title: VSL#3 protects against development of visceral pain in the neonatal maternal separation model: A whole genome microarray study

status: Public on Jun 26 2013

city: Perugia

first: Stefano

last: Fiorucci

address: Via E dal Pozzo

institute: Universita di Perugia

summary:
Background & Aims: Irritable bowel syndrome (IBS) is a disorder characterized by chronic abdominal pain and is linked to post-inflammatory and  stress-correlated factors that cause changes in the perception of visceral events. Increased evidence indicates that probiotic bacteria may be useful in treating IBS. Our aims were to evaluate the efficacy of treatment with  VSL#3, a mixture of 8 probiotic bacteria strains,  in the neonatal maternal separation (NMS)-induced visceral hypersensitivity rat model and to determine whether it modulates the colonic expression of pain-related genes.

Methods: Male NMS pups were treated orally with placebo or VSL#3 at days 3-60, while normal, not separated  rats were used as control. After 60 days from birth, perception of  painful sensation induced by colorectal distension (CRD) was measured by assessing the abdominal  withdrawal reflex (score 0-4). The colonic gene expression analysis was assessed by using Agilent Whole Rat Genome Oligo Microarrays.

Results: NMS rats exhibited both hyperalgesia and allodynia when compared with controls.  VSL#3 showed a potent analgesic effect on CRD-induced pain without modifying  colorectal compliance. The microarray analysis demonstrated that NMS rats  had both over- and downregulation of several genes involved in inflammatory and painful processes and VSL#3 was able to counteract these alterations.

Conclusions: This study  indicates that VSL#3  is effective in reducing visceral pain in an experimental model of IBS by  induction or suppression of pain-modulating   genes. These observations provide support for the use of VSL#3 in the treatment of  painful conditions related to IBS.

overall_design: The dataset comprises 12 samples divided into three sample groups each representing a certain treatment condition of male rats.

first: Eleonora

last: Distrutti

first: Sabrina

last: Cipriani

first: Andrea

last: Mencarelli


title: Identification of WRKY22 targets under submergence in Arabidopsis (mRNA)

status: Public on Jul 03 2013

city: Taipei

first: Fu-Chiun

last: Hsu

address: No. 128, Sec. 2, Academia Road, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

summary: We analyzed global transcriptional changes in submerged Arabidopsis seedlings comparing control untreated seedlings.  The same analysis were also applied on wrky22-ko2 seedling to identify WRKY22 targets under submergence.

overall_design: Time course experiments (1, 3, and 6 for Columbia and wrky22-ko2).  Tissues from submerged seedlings vs. Tissues from un-submerged seedlings.  Biological replicates: 4 replicates for each time point, independently grown, treated, and harvested. One replicate per array.  2 of 4 replicates are dye-swapped.

first: Hsu

last: Fu-Chiun

first: Chou

last: Mei-Yi

first: Peng

last: Hsiao-Ping

last: Shu-Jen

first: Shih

last: Ming-Che


title: Expression data from murine skin of tamoxifen-induced Ugcgfl/fl K14CreERT2 vs. Ugcgfl/fl

status: Public on Jun 12 2013

city: Heidelberg

first: Nicole

last: Amen

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

summary: Tamoxifen-induced deletion of endogenous GlcCer-synthesizing enzyme UDP-glucose:ceramide glucosyltransferase (UGCG) in keratin K14-positive cells results in epidermal GlcCer depletion. We used microarrays to investigate the molecular consequences of Ugcg-depleted mouse epidermis.

overall_design: Ugcgfl/fl K14CreERT2 vs. Ugcgfl/fl samples taken at day 21 post tamoxifen induction


title: Right ventricular failure due to pulmonary banding

status: Public on Jun 11 2013

city: Uppsala

first: Per

last: Vikholm

address: Akademiska sjukhuset

department: Cardiothoracic Surgery

country: Sweden

institute: Uppsala University

summary: Right ventricular failure was induced thourgh pulmonary banding in 11 pigs. Right ventricular failure was defined as a SRVP >50 mmHg during two hours. After right ventricular failure was induced, half the pigs were treated with a Glenn-shunt combined with pulmonary banding for one hour, and the other half served as control group with pulmonary banding only. The aim was to study the change in global gene expression during right ventricular failure due to pulmonary banding, and the effect of volume unloading during pulmonary banding.

overall_design:
11 pigs. Samples at the following time periods: 1) Baseline 2) Right ventricular failure 3) Treatment with modified Glenn-shunt/Control. After Right ventricular failure, pigs were randomized into two groups
a) Treatment with modified Glenn-shunt or b) Control group

first: Petter

last: Schiller

first: Laila

last: Hellgren


title: Cooperative function of the three different kinds of nucleoid-associated proteins encoded on the IncP-7 plasmid pCAR1

status: Public on Dec 07 2013

city: Tokyo

first: Hideaki

last: Nojiri

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

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

type: Expression profiling by genome tiling array

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

platform_organism:
Pseudomonas
Pseudomonas putida KT2440

overall_design: Refer to individual Series


title: Distinct transcriptional networks in quiescent myoblasts: a role for Wnt signaling in reversible vs irreversible arrest

status: Public on Apr 16 2013

city: SAN ANTONIO

first: PRETHISH

last: SREENIVAS

state: TX

address: 8403 Floyd Curl Dr

department: GCCRI

country: USA

institute: UTHSCSA

summary: Using cDNA arrays, we compared G0 myoblasts (S48) with post-mitotic myotubes. Our findings define the transcriptional program of quiescent myoblasts in culture which show important similarities with muscle satellite cells, and establish that distinct gene expression profiles characterize irreversible and reversible arrest

overall_design: Cell were synchronized in G0 by resuspending them in semi-solid media for 48  hours and harvested for RNA isolation

first: Sindhu

last: Subramanian

first: Prethish

last: Sreenivas

first: Sirisha

last: Cheedipudi

first: V

middle: R

last: Reddy

first: L

middle: S

last: Shashidhara

first: C

last: Kumar

first: Madhavi

last: Mylavarapu


title: Transmission of xanthomonads to Medicago truncatula seeds

status: Public on Jul 31 2013

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

summary: Plant pathogenic bacteria disseminate and survive through transmission to and by seeds of hosts and non-hosts plants. To investigate the interaction between xanthomonads and developing seeds of Medicago truncatula,   plants at the ﬂower bud stage were spray inoculated until runoff with xanthomonads suspensions. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed on seeds to characterize the molecular dialogue between Xanthomonas campestris pv. campestris in an incompatible situation with M. truncatula seeds and Xanthomonas alfalfae pv. alfalfae in a compatible situation at two developmental time points (16 and 32 days atfter pollination (DAP).

overall_design: Six-condition experiment, 16dap_Mock versus 16dap_Xaa, 16dap_Mock versus 16dap_Xcc, 32dap_Mock versus 32dap_Xaa, 32dap_Mock versus 32dap_Xcc. Biological replicates: 6 controls (16dap_Mock, 32dap_Mock), 12 treatments (16dap_Xaa, 16dap_Xcc, 32dap_Xaa, 32dap_Xcc), independently grown and harvested. One replicate per array.

first: Emmanuel

last: Terrasson

first: Olivier

last: Leprince

first: Marie-Agnès

last: Jacques

first: Julia

last: Buitink


title: DNA methylation profiles across different brain regions in Alzheimer disease mice models

status: Public on Sep 16 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal and disease samples from different mice models. A custom Illumina Golden Gate DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 800 CpGs.

overall_design: Bisulphite converted DNA from the 35 samples were hybridised to the Illumina custom golden gate DNA methylation array.

first: Jose

middle: V

last: Sanchez-Mut


title: Gene expression analysis of human heart valves

status: Public on Apr 06 2013

city: Boeblingen

first: Shannon

last: Layland

address: Nobelstrasse 12

institute: Fraunhofer IGB

summary: Semilunar valve leaflets have a well-described trilaminar histoarchitecture with a sophisticated elastic fiber network. It was previously proposed that elastin-containing fibers play a subordinate role in early human cardiac valve development; however, this assumption was based on data obtained from mouse models and human second and third trimester tissues. Here, we systematically analyzed tissues from human fetal first (4-12 weeks) and second (13-18 weeks) trimester, adolescent (14-19 years) and adult (50-55 years) hearts to monitor the temporal and spatial distribution of elastic fibers, focusing on semilunar valves. Global gene expression analyses revealed that the transcription of genes essential for elastic fiber formation starts early within the first trimester. These data were confirmed by quantitative PCR and immunohistochemistry employing antibodies that recognize fibronectin, fibrilin-1, -2 and -3, EMILIN-1, fibulin-4 and fibulin-5, which were all expressed at the onset of cardiac cushion formation (~week 4 of development). Tropoelastin/ elastin protein expression was first detectable in leaflets of 7-week hearts.   We revealed that immature elastic fibers are organized in early human cardiovascular development, and mature elastin-containing fibers first evolve in semilunar valves when blood pressure and heartbeat accelerate. Our findings provide a conceptual framework with the potential to lead to novel hypotheses in human cardiac valve development and disease.

