title: Genome wide expression analysis of psaA and psbA tobacco mutant plants.

status: Public on Aug 02 2011

city: New delhi

first: Padmalatha

address: Pusa campus

institute: NRCPB

summary:
Transcriptome analysis in tobacco mutant plants using tomato Genechip Genome array
Tobacco (Nicotiana tabacum cv. Petit Havanna) psaA and psbA deletion  mutants were constructed through a targeted deletion of 767 and 1152 nucleotides of coding regions, respectively with two gene cassettes: psbAproR:uidA:psbterR and rrnR:aadA:rbcLterR coding for GUS reporter and spectinomycin selectable marker genes, respectively. Standard established procedures were followed for chloroplast transformation to generate the psaA and psbA deletion mutants based on the homologous recombination. Gene expression profiles in psaA and psbA tobacco mutant plants were analyzed using tomato Genechip Genome array to study the global changes in the expression of genome.

overall_design: Total RNA was isolated from psaA and psbA tobacco mutant plants along with the wild type plants. Biotin labeled cRNA was hybridized on tomato GeneChip Genome Array following the Affymetrix protocols. Two independent biological replicates were maintained.

first: K

last: Padmalatha

first: G

last: Dhandapani

first: M

last: Kanakachari

first: Jain

last: Neha

first: Solanke

middle: U

last: Amolkumar

first: Reddy

last: Siva

first: Kumar

last: Ananda


title: Gene expression variation in horse placental tissue, and resting and stimulated horse lymphocytes [Agilent-021322]

status: Public on Feb 14 2012

city: Ithaca

first: Donald

last: Miller

state: NY

address: Hungerford Hill Rd.

department: Baker Institute for Animal Health

country: USA

institute: Cornell University

summary: We undertook gene expression microarray experiments to identify genes that are differentially expressed in invasive (Chorionic Girdle) and non-invasive (Chorion) placental tissue, and resting and Pokeweed Mitogen (PWM) stimulated horse lymphocytes.  Conceptus tissues were dissected to obtain chorionic girdle, and chorion.  Freshly isolated horse peripheral blood lymphocytes were split and harvested immediately, or stimulated with PWM and harvested over a five day period. These experiments utilized a commercially available Agilent horse array that featured >43,000 probes on a 4x44k array format.

overall_design: Three day 33-35 chorionic girdle RNAs were compared to matching chorion RNAs. Gene expression in resting lymphocytes was compared to gene expression in PWM treated lymphocytes.

first: Douglas

middle: F

last: Antczak


title: Expression data from transgenic Nicotiana tabacum expressing a variant of coat protein and movement protein from Tobacco mosaic virus

status: Public on Dec 01 2012

city: Buenos Aires

first: Gabriela

last: Conti

address: N. repetto y Los Reseros

country: Argentina

institute: INTA

summary:
Transgenic expression of viral proteins in natural host plants is a useful simplified system with the potential to understand the individual effect of each viral component. Transgenic expression of movement  (MP) and a variant from coat protein (CPT42W) in tobacco, a TMV natural host, produces severe morphological changes, altered miRNAs accumulation and poor fertility.
We used microarrays to characterize the gene expression changes caused by the co-expression of TMV capsid and movement proteins in Nicotiana tabacum comparing two isogenic lines MPxCPT42W  and mpxcpT42W* (a line with both transgenes spontaneously silenced and with normal phenotype).

overall_design: Leaf tissues from 6-week old tobacco plants MPxCPT42W and mpxcpT42W* were collected for RNA extraction and hybridization on Affymetrix microarrays. We collected pools of three plants (one biological replicate) and analyzed three independent biological replicates for each transgenic line.

first: Sebastian

last: Asurmendi


title: Transcriptomic and metabolic responses of mycorrhizal roots to nitrogen patches under field conditions

status: Public on Jun 29 2011

city: St. Louis

first: Dan

last: Ruzicka

state: MO

address: 975 N. Warson Rd.

