summary: Whole genome gene expression level changes in E. coli DH1 exposed to 150 mM [C2mim]Cl in mid exponential growth, and compared to a non-exposed strain.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Total RNA was isolated from three biological replicates for each condition: 150 mM [C2mim]Cl exposed at OD(600nm) 0.6, after 30 and 60 min, no exposure to [C2mim]Cl at OD(600 nm) 0.6 after 30 and 60 min.

first: Kimmo

last: Hutter

first: Aindrila

last: Mukhopadhyay


title: Transcriptional approach to study porcine tracheal epithelial cells individually or dually infected with swine influenza virus and Streptococcus suis

city: Mississauga

first: Claude

last: Lachance

state: Ontario

address: 1329 Meyerside Drive

institute: Bio-Rad

summary: Background: Swine influenza is a highly contagious viral infection in pigs affecting the respiratory tract that can have significant economic impacts. Streptococcus suis serotype 2 is one of the most important post-weaning bacterial pathogens in swine causing different infections, including pneumonia. Both pathogens are important contributors to the porcine respiratory disease complex. Outbreaks of swine influenza virus with a significant level of co-infections due to S. suis have lately been reported. In order to analyze a global response to the dual infection, we carried out a comprehensive gene expression profiling using a microarray approach to study the swine tracheal epithelial (NPTr) cell response to a co-infection with H1N1 swine influenza virus (swH1N1) and S. suis serotype 2. Results: Gene clustering showed that the swH1N1 and swH1N1/S. suis infections modified the expression of genes in a similar manner. Additionally, infection of NPTr cells by S. suis alone did not result in many differentially expressed genes compared to mock-infected cells. However, some important genes coding for inflammatory mediators, such as chemokines, interleukins, cell adhesion molecules and eicosanoids, were significantly upregulated in the presence of both pathogens comparing to infection with each pathogen taken individually. This synergy may also be the consequence of an increased adhesion/invasion of epithelial cells previously infected by swH1N1, as recently reported. Conclusion: In a co-infection situation, influenza virus would replicate in the respiratory epithelium inducing an inflammatory infiltrate comprised of mononuclear cells and neutrophils. Despite that these cells are unable to phagocyte and kill S. suis, they are highly activated by this pathogen. S. suis is not considered a primary pulmonary pathogen, but an exacerbated production of pro-inflammatory mediators during a co-infection with influenza virus may be of critical importance in the pathogenesis and outcome of this respiratory disease complex.

overall_design: Total RNA obtained from NPTr cells infected with S. suis, H1N1, or S. suis & H1N1. Four replicates in both groups.

first: Yuan

last: Dang

first: Yingchao

last: Wang

first: Carl

last: Gagnon

first: Christian

last: Savard

first: Mariela

last: Segura

first: Daniel

last: Grenier

first: Marcelo

last: Gottschalk