overall_design: Total RNA obtained from fetal cardiac valve cushions, developed fetal heart valves, adolescent heart valves, and adult heart valves.

first: Katja

last: Schenke-Layland

first: Miriam

last: Votteler


title: Expression data from Shox2 knockout and wildtype right atria of E11.5 mouse hearts

status: Public on Jun 03 2013

last: Hoffmann

address: Im Neuenheimer Feld 366

department: Department of Human Molecular Genetics

institute: Institute of Human Genetics

summary:
The heart’s rhythm is initiated and regulated by a group of specialized cells in the sinoatrial node (SAN), the primary pacemaker of the heart. Abnormalities in the development of the SAN can result in irregular heart rates (arrhythmias). Although several of the critical genes important for SAN formation have been identified, our understanding of the transcriptional network controlling SAN development remains at a relatively early stage. The homeodomain transcription factor Shox2 plays an essential early role in the specification and patterning of the SAN.
Here, we compared gene expression levels in the right atria of wildtype and Shox2-/- hearts using microarray experiments to identify Shox2 target genes.

overall_design: Right atria of E11.5 mouse embryos were dissected and genotyped for RNA extraction. RNA from 6 embryos and 2 independent pregnancies was pooled per genotype (Wildtype and Shox2 Knockout) and compared.

first: Norbert

last: Gretz


title: Gene expression of Alveolar Soft Part Sarcomas [mRNA]

status: Public on Apr 12 2013

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: Alveolar soft part sarcoma (ASPS) is a soft tissue sarcoma with poor prognosis. We analysed primary and metastatic ASPS samples to elucidate candidate molecular pathways involved in tumor pathogenesis. Differential gene expression analysis revealed the neural origin for ASPS and implication of fusion genes expression in the pathogenesis of ASPS.

overall_design: Total RNA was extracted, cleaned up, and eluted using the RNeasy MiniKit and RNeasy MinElute Cleanup Kit, respectively (Qiagen), according to the manufacturer’s protocol. The total RNA yield per sample ranged from 191ng to 2ug. cDNA-mediated annealing, selection, ligation, and extension (DASL) expression assay (Illumina) was performed as per manufacturer’s instructions on a panel comprising 24,526 probes for a total of 18,631 genes (Human Ref-8 Expression; BeadChip).

first: Richie

last: Flavin

first: Saumyadipta

last: Pyne


title: Gene Expression Analysis of Postnatal Day 6 Testes Sired by Paternally Exposed Males to Saline or BEP

status: Public on May 15 2013

city: Montreal

first: Jennifer

last: Maselli

state: Quebec

address: 3655 Prom Sir William Osler

country: Canada

institute: McGill University

summary: To determine the changes in gene expression of testes from postnatal day 6 pups, a window in development where spermatogonial stem cells is predominant, following paternal exposure to saline or BEP, a chemotherapeutic coktail used to treat testicular cancer

overall_design: Postnatal day 6 testes (2) of pups sired by males treated with saline (n=5) or BEP (n=5) for a 9 weeks followed by a 9-week recovery period

first: Barabara

middle: F

last: Hales

first: Bernard

last: Robaire


title: Reconstruction of the Mycobacterium tuberculosis Regulatory Network and Deconstruction of the Hypoxic Response

status: Public on Jan 12 2013

city: Seattle

first: Tige

last: Rustad

state: WA

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

institute: Seattle Biomedical Research Institute

summary:
Expression data from hypoxic time course and transcription factor over expression experiments.
(Abstract from paper will be appended after publication)

overall_design: Hypoxic time course experiments were done with a minimum of 3 replicates. TFOE are matched to the ChIP-seq experiment done simultaneously. This submission consists of the the gene expression component only.

first: Kyle

last: Minch

first: David

last: Sherman


title: Intra-tumoral heterogeneity in metastatic potential and survival signaling between iso-clonal HCT116 and HCT116b human colon carcinoma cell lines

status: Public on Feb 20 2013

city: Omaha

first: Sanjib

last: Chowdhury

state: Nebraska

address: 985950 Nebraska Medical Center

institute: University of Nebraska Medical Center

summary: Characterization of the intra-tumoral heterogeneity between two iso-clonal human colon cancer sublines HCT116 and HCT116b on their ability to undergo metastatic colonization and survive under growth factor deprivation stress (GFDS). Microarray analysis revealed an upregulation of survival and metastatic genes in the highly metastatic HCT116 primary colon tumor cells compared to the poorly metastatic HCT116b primary colon tumor cells.

overall_design: Total RNA obtained from isolated primary colon tumors of HCT116 and HCT116b xenograft transplanted animals obtained using the orthotopic implantation of HCT116 and HCT116b human colon cancer xenografts in the cecum of male athymic BALB/c nude mice were compared at their gene expression level.

first: Ashwani

last: Rajput


title: HAC1 protein arrays

status: Public on Nov 15 2012

city: Durham

first: Nikoleta

middle: G

last: Tsvetanova

state: NC

address: 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

summary:
Binding of in vitro synthesized HAC1 mRNA was studied using protein microarray. 3 replicates, plus 3 reverse dye replicates
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
is_reverse: no: HAC1 mRNA Cy5 labeled; yes: HAC1 mRNA Cy3 labeled


title: Ypt1 IPs

summary:
Yeast strains expressing either GST-tagged or untagged Ypt1 were grown in either normal media or in media treated with 10mM DTT, to induce UPR
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
GeneticModification: GST tagged/untagged YPT1
Media: DTT present/absent in media

platform_organism:
Methanocaldococcus jannaschii
Saccharomyces cerevisiae


title: Gene-expression profiles of formalin-fixed, paraffin-embedded human intrahepatic cholangiocarcinoma

status: Public on Jan 24 2013

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
BACKGROUND & AIMS: Cholangiocarcinoma, the second most common liver cancer, can be classified as intrahepatic (ICC) or extrahepatic. We performed an integrative genomic analysis of ICC samples from a large series of patients.
METHODS: We performed gene expression profile, high-density single nucleotide polymorphism array, and mutation analyses using formalin-fixed ICC samples from 149 patients. Associations with clinico-pathological traits and patient outcomes were examined for 119 cases. Class discovery was based on a non-negative matrix factorization algorithm and significant copy number variations (CNV) were identified by GISTIC analysis. Gene set enrichment analysis was used to identify signaling pathways activated in specific molecular classes of tumors, and to analyze their genomic overlap with hepatocellular carcinoma (HCC).
RESULTS: We identified 2 main biological classes of ICC. The inflammation class (38% of ICCs) is characterized by activation of inflammatory signaling pathways, overexpression of cytokines, and STAT3 activation. The proliferation class (62%) is characterized by activation of oncogenic signaling pathways (including RAS, mitogen-activated protein kinase, and MET), DNA amplifications at 11q13.2, deletions at 14q22.1, mutations in KRAS and BRAF, and gene expression signatures previously associated with poor outcomes for patients with HCC. CNV-based clustering was able to further refine these molecular groups. We identified high-level amplifications in 5 regions, including 1p13 (9%) and 11q13.2 (4%), and several focal deletions, such as 9p21.3 (18%) and 14q22.1 (12% in coding regions for the SAV1 tumor suppressor). In a complementary approach, we identified a gene expression signature that was associated with reduced survival times of patients with ICC; this signature was enriched in the proliferation class (P<0.001).
CONCLUSIONS: We used an integrative genomic analysis to identify 2 classes of ICC. The proliferation class has specific copy number alterations, many features of the poor-prognosis signatures for HCC, and is associated with worse outcome. Different classes of ICC, based on molecular features, might therefore require different treatment approaches.

overall_design: Gene-expression profiling was performed using formalin-fixed, paraffin-embedded intrahepatic cholangiocarcinoma tissues obtained at the time of surgical resection.

first: Daniela

last: Sia

first: Augusto

last: Villanueva

first: Vincenzo

last: Mazzaferro

first: Jordi

last: Bruix

first: Myron

last: Schwartz

first: Josep

middle: M

last: Llovet


title: Expressed sequences and polymorphisms in rohu carp (Labeo rohita, Hamilton) revealed by mRNA-seq

status: Public on Jan 01 2013

city: Ås

first: Matthew

last: Baranski

address: Osloveien 1

country: Norway

institute: Nofima Marin

type: Expression profiling by high throughput sequencing

type: Genome variation profiling by high throughput sequencing

summary: An integrated approach was used to identify genes associated with resistance to Aeromonas hydrophila, an important bacterial pathogen causing aeromoniasis in rohu Labeo rohita. DNA polymorphism and gene expression profiling in lines of L. rohita selected for resistance or susceptibility to challenge with A. hydrophila, and grown in a common environment, were studied using Illumina mRNA-seq of selectively pooled RNA samples.