institute: Donald Danforth Plant Science Center

summary: Arbuscular mycorrhizal (AM) fungi contribute to plant nutrient uptake in systems managed with reduced fertilizer inputs such as organic agriculture and natural ecosystems by extending the effective size of the rhizosphere and delivering mineral.  Connecting the molecular study of the AM symbiosis with agriculturally- and ecologically-relevant field environments remains a challenge and is a largely unexplored research topic.    This study utilized a cross-disciplinary approach to examine the transcriptional, metabolic, and physiological responses of tomato (Solanum lycopersicum) AM roots to a localized patch of nitrogen (N).   A wild-type mycorrhizal tomato and a closely-related nonmycorrhizal mutant were grown at an organic farm in soil that contained an active AM extraradical hyphal network and soil microbe community.    The majority of genes regulated by upon enrichment of nitrogen were similarly expressed in mycorrhizal and nonmycorrhizal roots, suggesting that the primary response to an enriched N patch is mediated by mycorrhiza-independent root processes.  However where inorganic N concentrations in the soil were low, differential regulation of key tomato N transport and assimilation genes indicate a transcriptome shift towards mycorrhiza-mediated N uptake over direct root  supplied N.  Furthermore, two novel mycorrhizal-specific tomato ammonium transporters were also found to be regulated under low N conditions.  A conceptual model is presented integrating the transcriptome response to low N and highlighting the mycorrhizal-specific ammonium transporters.  These results enhance our understanding of the role of the AM symbiosis in sensing and response to an enriched N patch, and demonstrate that transcriptome analyses of complex plant-microbe-soil interactions provide a global snapshot of biological processes relevant to soil processes in organic agriculture.

overall_design: 30 samples were analyzed.  There were 2 genotypes (wildtype and mutant) and 3 treatments (two N treatments and a water control) for a total of 6 groups.  Each group had 5 biological replicates.

first: Daniel

middle: R

first: Natasha

middle: T

last: Hausmann

first: Felipe

middle: H

last: Barrios-Masias

first: Louise

middle: E

last: Jackson

middle: P

last: Schachtman


title: Multi-tissue gene expression profiles of human brain (PFC)

status: Public on Apr 25 2013

city: New York

first: Jun

last: Zhu

address: One Gustave L Levy, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn Medical School at Mount Sinai

summary: The genetics of complex disease produce alterations in molecular interactions of cellular pathways which collective effect may become clear through the organized structure of molecular networks. To characterize molecular systems associated with late-onset Alzheimer´s disease (LOAD), we constructed gene regulatory networks in hundreds of autopsied brain tissues from LOAD patients and non-demented subjects. We demonstrate that LOAD reconfigures specific portions of the molecular interaction structure, and via an integrative network-based approach we rank ordered these sub-networks (modules) for relevance to LOAD pathology, highlighting the immune/microglia module as the top ranking. Through a Bayesian inference approach we identified multiple key causal regulators for LOAD brains.

overall_design: Autopsied tissues from dorsolateral prefrontal cortex (PFC), visual cortex (VC) and cerebellum (CR) in brains of LOAD patients, and non-demented healthy controls, collected through the Harvard Brain Tissue Resource Center (HBTRC), were profiled on a custom-made Agilent 44K array (GPL4372_1). All subjects were diagnosed at intake and each brain underwent extensive LOAD-related pathology examination.  Gene expression analyses were adjusted for age and sex, postmortem interval (PMI) in hours, sample pH and RNA integrity number (RIN).  In the overall cohort of LOAD and non-demented brains the mean ± SD for sample PMI, pH and RIN were 17.8±8.3, 6.4±0.3 and 6.8±0.8, respectively.  230 samples with all PFC, VC, and CR tissue profiled were included for further multi-tissue analysis.

first: Bin

last: Zhang

first: Chris

last: Gaiteri

first: Liviu-Gabriel

last: Bodea

first: Zhi

last: Wang

first: Joshua

last: McElwee

first: Chunsheng

first: Tao

last: Xie

first: Linh

last: Tran

first: Radu

last: Dobrin

first: Eugene

last: Fluder

first: Brunce

last: Clurman

first: Manikandan

last: Narayanan

first: Christine

last: Suver

first: Hardik

last: Shah

first: Milind

last: Hahajan

first: John

last: Lamb

first: Cliona

last: Molony

first: David

middle: J

last: Stone

first: Vilmundur

last: Gudnason

first: Amanda

last: Myers

first: Eric

last: Schadt

first: Harald

last: Neumann

first: Valur

last: Emilsson


title: Expression data from roots and first two leaves of tomato seedlings growing on regular MS medium or MS medium supplemented with multi-wall carbon nanotubes (0, 50, 100, 200 ug/ml) or activated carbon (50 mg/ml)

status: Public on Dec 01 2010

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Applied Science

institute: University of Arkansas at Little Rock

summary:
To investigate effects of carbon nanotubes (CNTs) om total expression profile of tomato plants we introduced CNTs in MS agar medium in concentrationd 0, 50, 100, 200 ug/ml
Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in tomato seedlings in response to carnom nanotubes (CNTs).

overall_design: 10 day old root tips and first two leaves of  wild type tomato seedlings (cv. Micro-Tom) growing on regular MS agar medium or MS medium supplemented with carbon nanotubes (50, 100, 200 ug/ml) or MS medium supplemented with activated carbon (50 ug/ml) were selected for RNA extraction and hybridization on Affymetrix microarrays.


status: Public on Feb 29 2012

city: Delhi

first: arun

middle: k.

last: sharma

state: Delhi

address: Benito-juarez road

department: Plant Molecular Biology

country: India

institute: Delhi university

summary:
[original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes

A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening.  A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes.

overall_design: Three chronological stages of tomato (Solanum lycopersicon) fruit ripening were compared between wild type and rin mutant

first: Rahul

last: Kumar

first: Arun

middle: K

last: Sharma


title: Microarray analysis of gene expression induced by Phytophthora infestans in tomato leaves

status: Public on Oct 25 2011

city: Bonn

first: Muna

last: Sultan

address: nussalle 9

country: Germany

institute: university of Bonn

summary: Phytophthora infestans is most notorious oomycete causing a devastating disease on tomato called late blight. The molecular mechanisms involved in host-parasite interaction is still unexplored well. Investigation of changes in gene expression profile after pathogen infection to find out the mechanisms involved in infection process

overall_design: Second full expanded leaves from both healthy tomato plants (non-inoculated) and diseased tomato plants inoculated with Phytophthora infestans inoculum were used to extract total RNA for microarry analysis 12 hours post inoculation time.


title: embryo AVE neurons tiling array

status: Public on Nov 18 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

type: Expression profiling by genome tiling array

summary:
modENCODE_submission_3173
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC1750 (engineered, target gene opt-3 tagged by GFP); Tissue: embryo-AVE; Developmental Stage: Mixed stage of embryos 20dC; Genotype: KM173 (opt-3::GFP[pRF4]); hdIs32 (glr-1::DsRed2); Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain NC1750 (engineered, target gene opt-3 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue embryo-AVE

first: Bob

last: Waterston

last: Miller

first: Mark

last: Gerstein

first: Mike

last: Wilson

first: Ashish

last: Argiwal

first: Valerie

last: Reinke


title: A tomato fruit RNA extraction method that isolates mRNAs encoding secreted and endomembrane associated proteins