overall_design: mRNA-seq of pooled samples from resistant and susceptible lines of rohu for expression characterisation and SNP detection

first: Nicholas

last: Robinson

first: Pramoda

middle: K

last: Sahoo

first: Kanta

last: Das Mahapatra

first: Jatindra

middle: N

last: Saha

first: Sweta

last: Das

first: Yashowant

last: Mishra

first: Paramananda

first: Hirak

last: Barman

first: Ambekar

middle: E

last: Eknath


title: Adaptor candidates

first: Nikoleta

last: Tsvetanova

summary:
IP of candidate adaptor Ada5/Gdi1, tagged with HA, versus Mock (untagged) replicates. IP associated RNA was assayed.
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
GeneticModification: HA-tagged candidate gene or control


title: Knockdown strains

summary:
Expression profiling of Ypt1/Sec12 knockdown versus isogenic parental wild type BY4741:
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out.


title: Ypt1, Ada5/Gdi1, studies


title: Integrative Molecular Analysis of Intrahepatic Cholangiocarcinoma Reveals 2 Classes That Have Different Outcomes

first: Yujin

last: Hoshida

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

summary:
BACKGROUND & AIMS: Cholangiocarcinoma, the second most common liver cancer, can be classified as intrahepatic (ICC) or extrahepatic. We performed an integrative genomic analysis of ICC samples from a large series of patients.
METHODS: We performed gene expression profile, high-density single nucleotide polymorphism array, and mutation analyses using formalin-fixed ICC samples from 149 patients. Associations with clinico-pathological traits and patient outcomes were examined for 119 cases. Class discovery was based on a non-negative matrix factorization algorithm and significant copy number variations (CNV) were identified by GISTIC analysis. Gene set enrichment analysis was used to identify signaling pathways activated in specific molecular classes of tumors, and to analyze their genomic overlap with hepatocellular carcinoma (HCC).
RESULTS: We identified 2 main biological classes of ICC. The inflammation class (38% of ICCs) is characterized by activation of inflammatory signaling pathways, overexpression of cytokines, and STAT3 activation. The proliferation class (62%) is characterized by activation of oncogenic signaling pathways (including RAS, mitogen-activated protein kinase, and MET), DNA amplifications at 11q13.2, deletions at 14q22.1, mutations in KRAS and BRAF, and gene expression signatures previously associated with poor outcomes for patients with HCC. CNV-based clustering was able to further refine these molecular groups. We identified high-level amplifications in 5 regions, including 1p13 (9%) and 11q13.2 (4%), and several focal deletions, such as 9p21.3 (18%) and 14q22.1 (12% in coding regions for the SAV1 tumor suppressor). In a complementary approach, we identified a gene expression signature that was associated with reduced survival times of patients with ICC; this signature was enriched in the proliferation class (P<0.001).
CONCLUSIONS: We used an integrative genomic analysis to identify 2 classes of ICC. The proliferation class has specific copy number alterations, many features of the poor-prognosis signatures for HCC, and is associated with worse outcome. Different classes of ICC, based on molecular features, might therefore require different treatment approaches.

This SuperSeries is composed of the SubSeries listed below.

first: Daniela


title: Comparison of the genomic structures between S. cerevisiae strains ZGR3 and BYZ1

status: Public on Oct 10 2012

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

type: Genome variation profiling by genome tiling array

summary: To determine how does genomic structural variation changed the phenotypes of yeast. aCGH and RNA-Seq were performed to reveal the differeces in the genomic structures and transcription of ZTW1 and ZGR3.

overall_design: In the aCGH experiment, strain BYZ1 (S288c background) was used as the control. In the RNA-Seq experiment, the total RNA from three independent cultured cells of each yeast strain was extracted. Three cDNA libraries of one sample were mixed before sequencing.


title: genetic interactions

summary:
Strains lacking indicated genes were transformed with GST-YPT1.  Ypt1p was IPd with anti-GST ab and associated rna was analyzed.
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out.
GeneticModification: gene deleted from parent strain


title: Young and old HSCs from WT and Lnk-/- mice

status: Public on Oct 03 2012

city: Philadelphia

first: Wei

last: Tong

state: PA

address: 316A Abramson Bldg., 3615 Civic Center Blvd.

department: Pediatrics

institute: Children's Hospital of Philadelphia, and University of Pennsylvania School of Medicine

summary: The adaptor protein Lnk is an important negative regulator of HSC homeostasis and self-renewal. This study aims to investigate the role of Lnk in HSC aging. Here we performed expression profiling of bone marrow CD150+CD48-LSK LT-HSCs from young and old WT and Lnk-/- mice. Results identify select Lnk-mediated pathways with potential involvement in HSC self-renewal and aging.

overall_design: CD150+CD48-LSK HSCs were double sorted from WT and Lnk-/- mice at both young and old ages (2 months and 20 months, respectively). RNA was isolated using miRNeasy kit from QIAGEN and processed using the NuGEN Pico kit. The microarray analysis was performed at the Penn Molecular Profiling/Genomics Facility using GeneChip Mouse Gene 1.0ST array (Affymetrix).

first: Alexey

last: Bersenev

first: Krasimira

last: Rozenova

first: Joanna

last: Balcerek

first: Jing

last: Jiang

first: Chao

last: Wu


title: Loss of heat shock protein HSPA4 aggravates pressure overload-induced myocardial damage

city: Goettingen

first: belal

middle: Awd

last: Mohamed

state: Lower Saxony

address: Heinrich Dueker Weg 12

department: Institute of Human Genetics

institute: Medical university, Goettingen

summary: Failure of molecular chaperones to direct the correct folding of newly synthesized proteins leads to the accumulation of misfolded proteins in cells. HSPA4 is a member of the heat shock protein 110 family (HSP110) that acts as a nucleotide exchange factor of HSP70 chaperones. We found that the expression of HSPA4 is upregulated in murine hearts subjected to pressure overload and in failing human hearts. To investigate the cardiac function of HSPA4, Hspa4 knockout (KO) mice were generated and exhibited cardiac hypertrophy and fibrosis. Hspa4 KO hearts were characterized by a significant increase in heart weight/body weight ratio, elevated expression of hypertrophic and fibrotic gene markers, and concentric hypertrophy with preserved contractile functions. Cardiac hypertrophy in Hspa4 KO hearts was associated with enhanced activation of gp130-STAT3, CaMKII, and calcineurin-NFAT signaling. Further analyses revealed a significant increase in cross sectional area of cardiomyocytes, and in expression levels of hypertrophic markers in cultured neonatal Hspa4 KO cardiomyocytes suggesting that the hypertrophy of mutant mice was a result of primary defects in cardiomyocytes. Gene expression profile in hearts of 3.5-week-old mice revealed a differentially expressed gene sets related to ion channels and stress response. Taken together, these results reveal that HSPA4 is implicated in protection against pressure overload-induced heart failure.

overall_design: Total RNA was extracted from heart ventricles of 3.5-week-old Hspa4+/+ and Hspa4-/- males (n = 3 mice for each genotype).

first: Belal

first: Amal

last: Barakat

first: Wolfram-Hubertus

last: Zimmermann

first: Reginald

last: Bittner

first: Christian

last: Mühlfeld

first: Mark

last: Hünlich

first: Wolfgang

last: Engel

first: Lars

last: Maier

first: Ibrahim

last: Adham


title: Differentiated mouse podocytes (SVI)

status: Public on Oct 16 2012

city: Rostock

first: Gregor

last: Warsow

address: Ernst-Heydemann-Str. 8

department: Medical Department

institute: University of Rostock

summary:
Transcriptomes of differentiated cells of the conditionally immortalized mouse podocyte cell line SVI (Schiwek et al., Kidney Int. 66: 91-101, 2004) were determined as described in Kabgani et al. (PLoS One 7:e34907, 2012).
The transcriptomes of the podocyte cell line were mapped on a protein-protein interaction network of the podocyte (PodNet). Together with other transcriptomes taken from GEO, we analyzed differential gene regulation and differential regulation of protein-protein interactions between cultured podocytes and differentiated in vivo podocytes.

overall_design: Three independent batches were used.

first: Eric

last: Schordan

first: Sandra

first: Ravi

last: Chilukoti

first: Georg

last: Homuth

last: Fuellen

first: Nicole

last: Endlich

first: Karlhans


title: Apoptosis rate and transcriptional response of pancreatic islets exposed to the PPAR gamma agonist Pioglitazone

status: Public on Aug 16 2012

city: Columbus

first: Peter

last: White

state: OH

address: 700 Children's Drive

department: Microbial Pathogenesis

institute: Nationwide Children's Hospital

summary: To explore the molecular pathways underlying thiazolidinediones effects on pancreatic islets in conditions mimicking normo- and hyperglycemia, apoptosis rate and transcriptional response to Pioglitazone at both physiological and supraphysiological glucose concentrations were evaluated.

overall_design: Adult rat islets were cultured at physiological (5.6 mM) and supraphysiological (23 mM) glucose concentrations in presence of 10 mM Pioglitazone or vehicle. RNA expression profiling was evaluated with the PancChip 13k cDNA microarray after 24-h, and expression results for some selected genes were validated by qRT-PCR.

first: R

last: Lamounier

first: C

last: Coimbra

first: P

first: F

middle: L

last: Costal

first: L

last: Oliveira

first: D

last: Giannella-Neto

first: K

middle: H

last: Kaestner

first: M

last: Correa-Giannella


title: Transcriptomic profiling of formalin-fixed, paraffin-embedded human sarcoma specimens

status: Public on Jul 24 2012

city: Boston

first: Katherine

last: Hill

state: MA

address: 330 Brookline Avenue, DA-679

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary: A study which uses gene expression profiles to infer relative changes in miRNA activity across biological conditions (i.e. tumor versus normal)

overall_design: Fifteen unique human FFPE soft tissue sarcoma samples used for profiling with eight of them run in technical duplicate

first: Andrew

last: Kelly


title: Whole genome expression profiling based on paraffin embedded tissue can be used to classify diffuse large b-cell lymphoma and predict clinical outcome

status: Public on Sep 19 2012

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

summary: Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies for 172 patients with diffuse large b-cell lymphoma (DLBCL) using the Illumina DASL platform.  Classification into GCB, ABC or Type-III subtypes was carried out revealing a significant relationship between subtype and survival.

overall_design: A retrospective study of 172 patients, 140 treated with R-CHOP, 32 not treated with curative intent

first: Sharron

last: Barrans

middle: A


title: Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HumanRef-v3 samples]

status: Public on Oct 02 2012

city: Herston

first: Amy

middle: McCart

last: Reed

state: Queensland

address: Royal Brisbane & Women's Hospital Campus

department: UQ Centre for Clinical Research

country: Australia

institute: University of Queensland

summary: We performed an expression profiling study of 168 primary breast tumors, lymph node metastases, and autopsy samples of primary breast tumours and metastases to liver, chest wall, lymph node, lung, and spleen, as well as positive and negative RNA controls, with technical replicates, to assess quality control methodology and probe-level reproducibility of the Illumina DASL microarray assay.  The experiment included both Illumina DASL HumanRef-v3 and DASL HT-12; this series includes only the 120 HumanRef-v3 samples .

overall_design: This series includes 120 samples in total: 19 autopsy tissues of the chest wall, liver, lymph nodes, lung, spleen, liver, and breast, 5 negative controls, 6 positive controls, and 90 lymph node metastases.

middle: T

last: Simpson

first: Ana

middle: C

last: Vargas

first: Margaret

last: Cummings

first: Sunil

last: Lakhani

first: Levi

middle: D

last: Waldron


title: Gene expression profiling of colorectal tissues in the early adenoma-carcinoma sequence

status: Public on Aug 25 2012

city: Leicester

first: James

middle: Howard

last: Pringle

state: Leicestershire

address: Robert Kilpatrick Clinical Sciences Building Leicester Royal Infirmary

department: Department of Cancer Studies and Molecular Medicine

institute: University of Leicester

summary: Colorectal cancer (CRC) is the third most common cancer worldwide. Colorectal polyps are recognised pre-cursors of CRC, however hyperplastic polyps lack malignant potential. The purpose of this study was to identify differences in gene expression between normal colonic mucosa, hyperplastic and adenomatous polyps from disease-free individuals. By comparing polyps believed to have malignant potential (adenomatous polyps) with hyperplastic polyps it is hoped that new insights into colorectal carcinogenesis can be achieved.

overall_design: 24 colonic samples comprising 8 normal colonic mucosa, 8 hyperplastic polyps and 8 adenomatous polyps.

first: Katie

last: Thomas

first: Kevin

middle: P

last: West

first: Jacqui

last: Shaw


title: Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues

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

overall_design: Refer to individual Series

first: Peter

middle: R


title: Expression data from one-year-old leaves of Populus simonii treated with short-term water deficit

status: Public on Apr 27 2012

city: Beijing

first: Jin

middle: Hui

last: Chen

state: Beijing

address: No. 35, Qinghua East Road

department: College of Biological Sciences and Biotechnology, Beijing Forestry University

institute: Beijing Forestry University

summary: We take one-year-old plants for short-term water deficit treatments and controls. We use the Affymetrix Poplar GeneChip to decrypt the gene functions and mechanisms in Populus simonii leaves and detail the global program of gene expression during water deficit treatments.

overall_design: Populus simonii leaves were taken from short-term water-deficit-treated plants and control plants for RNA extraction and hybridization on Affymetrix microarrays. D1 and D2 are from water-deficit-treated plants, CK1 and CK2 are controls.

first: Jinhui

first: Deqiang

last: Zhang

first: He


title: Expression profiling of archival tissues for long-term health studies

address: 655 Huntington Avenue

department: Biostatistics

institute: Harvard School of Publich Health

summary: Over 20 million archival tissue samples are stored annually in the United States as formalin-fixed, paraffin-embedded (FFPE) tissue blocks, but only recently has whole-genome expression profiling from these samples become technically feasible. Here, we introduce novel general methods for assessing, summarizing, and visualizing expression data quality from archival samples. We validated these methods in technical study of 144 clinical breast cancer and autopsy samples and in an overview of all current publicly available FFPE whole-genome expression data. We additionally performed a case study incorporating over 1,000 colorectal cancer (CRC) samples collected from patients across the United States over a period of more than 25 years, integrating clinicopathological information, tumor molecular data, and archival tissue gene expression on an unparalleled scale. Both large-scale clinical studies presented a much greater range of data quality than previous smaller studies, emphasizing the need for rigorous quality control in translational applications of archival tissue gene expression profiling.

overall_design: This series includes 1,003 FFPE-preserved CRC tumors, assayed by Illumina HumanRef-v3 WG-DASL microarray.

first: Shuji

last: Ogino

first: Yujin

last: Hoshida

first: Kaori

last: Shima

first: Yoshifumi

last: Baba

first: Katsuhiko

last: Nosho

first: Todd

last: Golub

first: Charles

middle: S

last: Fuchs

first: Giovanni

last: Parmigiani

first: Curtis

last: Huttenhower


title: A transcriptomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation [2010]

status: Public on Apr 01 2012

city: MONTPELLIER

first: Sylvie

last: Dequin

address: 2 PLACE PIERRE VIALA

institute: INRA

summary: Experience 2: 59A vs. 59A NADH Bdh200 mM, 59A NADPH Bdh200mM and 59A NADPH Bdh300 mM

overall_design: Analysis used RNA samples of three replicates by strain extracted from cells harvested at mid-exponential phase of wine fermentation

first: Magalie

last: Celton


title: A transcriptomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation [2009]

summary: Experience 1: 59A vs. 59A NADPH Bdh100mM

overall_design: Analysis used RNA samples of three independent replicates by strain extracted from cells harvested at mid-exponential phase of oenological fermentation


title: A transcriptomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation


title: ChIP-Seq of H3K9 acetylation for wildtype and ada2Δ cells in Cryptococcus neoformans

status: Public on Jan 01 2012

city: St. Louis

first: Brian

middle: Clifton

last: Haynes

state: MO

address: 4444 Forest Park Ave

department: Computer Science

institute: Washington University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SAGA member Ada2 is required for the majority of H3K9 acetylation in C. neoformans. To identify specific genomic loci that exhibit Ada2-dependent H3K9 acetylation, we performed ChIP-Seq against H3K9ac in wildtype and ada2Δ cells.

overall_design: ChIP-Seq was performed using antibodies for H3K9ac in KN99 wildtype cells and ada2Δ cells.  Input and IPed DNA was collected in triplicate from each strain and sequenced on an Illumnina HiSeq 2000 flow cell producing 84 million reads.  Due to the lack of quality scores, raw reads are omitted from the submission.

first: Stacey

last: Gish

first: Michael

last: Skowyra

last: Brent

first: Tamara

last: Doering


title: Cryptococcal H99 cells grown in 8 conditions for capsule induction

summary:
To understand the relationship between gene expression and capsule formation, H99 cells were cultured overnight at 37ºC in the following eight conditions:
low iron medium with or without both 500 mM ethylenediaminetetraacetic acid (EDTA) and 10 mM bathophenanthroline disulfonate (BPDS); phosphate-buffered saline (PBS) with or without 10% v/v fetal bovine serum; Dulbecco's Modified Eagle's Medium (from Sigma) in ambient air or 5% CO2; and Littman's medium with either 0.01 µg/ml or 1 µg/ml thiamine.

overall_design: All samples were hybridized against a common reference pool of total RNA.  Three biological replicates were performed for each growth condition, with the exception of growth in DMEM.


title: Highly Parallel Genome-Wide Expression Analysis of Single Mammalian Cells (Optimization)

status: Public on Feb 27 2012

city: San Diego

first: Craig

last: April

state: CA

address: 9885 Towne Centre Drive

institute: Illumina, Inc.