status: Public on Jan 21 2011

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

summary: Background: During the analysis of ripening related gene expression in tomato fruit, we observed a bias towards certain classes of messenger RNA based upon the type of buffer used in the initial step of the extraction procedure. We postulated that there was a functional association of the separated transcripts.  To test this hypothesis, we carried out extractions from the same tissue sample where only the buffer varied.  Transcripts were hybridised to Affymetrix oligo arrays and the data was analysed according to the predicted cellular component of the encoded proteins. Results: The use of an extraction buffer that lacked high levels of caeotropic agents resulted in a reduction of mRNAs encoding proteins that were either secreted or were predicted to be routed through the endomembrane system and hence could have been bound to the endoplasmic reticulum in polyribosomes. Extraction of the cell debris immediately following the initial buffer based extraction and subsequent micro array analysis revealed that the expected transcripts could be recovered. This demonstrated that the buffer was separating the mRNAs based on the cellular component of the encoded proteins.  Analysis of selected transcripts by northern hybridisation again supported this theory. Conclusions: Some traditional buffers used for fruit RNA extraction selectively deplete for transcripts encoding proteins that are membrane-associated or secreted.  This can be explained if polyribosomes that are bound to the endoplasmic reticulum (ER) are not effectively disrupted when the extraction buffer lacks either detergent or organic solvents. These findings have important implications with respect to experimental bias, as well as opportunities for message enrichment and protein characterisation.

overall_design: GeneChip analyses were performed to analyse the effect of using different extraction protocols on Solanum lycopersicum pericarp.

first: Mervin

last: Poole

first: Katalin

last: Kovács

first: Colin

last: Watson

first: Neil

middle: S

last: Graham

first: Martin

last: Broadley

first: Graham

middle: B

last: Seymour

first: Sean

last: May

first: Rupert

middle: G

last: Fray

first: Donald

last: Grierson


title: Multi-tissue gene expression profiles of human brain

first: Jun

last: Zhu

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

overall_design: Refer to individual Series


title: Multi-tissue gene expression profiles of human brain (VC)

first: Bin

last: Zhang

first: Chris

last: Gaiteri

first: Liviu-Gabriel

last: Bodea

first: Zhi

last: Wang

first: Joshua

last: McElwee

first: Chunsheng

first: Tao

last: Xie

first: Linh

last: Tran

first: Radu

last: Dobrin

first: Eugene

last: Fluder

first: Brunce

last: Clurman

first: Manikandan

last: Narayanan

first: Christine

last: Suver

first: Hardik

last: Shah

first: Milind

last: Hahajan

first: John

last: Lamb

first: Cliona

last: Molony

first: David

last: Stone

first: Vilmundur

last: Gudnason

first: Amanda

last: Myers

first: Eric

last: Schadt

first: Harald

last: Neumann

first: Valur

last: Emilsson


title: Tomato fruit wound inoculation by C. coccodes and ammonium treated

status: Public on Jun 01 2011

city: Rehovot

first: Robert

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

summary: Colletotrichum coccodes secretes ammonium during germination and colonization of host tissue as a mechanism for dual activation of fungal pathogenicity factors and plant cell death via activation of host NADPH oxidase. Ammonium accumulation during colonization of tomato fruits by C. coccodes induced host nucleus integrity changes and program cell death (PCD). Transcriptome analysis at the leading edge of colonized tissue and ammonium treated tomato fruits revealed 82 and 237 common up-regulated and common down-regulated genes, respectively. The common-up-regulated genes showed over representation of pathogen related (PR) proteins, salicylic acid (SA) dependent and systemic acquired resistance (SAR) related genes and genes related to biotic stress. The down regulated genes showed over representation of Jasmonic acid (JA) dependent genes. Consistent with this observation the direct application of SA enhanced C. coccodes colonization, whereas the application of JA delayed colonization. Candidate genes were selected for QRT-PCR analysis of transcripts in normal and transgenic RBOH antisense plants and showed dependence on RBOH regulation. In all, the results suggest that ammonia accumulation during C. coccodes colonization activates SA and suppress JA pathways through activation of RBOH. The effects of ammonium on the expression of the selected up-and down regulated genes were examined in fruit of different maturation stages. Red, susceptible and green resistant, tomato fruit displayed similar behavior, suggesting that resistance of green fruits to C. coccodes colonization is not modulated by the JA and SA pathways but depends on other factors

overall_design:
Ten micrograms of total RNA was processed for the microarray hybridizations using the Affymetrix GeneChip one-cycle target-labeling kit (Affymetrix). The four treatments were: C. coccodes "mat inoculation" compared to a wound control (24 hours after the tomato fruit peel was removed). 5 mM Ammonium treatment in PBS compared to PBS treatments as a control for ammonium treatment, the treatments applied every four hours. Each treatment had a duplicate. The biotinylated complementary RNA was fragmented and hybridized to the GeneChip Tomato Genome Array (10,038 tomato probe sets for more than 9,200 tomato genes). The arrays were washed, stained, and scanned at the biological services (Weizmann institute of science, Rehovot, Israel).
CEL files for the Affymetrix microarray data arising from the microarray experiments were analyzed utilizing the Partek genomics software (Downey, 2006).