summary: Pre-Amplification Assay Optimization for Low RNA Inputs and Single Cells

overall_design: Low Input Total RNA


title: Highly Parallel Genome-Wide Expression Analysis of Single Mammalian Cells


title: Resolving phenylalanine metabolism sheds light on natural synthesis of benzylpenicillin in Penicillium chrysogenum

status: Public on Nov 05 2011

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: Industrial production of penicillin G by Penicillium chrysogenum requires medium supplementation with the side chain precursor phenylacetate. However, P.chrysogenum grown in presence of phenylalanine as sole nitrogen source formed detectable extracellular amounts of phenylacetate and penicillin G. To get more insights in the metabolism implicated, chemostat-cultivation in presence of 13C9-phenylalanine were carried out.  Quantification and modeling of the labeled metabolite pools indicated that phenylalanine was i) incorporated in nascent protein, ii) transaminated to phenylpyruvate and further converted by oxidation or by decarboxylation and iii) oxidized into tyrosine and subsequently assimilated in the homogentisate pathway. Comparative transcriptome analysis of phenylalanine and (NH4)2SO4 grown P.chrysogenum cultures enabled to identify two putative 2-oxo acid decarboxylases Pc13g9300 and Pc18g01490. Both cDNAs were cloned and expressed in the decarboxylase-free Saccharomyces cerevisiae CEN.PK711-7C (pdc1delta, 5delta, 6delta, aro10delta, thi3delta) strain that has lost the ability to grow on glucose as sole carbon source or on phenylalanine as sole nitrogen source. Only Pc13g09300 was able to restore growth on glucose and on phenylalanine, demonstrating that this gene encodes a dual substrate pyruvate, phenylpyruvate decarboxylase. This newly identified thiamine-dependent 2-oxo acid decarboxylase provides clues to explain the formation of phenylacetate via an Ehrlich-like pathway in P.chrysogenum.

overall_design: Penicillium chrysogenum DS17690 was grown in aerobic glucose limited chemostat at 25oC, pH 6.5 and a dilution rate of 0.03h-1 with either amonia or phenylalanine

first: Tania

middle: V

last: Dos Innocentes


title: Impact of Velvet complex on transcriptome and penicillin G production in glucose-limited chemostat cultures of a beta-lactam high-producing Penicillium chrysogenum strain

status: Public on Dec 06 2011

summary: The multi-component global regulator Velvet complex has been identified as a key regulator of secondary metabolite production in Aspergillus and Penicillium species. Previous work indicated a massive impact of PcvelA and PclaeA deletions, two key components of the Velvet complex, on penicillin production in prolonged batch cultures of P. chrysogenum, as well as substantial changes in transcriptome. The present study investigates the impact of these mutations on product formation and genome-wide transcript profiles under glucose-limited, aerobic conditions, relevant for industrial production of β-lactams. The gene-deletion cassette for PcvelA or PclaeA was integrated in a hdfA mutant of the penicillin high-producing strain P. chrysogenum DS17690. Predicted amino acid sequences of PcVelA and PcLaeA in this strain were identical to those in its ancestor Wisconsin54-1255. Controls were performed to rule out transformation-associated loss of penicillin-biosynthesis clusters which, in preliminary studies, led to a massive reduction of penicillin production in a PcvelA deletion mutant. The correct PcvelA and PclaeA deletion strains revealed a significant (up to 30 %) reduction of penicillin-G productivity relative to the reference strain, which is a much smaller reduction than previously reported for prolonged batch cultures of P. chrysogenum strains. Chemostat-based transcriptome analysis yielded only 23 genes with a consistent response in the PcvelAΔ and PclaeAΔ mutants when grown in the absence of the penicillin-G side-chain precursor phenylacetic acid. 11 of these genes belonged to two small gene clusters (with 5 and 6 genes, respectively), one of which contains a gene with high homology to an aristolochene synthase.  These results provide a clear caveat that the impact of the Velvet complex on secondary metabolism in filamentous fungi may be strongly context dependent

overall_design: Previous studies on the impact of the Velvet complex in P. chrysogenum were performed in prolonged batch cultures. Time course analysis revealed that the impact of PcvelA and PclaeA mutations was most pronounced after prolonged incubation {Hoff, 2010 6 /id}, but the physiological status of these cultures was not precisely defined. Industrial production of β-lactam antibiotics is performed in sugar-limited, aerobic fed-batch cultures {Menezes, 1994 76 /id}. The aim of the present study is to investigate the impact of the Velvet complex on physiology, penicilllin production and transcriptional regulation under industrially relevant conditions. To this end, we studied the impact of PcvelA and PclaeA deletions in aerobic, glucose-limited chemostat cultures of the penicillin high-producing strain P. chrysogenum DS17690.

first: Ishtar

middle: I

last: Snoek

first: Jack

last: Pronk


title: Identification and validation of gene expression models that predict clinical outcome in patients with early stage laryngeal cancer

status: Public on Nov 26 2011

city: Thessaloniki

first: elena

last: fountzilas

address: School of Medicine, Pathology Department

department: Medical Oncology

country: Greece

institute: Aristotle University of Thessaloniki, Greece

summary:
Background
Despite improvement in diagnostic and therapeutic techniques, a significant percentage of patients with early stage laryngeal cancer still recur after treatment. Gene expression models prognostic of recurrence risk could suggest which patients with early stage laryngeal cancer would be more appropriate for testing adjuvant strategies.

Patients and Methods
Expression profiling using whole genome DASL arrays was performed on 56 formalin-fixed paraffin-embedded tumor samples of patients with early stage laryngeal cancer, treated with surgery or radiation therapy. We split the samples into a training set and a validation set. Using the supervised principal components survival analysis in the first cohort, we identified multiple gene expression profiles that predict the risk of recurrence. These profiles were then validated in the second independent cohort.

Results
Gene models comprising different number of genes (40-100) identified a subgroup of patients who were at high risk of recurrence. Of these, the best prognostic model distinguished between a high- and a low-risk group (median DFS: 92 and 123 months, log rank p<0.005, permutation p<0.05), Hazard Ratio (HR): 8.51 (95% CI, 1.01 to 71.77; p<0.05). These models performed similarly in the independent cohort of our study (median DFS: 38 vs 161 months, log rank p=0.018), HR=5.19 (95% CI, 1.14 to 23.57; p<0.05).

Conclusions
We have identified gene expression prognostic models which can refine the estimation of a patient’s risk of recurrence. These findings, if further validated, should aid in patient stratification for testing adjuvant treatment strategies.

overall_design: 56 patients with early stage laryngeal cancer were included in this study.

first: Elena

last: Fountzilas

first: Dimitrios

last: Spentzos


title: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FFPE samples)

status: Public on Jun 22 2011

city: Toronto

first: Dong-Yu

last: Wang

address: 610 University Ave

institute: UHN-PMH-OCI

summary: The Formalin-Fixed Paraffin-Embedded (FFPE) samples on selected breast cancer subtypes (ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2-) and their paired fresh fine needle aspirated biopsies (FNA) were investigated. The cases represented different subtypes of breast cancers based on their clinical receptors ER (E) and Her2 (H) status to demonstrate the ability of gene profiles to differentiate these tumors. Compared to FNA specimens, FFPE samples yielded relatively more degraded RNA, and 80% of the samples deemed suitable for cDNA-mediated annealing, selection, extension and ligation (DASL) assay. It is able to demonstrate that gene profiles from FFPE microarrays were reproducible and correlated well with the corresponding gene profiles from FNA microarrays. The gene profiles from both FNA and FFPE could differentiate the four breast cancer subtypes, and the expression levels of corresponding gene set were consistent with qRT-PCR and correlated to the clinical outcomes on published microarray data. It supports the use of FFPE specimens to develop a prognostic tool for breast cancers which can obviate the need for fresh specimens.

overall_design: 25 FFPE specimens were processed for whole genome DASL assays using Illumina Human-Ref8 version 3 BeadChips. Invasive ductal carcinoma (IDC)-type subtypes ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2- (ER: estrogen receptor, HER2: human epidermal growth factor receptor 2) were analyzed.

first: Dong

middle: Y

first: Al

middle: M

last: Sadi

first: Wey

last: Leong


title: Gene expression analysis of pluripotent stem cells

status: Public on Apr 19 2011

city: Los Angeles

first: ANYOU

last: WANG

address: Gonda BLDG

department: Human Genetics

institute: UCLA

summary:
Analysis of genome-wide gene expressions of iPS stem cell with controls, both stem cells and parental cells. Results provide insight into the molecular basis of stem cell differentiation.

Keywords: Expression profiling by array, count

overall_design: Total RNA obtained from 9 iPS stem cell, 4 stem cells, and 3 somatic cells. 2 replicates for most of them.

first: Guoping

last: Fan

first: Anyou


title: Comparative transcriptome analysis between an original and a recombinant wine yeast strain defective for KNR4/SMI1

status: Public on Feb 28 2011

city: LOGROÑO

first: Vanessa

last: Penacho

state: LA RIOJA

address: c/ Madre de Dios, 51

department: Oenology & Viticulture

institute: ICVV/CSIC

summary:
EKD-13 is among the recently developed mannoprotein overproducing strains. It is a recombinant derivative of the well known EC1118 commercial strain, in which the ORF of all the alleles of KNR4/SMI1 was replaced by different integration cassettes. Lack of Knr4p resulted in a negligible impairment in fermentation kinetics and a net reduction in bentonite requirements to attain complete protein stabilization of white wines made out of natural grape must.
In order to improve the technological characterization of this strain, and to better understand the mechanisms underlying mannoprotein oversecretion, we have analyzed kinetics of mannoprotein release and autolysis during fermentation and aging, and we have performed a genome wide expression analysis in two different steps of the fermentation process. The results give some additional clues on KNR4 function in S. cerevisiae as well as on the best application conditions for this recombinant strain.

overall_design:
A comparative transcriptome analysis between the S. cerevisiae recombinant strain (EKD-13) defective for KNR4/SMI1 and the wild-type strain (EC1118) was implemented.
At every step of the fermentation (mid-exponential growth phase of fermentation advancement as 10 g of released CO2 and stationary-growth phase as 70 g of CO2 released) a recombinant and a WT yeast samples are put on a slide. There are three biological replicates that are labeled in dye-switch way (sometimes called biological dye-swap) for each step of fermentation leading to 3 independent intensity values for each gene (spots) on the microarrays. This experimental design minimizes the intrinsic biological noise between identical culture conditions and the technical variations inherent to the DNA microarray technology. In summary, there are six samples, each corresponding to comparisons between independent fermentations of both strains.

first: V

first: B

last: Blondin

first: E

last: Valero

first: R

last: Gonzalez


title: Comparison of root and leaf samples from Brassica rapa

status: Public on Sep 10 2010

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary: Root and leaf samples from Brassica rapa line R-O-18 were compared. The results will be compared to the same samples hybridised to the Affymetrix Brassica Exon 1.0 ST array.

overall_design: 6 samples were hybridised. Triplcate samples of 11 day old roots and 2 semi-expanded leaves from 23 day old Brassica rapoa R-O-18 plants.

first: Chris

middle: G

last: Love

first: Neil

last: Graham

first: Seosamh

middle: O

last: Lochlainn

first: Sean

last: May

first: Helen

last: Bowen

first: Philip

middle: J

last: White

first: Martin

last: Broadley

first: John

last: Hammond

first: Graham

last: King


title: Time-course gene expression data from deletion strains of Penicillium chrysogenum

status: Public on Jun 17 2010

city: Bochum

first: Jens

last: Kamerewerd

address: Universitätsstrasse 150

department: General and Molecular Botany

institute: Ruhr-University Bochum

summary: The recent discovery of a velvet complex containing several regulators of secondary metabolism in the model fungus Aspergillus nidulans raises the question whether similar type complexes direct fungal development in genera other than Aspergillus. Penicillium chrysogenum is the industrial producer of the antibiotic penicillin, whose biosynthetic regulation is barely understood. Here we provide a functional analysis of two major homologues of the velvet complex in P. chrysogenum, that we have named PcvelA and PclaeA. Data from array analysis using a ΔPcvelA deletion strain indicate a significant role of PcvelA on the expression of biosynthesis and developmental genes, including PclaeA. Northern hybridization and HPLC quantifications of penicillin titres clearly show that both PcvelA and PclaeA play a major role in penicillin biosynthesis. Both regulators are further involved in different and distinct developmental processes. While PcvelA deletion leads to light independent conidial formation, dichotomous branching of hyphae and pellet formation in shaking cultures, a ΔPclaeA strain shows a severe impairment in conidiophore formation in both the light and dark. Bimolecular fluorescence complementation assays finally provide evidence for a velvet-like complex in Penicillium chrysogenum, with structurally conserved components that have distinct developmental roles, illustrating the functional plasticity of these regulators within filamentous ascomycetes.

overall_design: Transcriptomes of PcvelA- and PclaeA- deletion mutants were compared with expression data from recipient strain deltaPcku70 and reference strain P2niaD18 as a control

first: Birgit

last: Hoff

first: Claudia

last: Sigl

first: Rudolf

last: Mitterbauer

first: Ivo

last: Zadra

first: Hubert

last: Kürnsteiner

first: Ulrich

last: Kück


title: ATR1 Boron Transporter is Regulated by Gcn4 Transcription Factor in Response to Boron Stress

status: Public on Jul 20 2011

city: Lincoln

first: Dmitri

middle: E

last: Fomenko

state: NE

department: Biochemistry

institute: University of Nebraska

summary: Transcriptional profiling of yeast wild type BY4741, gcn4 and yap1 mutants  in response to boron treatment.

first: Ahmet

last: Koc


status: Public on Jan 04 2011

city: Kundl

state: Tyrol

address: Biochemiestr. 10

department: Anti Infectives Microbiology

country: Austria

institute: SANDOZ GmbH

summary:
In filamentous fungi, secondary metabolism is often linked with developmental processes such as conidiation. In this study we analyzed the link between secondary metabolism and conidiation in the main industrial producer of the β-lactam antibiotic penicillin, the ascomycete Penicillium chrysogenum. Therefore, we generated mutants defective in two central regulators of conidiation, the transcription factors BrlA and StuA, respectively. Inactivation of both BrlA and StuA blocked conidiation and altered hyphal morphology during growth on solid media, as shown by light and scanning electron microscopy, but did not affect biomass production during liquid submerged growth. Genome-wide transcriptional profiling identified a complex StuA- and BrlA-dependent regulatory network, including genes previously shown to be involved in development and secondary metabolism. Remarkably, inactivation of StuA, but not BrlA, drastically down-regulated expression of the penicillin biosynthetic gene cluster during solid and liquid submerged growth. In agreement, penicillin V production was wild type-like in BrlA-deficient strains but 99 % decreased in StuA-deficient strains during liquid submerged growth as shown by HPLC analysis. Thus, among identified regulators of penicillin V production StuA has the most severe influence. Over-expression of StuA increased the transcript levels of BrlA and AbaA (another developmental regulator), de-repressed conidiation during liquid submerged growth, but did not affect penicillin V productivity. Taken together, these data demonstrate an intimate but not exclusive link between regulation of development and secondary metabolism in P. chrysogenum.
Transcriptomes of PcbrlA- and PcstuA- deletion mutants were compared with expression data from recipient strain deltaPcku70 as a control

overall_design: Mycelia from the transformants and the reference strain were harvested at successive stages of development for RNA extraction and hybridization on Affymetrix microarrays.

first: Hubertus

last: Haas

first: Thomas

last: Specht


title: Transcriptional profiling of CD4 T-cells in HIV-1 infected patients

status: Public on Jan 01 2011

city: Charlestown

first: Matthew

last: Woods

address: 149 13th Street

department: Computational Biology Core

institute: The Ragon Institute of MGH, MIT, and Harvard

summary: HIV-1 elite controllers maintain undetectable levels of viral replication in the absence of antiretroviral therapy, but their underlying immunological and virological characteristics may vary. Here, we used a whole-genome transcriptional profiling approach to characterize gene expression signatures of CD4 T cells from an unselected cohort of elite controllers. In the majority of elite controllers, transcriptional profiles were similar to HAART-treated patients, while being different from HIV-1 negative persons. Yet, a smaller proportion of elite controllers showed an opposite gene expression pattern that was indistinguishable from HIV-1 negative persons, but different from HAART-treated individuals. Elite controllers with this gene expression signature had significantly higher CD4 T cell counts, smaller levels of HIV-1-specific CD8+ T cell responses and tended to have lower residual HIV-1 viremia as determined by ultra-sensitive single-digit PCR, but did not differ from other elite controllers in terms of HLA class I alleles, age or sex. Thus, these data identify a specific subgroup of elite controllers whose clinical, immunological and gene expression characteristics approximate those of HIV-1 negative persons.

overall_design: PBMC from study persons were stained with monoclonal antibodies against CD3, CD4 and HLA-DR, and subsequently subjected to live sorting at 70 psi using an ARIA cell sorting device (Becton Dickinson) located in a specifically designated biosafety cabinet. Following mRNA extraction form the sorted cells (RNAeasy kit, Qiagen), whole genome transcriptional profiling was performed using WG-DASL microarrays (Illumina) according to standard protocols.  We included an unselected cohort of elite controllers (n = 12) and two background populations of HIV-1 negative persons (n = 9) and HIV-1 infected persons effectively treated with HAART (n = 14).  Four replicates were included in the study.