first: Noam

last: Alkan

last: Flohr

first: Dov

last: Prusky


title: Transcript profiling of tomato mutants producing anthocyanins in the fruit

status: Public on Jul 31 2010

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

summary:
Anthocyanins are high value plant antioxidants which are not present in the fruits of cultivated tomato. However, both the dominant gene Anthocyanin fruit (Aft) and the recessive gene atroviolacea (atv), introgressed into domesticated tomato from two different wild Solanum species, stimulate a limited anthocyanin pigmentation. Surprisingly, double mutant Aft/Aft atv/atv tomatoes are characterised by the presence of anthocyanins in the fruit peel, resulting in intensely purple pigmented fruit.
We carried out a transcript profiling analysis using GeneChip® Tomato Genome Arrays, in order to identify differentially expressed genes when comparing wild type,  Aft/Aft, atv/atv, and Aft/Aft atv/atv fruits. The expression pattern of several genes involved in the anthocyanin pathway was analyzed in detail. Among the fruit peel-associated differentially expressed transcripts, genes involved in phenylpropanoid pathway, cell wall composition, biotic and abiotic stress responses, sugar and hormone metabolism were overrepresented in Aft/Aft atv/atv. Transcriptomic analysis thus revealed that the activation of anthocyanin synthesis in tomato fruit was accompanied by a complex remodulation of gene expression, likely affecting important agronomic and merceological traits.

overall_design: Wild type (Cv. Ailsa Craig, accession number LA2838A), Aft/Aft (accession number LA1996), atv/atv (accession number LA0797) and double mutant (Aft/Aft atv/atv) were grown during the winter season in a controlled heated greenhouse. Fruits were collected at mature green, turning red and red stages of development. The transcriptional profile in Aft/Aft, atv/atv, and Aft/Aft atv/atv fruits when compared to the wild type was analyzed using the GeneChip® Tomato Genome Array.

first: Giovanni

last: Povero

first: Silvia

last: Gonzali


title: The Histoplasma capsulatum virulence factor CBP1 mediates a unique transcriptional signature associated with host-cell lysis

status: Public on Oct 01 2010

city: San Francisco

first: Sajeev

last: Batra

state: CA

institute: UCSF

summary:
keywords: murine bone marrow-derived macrophages response to Histoplasma capsulatum yeast infection
In order to gain a better understanding of the macrophage response to infection with H. capsulatum, an intracellular fungal pathogen, we conducted a microarray timecourse analysis of gene expression in bone marrow-derived macrophages infected with H. capsulatum yeasts.  The H. capsulatum gene CBP1 is required for virulence in animals, and is also necessary for macrophage lysis. Cbp1 protein is secreted, thus we hypothesized that it may interfere with macrophage signaling and/or gene expression. To test this, we compared macrophage gene expression profiles following infection with wild-type or cbp1 mutant yeasts. Additionally, we infected with UV-treated yeasts, which are phagocytosed and quickly degraded in the macrophage. Immediately following infection with either live, UV-treated, or cbp1 mutant yeasts, we observed a canonical inflammatory response signature from 1-3 hpi. At later time points following infection, we observe upregulation of several genes, including the pseudo-kinase Tribbles homolog 3, that have been linked to stress response and cell death in other cell types. The expression of these genes is dependent on CBP1, suggesting that this infection regulon may cause or respond to the initiation of a lytic program.