first: Francois

last: Vigneault

first: Maria

last: Buzon

first: Florencia

last: Pereyra

first: Ildeko

last: Toth

first: George

last: Church

first: Eric

last: Rosenberg

first: Javier

last: Martinez-Picado

first: Amalio

last: Telenti

first: Xu

last: Yu

first: Mathias

last: Lichterfeld


title: Expression quantitative trait loci (eQTL) analysis of Brassica rapa under varying soil phosphorus (P) supplies

status: Public on Jun 29 2011

city: Crawley

first: John

last: Hammond

state: WA

address: 35 Stirling Highway

department: School of Plant Biology

institute: University of Western Australia

summary: The aim of this study was to identify eQTL in Brassica rapa grown under altered soil phosphorus (P) supply, to understand better the genetic architecture of P-use efficiency (PUE) in plants. Recombinant inbred lines (RILs) of the BraIRRI mapping population were grown at adequate and growth-limiting soil P. Variation in leaf gene expression was quantified using an Agilent Brassica 95k oligonucleotide array. Informative gene expression markers (GEMs) were used to map eQTL and PUE-related QTL. Gene expression was highly dependent on soil P supply. However, the altered expression of many genes, including known P-responsive genes, was highly heritable. Interval mapping using P supply as a covariate revealed 18,876 eQTL, representing 15,912 unique probes. Notable trans-eQTL hotspots occurred on chromosomes A06 and A01; these were enriched with protein modification and phosphorus metabolism-related (A06), as well as chloroplast and photosynthesis-related (A01) transcripts. Regulatory loci and genes associated with P-use efficiency identified through eQTL analysis are potential targets for further characterisation and may have potential for crop improvement. Availability of the annotated B. rapa genome sequence will facilitate their study, including the separation of cis- and trans- effects.

overall_design: The experiment was designed to identify expression QTL associated with availability of phosphorus in Brassica rapa. Seventy-eight informative lines from the “BraIRRI” mapping population of Brassica rapa L. (2n = 2x = 10; A-genome) and the two parent lines (IMB211, female; R500, male) were selected for study. The establishment of the BraIRRI population is described by Iniguez-Luy et al. (2009). Plants were grown from seed in compost, under two [P]ext treatments of 9 mg L-1 (low) or 30 mg L-1 (optimal) Olsen extractable P. RNA was extracted from leaf samples from one experimental run (78 lines at low and optimal [P]ext, with one line duplicated i.e. 158 samples), and from leaf samples from the parent lines at low and optimal P in all three experimental runs (12 samples) using a modified TRIzol extraction method (Hammond et al., 2006).

first: Sean

last: Mayes

first: Helen

last: Bowen

first: Neil

last: Graham

first: Rory

last: Hayden

first: Christopher

last: Love

first: William

last: Spraklen

first: Jun

last: Wang

first: Sue

last: Welham

first: Philip

last: White

first: Graham

last: King

first: Martin

last: Broadley


title: Early gene expression differences in inbred mice predict susceptibility to spontaneous pulmonary adenomas

status: Public on Jun 17 2011

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

summary: We examined if gene expression profiles differed between healthy (tumor-free) mice of strains that are known to have different pulmonary adenoma susceptibility (severity and frequency).

overall_design: Three females of 11 week old mice of 9 (129S1/SvlmJ, A/J, BALB/cJ, C3H/HeJ, C57BL/6J, C57L/J, DBA/2J, KK/HlJ, and MRL/MpJ) strains were selected for RNA extraction and hybridization on GeneChip® Mouse Gene 1.0 ST Arrays (Affymetrix, Santa Clara, CA). Each strain was compared to all other strains (36 unique comparisons total) to identify the most common differentially expressed probe sets among the population.  The most common probesets were then compared between strain groups (increased vs. decreased spontaneous pulmonary adenoma frequency and severity).

first: Annerose

last: Berndt


title: Effects of Ethanol Stress on Gene Expression in Saccharomyces cerevisiae

status: Public on Mar 30 2010

city: East Geelong

first: Dragana

last: Stanley

state: Victoria

address: 5 Portarlington Rd

department: AAHL

institute: CSIRO

summary: To identify genes involved in acclimatization of yeast to non-lethal ethanol stress, S. cerevisiae strain W303-1A was grown separately at 0% and 6.5% (v/v) ethanol, and gene expression profiles were compared using microarray analysis.  A t-test with a p-value of 0.05 was applied for differences in gene expression across unstressed and stressed replicates of W303-1A.  There were 1049 genes with significant differences in expression.  Among the genes that passed the t-test, 46 genes were up-regulated 5-fold and more in ethanol stress and 149 by more than 3-fold.  There were 40 genes down-regulated by more than a factor of 5 and 161 by more than a factor of 3; the remaining genes that passed the t-test had expression level differences lower than 3-fold. GenowizTM bioanalysis results that identify GO categories comprising stress induced (more than 3-fold) genes show the two highest ethanol stress induced categories to be Retrotransposition Nucleocapsid (z-score of 15.69) and Transposition RNA Mediated (z-score of 15.54).  These categories were not reported in previous gene expression studies on ethanol stress (Alexandre et al. 2001, Chandler et al. 2004, Fujita et al. 2004, Hirasawa et al. 2007). Our further investigaition identifies lack of annotation and omission of the genes from the retrotransposition-associated categories in slide printing as possible causes of this inconsistency.

overall_design: Two conditions: 0% and 6.5 % (v/v) ethanol added to the culture growth medium. One set of triplicates with one dye swap for each condition. Each triplicate was prepared from different biological replicate (i.e. different culture).

first: Sarah

last: Fraser

first: Grant

middle: A

first: Paul

last: Chambers


title: Gene Expression Profiling of Formalin Fixed Paraffin Embedded Familial Breast Tumours Using the Whole Genome-DASL Assay

status: Public on Jun 09 2010

city: Brisbane

first: Nic

last: Waddell

address: St Lucia

institute: Queensland Centre for Medical Genomics

summary: Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin fixed paraffin embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumor banks. Once samples are fixed in formalin the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study we have evaluated the whole genome DASL assay from Illumina to perform transcriptomic analysis from archived breast tumor tissue fixed in formalin paraffin embedded blocks. We profiled 76 familial breast tumors from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r2=0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumor molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterisation of many diseases.

overall_design: RNA was extracted from FFPE Familial breast tumours and analysed using the WG-DASL assay for Illumina.


title: Transcription profiling of Brassica lines

status: Public on May 03 2009

city: Norwich

first: Andreas

last: Magusin

address: Norwich Research Park

department: Crop Genetics

institute: John Innes Centre

summary:
Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II

The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes.

sample_organism:
Brassica napus
Brassica rapa
Brassica oleracea

overall_design: Four-condition experiment, comparison of transcription profiles of the genomes. Four biological replicates were used, independently grown and harvested. One replicate per array.

last: Trick

first: Foo

last: Cheung

first: Nizar

last: Drou

first: Fiona

first: Edward

middle: K

last: Lebenhofer

first: Patrick

last: Hurban

middle: D

last: Town

first: Ian

last: Bancroft


title: Differential gene expression in CadA strain vs D398A control strain upon 1 μM cadmium treatment

status: Public on Apr 20 2010

city: Gif-sur-Yvette cedex

first: Jean-Christophe

last: AUDE

address: CEA Saclay Bâtiment 142 - PC 21

department: IBITEC-S

institute: CEA

summary: Differential gene expression in W303-1A strain expressing CadA relative to the W303-1A strain expressing an inactive form of CadA (D398A). The two strains grown to exponential were treated for 1h with 1uM cadmium.

overall_design: W303-1A cells expressing CadA or D398A were grown to exponential phase (OD600 = 0.4) in SD minimal medium + all amino acids plus adenine at 30°C. Cells were treated with 1 µM cadmium and harvested after 1h incubation. Total RNA extraction and microarray hybridization were performed as previously described (Laferte et al., 2006).

first: A

last: Gardarin

first: S

last: Chédin

first: G

last: Lagniel

last: Aude

first: E

last: Godat

first: P

last: Catty

first: J

last: Labarre


title: Gene expression in Calu-3 cells after influenza H3N2 and H11N9 infection

status: Public on Dec 19 2009

city: Newcastle

first: Alan

middle: Chen-Yu

last: Hsu

state: NSW

address: Lvl 3 HMRI, John Hunter Hospital, Lookout Rd, New Lambton Height

department: Respiratory Medicine

institute: University of Newcastle

summary: Airway epithelial cells are the initial site of infection with influenza viruses. The innate immune responses of airway epithelial cells to infection have the potential to limit virus replication and induce effective adaptive immune responses. However, relatively little is known about the importance of this innate anti-viral response to infection. Avian influenza viruses are a potential source of future pandemics, therefore it is critical to examine the effectiveness of the host anti-viral system to different influenza viruses. We used a human influenza (H3N2) and a low pathogenic avian influenza (H11N9) to assess and compare the anti-viral responses of bronchial epithelial cells (BECs). After infection, the H3N2 virus replicated more effectively than the H11N9 strain in BECs. This was not due to differential expression of different sialic acid residues on BECs but was attributed to the interference of the host anti-viral responses by H3N2. The H3N2 strain induced a delay in anti-viral signaling and impaired release of type I and type III interferons (IFNs) compared to the H11N9 virus. We then transfected the gene encoding for non-structural (NS) 1 protein into the BECs and the H3N2 NS1 induced a greater inhibition of anti-viral responses compared to the H11N9 NS1. While the low pathogenic avian influenza virus was capable of infecting BECs, the human influenza virus replicated more effectively than avian influenza virus in BECs and this may be at least in part due to a differential ability of the two NS1 proteins to inhibit anti-viral responses. This suggests that the subversion of human anti-viral responses may be an important requirement for influenza viruses to adapt to the human host and induce disease.

overall_design:
One (2hr) or three (6hr, 24hr) replicates of each infection (H3N2, H11N9) and two replicates of media control samples (24hr) were performed and hybridized onto the beadchip.

The supplementary file 'GSE19580.non-normalized.txt' file contains non-normalized data for Samples GSM487974-GSM487989.

middle: C

last: Barr

first: Philip

last: Hansbro

first: Peter

last: Wark


title: Molecular analysis of a microbial strain improvement paradigm

status: Public on Dec 01 2008

city: Delft

first: Marco

middle: Alexander

last: van den Berg

address: PO Box 425

institute: DSM Anti Infectives

summary:
Industrial production of penicillins with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. Sequencing of the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 revealed many genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and alpha-aminoadipic acid, the amino-acid precursors for penicillin biosynthesis, as well as genes encoding microbody proteins, increased in the high-producing strain. Many key (intra)cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven functional analysis.
Keywords: genetic modification

overall_design: Transcriptome analysis was performed on aerobic, glucose-limited chemostat cultures (D=0.03h-1)of the Wisconsin54-1255 strain and the derived industrial, penicillinG high-producing strain DS1769032. Chemostat cultivation offers the possibility to keep specific growth rate and other key parameters constant33. Some intermediates of β-lactam biosynthesis are produced in the absence of the side-chain precursor phenylacetic acid (PAA), but penicillinG biosynthesis is strictly dependent on PAA addition to culture media.

first: JM

last: Daran

first: D

last: Harris

middle: T

last: Pronk

first: M


title: Identification of ACLA, an adipoyl Co enzyme A ligase in Penicillium chrysogenum, a key enzyme of cephem antibiotics

status: Public on Aug 01 2009

first: Jean-Marc

address: Julianalaan 67

institute: Delft University of Technology

summary: Production of cephalosporin precursors with recombinant strains of Penicillium chrysogenum has improved the economics and reduced the environmental impact of industrial cephalosporin production. The engineered P. chrysogenum strains used in these processes express heterologous enzymes that convert the intermediate acyl-6-aminopenicillanic acid into different tailor-made compounds. Activation of the cephalosporin side-chain precursor to its corresponding CoA thioester is an essential step for its incorporation into the β-lactam backbone. To identify the acyl-CoA ligase involved in activation of adipic acid, a frequently used cephalosporin side-chain precursor, we searched the genome of P.chrysogenum for putative structural genes encoding acyl-CoA ligases. Chemostat-based transcriptome analysis was then used to identify the one presenting the highest expression level when cells were grown in the presence of adipic acid. Deletion of the  gene renamed aclA, led to a 32% decreased specific rate of adipic acid consumption and a three-fold reduction of adipoyl-6-aminopenicillanic acid levels in chemostat cultures of P. chrysogenum, but did not affect penicillin production. After cloning the gene and overexpressing it in Escherichia coli, its purified protein product was shown to have adipoyl-CoA ligase, but no phenylacetyl-CoA ligtase activity. Finally, by fusing the gene to a sequence encoding cyan fluorescent protein, the resulting fusion protein localized to microbodies, which indicates that activation of the side-chain precursor adipic acid takes place in this compartment, where also the subsequent acyltransferase step takes place. Identification and functional characterization of this adipoyl-CoA ligtase gene may aid in developing future metabolic engineering strategies for improving the production of different cephalosporins.

overall_design: This study describes the first successful identification of a fungal adipoyl-CoA ligase, an essential enzymatic activity in the activation of the side-chain precursor adipic acid during production of cephalosporin precursors with recombinant P. chrysogenum strains. The gene encoding for the protein was identified by means of transcriptomics. The strain DS17690 a high penicillinG producing strain was grown in chemostat culture, in the three conditions, with phenylacetate, adipate and without any side chain.

first: Andreas

last: Gombert

first: Jack


title: Characterization of the  Ku70 homologue HdfA deletion in Penicillium chrysogenum

status: Public on Mar 09 2009

summary: Targeting an engineered DNA fragment to a specific site in chromosomes in order to disrupt, overexpress or modify the nucleotide sequence of a gene requires homologous recombination repair mechanism. This DNA repair mechanism is not predominant in fungi, resulting in extremely low targeting efficiency. To increase this efficiency, it is becoming common practice to disable the non homologous end joining (NHEJ) pathway that causes random integration, by deleting homologous gene to human KU70 and KU80 which encode proteins functioning in the NHEJ pathway. These genes have been successfully deleted in several organisms, including the yeast Kluyveromyces lactis and the fungi Neurospora Crassa and several Aspergilli species. In this study we investigated the behavior of high penicillinG-producing Penicillium chrysogenum strains, in which the KU70 or KU80 homologues, HdfA or HdfB, had been deleted. Targeting efficiency in these mutant strains was significantly increased relative to the reference strain. Both physiological and transcriptome data of chemostat cultivations of the hdfA deletion strain and the reference strain showed minimal differences. However, in a direct competition experiment to assess global strain fitness, the reference strain had a clear advantage over the deletion strain. The full characterization of these recombinant host strains is an essential step to guide the future construction of a whole genome knock-out mutant collection.

overall_design: Penicillium chrysogenum is a filamentous fungus that is used to industrially produce the beta-lactam antibiotics. After decades of classical strain improvement, the genome sequence has been deciphered and annotated. The combination of the P. chrysogenum genome sequence and a strain exhibiting increased targeting efficiency would paved the way to the construction of deletion or expression libraries that  would be a tremendous help in understanding the nature of the productive capabilities of this organism. This study reports the effect of the deletions of the Ku70 and Ku80 homologues, HdfA and HdfB respectively, in P. chrysogenum. A detailed analysis of the physiology, transcriptome and phenotype was performed to assess the use of these strains as platform for functional genomics study.

first: Isthar

middle: S

last: Snoek


title: Engineering of Penicillium chrysogenum for fermentative production of a novel carbamoylated cephem antibiotic precursor

status: Public on Jan 05 2009

summary: Penicillium chrysogenum was successfully engineered to produce a novel carbamoylated cephalosporin that can be used as a synthon for semi-synthetic cephalosporins. To this end, structural genes for Acremonium chrysogenum expandase/hydroxylase and Streptomyces clavuligerus carbamoyltransferase were expressed in a penicillinG high-producing strain of P. chrysogenum. Growth of the engineered strain in the presence of the side-chain precursor adipic acid resulted in production of adipoyl-7-amino-3-carbamoyloxymethyl-3-cephem-4-carboxylic acid (ad7-ACCCA) and of several adipoylated pathway intermediates. A combinatorial chemostat-based transcriptome study, in which the ad7-ACCCA- producing strain and a strain lacking key genes in β-lactam synthesis were grown in the presence and absence of adipic acid, enabled the dissection of transcriptional responses to adipic acid per se and to ad7-ACCCA production. In chemostat cultures of both strains, adipic acid served as an additional carbon source. Transcriptome analysis supported an earlier proposal, based on 13C-labelling studies, that adipic acid catabolism in P. chrysogenum occurs via β-oxidation and enabled the identification of putative genes for enzymes involved in mitochondrial and peroxisomal β-oxidation pathways. Several of the genes that showed a specifically altered transcript level in ad7-ACCCA-producing cultures were previously implicated in oxidative stress responses. As strain improvement programmes lead to increased specific productivity and yields, a deeper understanding of these stress responses is likely to be important to also achieve high ad7-ACCCA titers with engineered strains of P. chrysogenum.

overall_design: The goal of the present study was to explore the metabolic engineering of P. chrysogenum for the production of the important semisynthetic cephalosporin precursor ad7-ACCCA. In this way, new fermentation processes for the production of this compound can be designed, resulting in a reduction of the use of environmentally unfriendly chemicals as well as a cost reduction. Genetic engineering for this purpose involved the introduction into P. chrysogenum of the cefEF gene from A. chrysogenum and the cmcH gene of S. clavuligerus. To investigate the physiological impact of the introduction of this novel pathway, physiological and genome-wide transcriptional studies were performed in batch and chemostat cultures of the engineered P. chrysogenum strains grown in the absence and presence of the side-chain precursor adipic acid. To distinguish between effects of the side-chain precursor per se and effects of ad7-ACCCA production, parallel experiments were run with a congenic strain that lacks three key genes for beta-lactam biosynthesis.

first: Diana

first: Zita

last: Krogt