overall_design: Bone marrow-derived macrophages were isolated from 8 week-old female C57BL/6 mice and either mock-infected, or infected with live H. capsulatum yeasts (strain G217B), UV-treated yeasts, or yeasts harboring an insertion in the gene encoding the virulence factor CBP1. At various time points following infection, we isolated macrophage total RNA and subjected to RNA amplification to generate aRNA. aRNAs were hybed to 64 MEEBO arrays.

first: Charlotte

middle: A

last: Berkes

first: Dervla

last: Isaac

first: Davina

last: Hocking Murray

first: Anita

last: Sil


title: Expression data of fruits in the wildtype and ORR tomato plants

status: Public on Jun 05 2010

city: Potsdam

first: Björn

last: Usadel

address: Am Mühlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

summary:
An Ac/Ds transposon tagged mutant population was screened for changes in visible fruit phenotypes. One line showed orange, yellow sectors in the fruit and was named Orange ripening (Orr), its transposase free offspring showed Mendelian segregation yielding red, yellow and orange fruit bearing plants in a ratio of 1:2:1. Crossing the an orange fruit plant line to the wild-type yielded only plants bearing yellow fruit. A cross between the yellow fruit bearing progeny yielded 26 plants having red and 17 plants having yellow fruit, suggesting an over-dominant allele. Using inverse PCR analysis showed an insertion in the putative subunit M of the tomato Ndh complex. Subsequently, an Orr Ds transposon excision line was recovered which only showed red pigmented fruit. Here, we describe microarray profiling of tomato fruits from wild-type, heterozygous and homozygous Orr insertion plants and from fruits harvested from the Orr excision line.

Keywords: mutant wild type

overall_design:
Tomato fruits were harvested at breaker stage using wild-type, ORR homozygouse and heterozygous lines as well as Orr excision lines.
To investigate the expression changes in the ORR mutants, wildtype and ORR mutant line fruits were harvested at the breaker stage and subjected to Affymetrix microarray profiling

first: Nashilevitz

last: Shai

first: Melamed-Bessudo

last: Cathy

first: Rogachev

last: Ilana

first: Itkin

last: Maxim

first: Pankratov

last: Ilya

first: Hirschberg

last: Joseph

first: Wolf

last: Shmuel

first: Usadel

last: Björn

first: Itzkovich

last: Yinon

first: Levy

last: Avraham A

first: Rumeau

last: Dominque

first: Aharoni

last: Asaph


title: Tomato root transcriptome response to a nitrogen-enriched soil patch

status: Public on Mar 24 2010

first: Dan

last: Ruzicka

summary: Nitrogen (N), the primary limiting factor for plant growth and yield in agriculture, has a patchy distribution in soils due to fertilizer application or decomposing organic matter. Studies in solution culture over-simplify the complex soil environment where microbial competition and spatial and temporal heterogeneity challenge roots’ ability to acquire adequate amounts of nutrients required for plant growth.  In this study, various ammonium treatments (as 15N) were applied to a discrete volume of soil containing tomato (Solanum lycopersicum) roots to simulate encounters with a localized enriched patch of soil.  Transcriptome analysis was used to identify genes differentially expressed in roots 53 hrs after treatment.  Results:  The ammonium treatments resulted in significantly higher concentrations of both ammonium and nitrate in the patch soil. The plant roots and shoots exhibited increased levels of 15N over time, indicating a sustained response to the enriched environment.  Root transcriptome analysis identified 585 genes differentially regulated 53 hrs after the treatments.  Nitrogen metabolism and cell growth genes were induced by the high ammonium (65 ug NH4+-N g-1 soil), while stress response genes were repressed.  The complex regulation of specific transporters following the ammonium pulse reflects a simultaneous and synergistic response to rapidly changing concentrations of both forms of inorganic N in the soil patch.  Transcriptional analysis of the phosphate transporters demonstrates cross-talk between N and phosphate uptake pathways and suggests that roots increase phosphate uptake via the arbuscular mycorrhizal symbiosis in response to N.    Conclusion:  This work enhances our understanding of root function by providing a snapshot of the response of the tomato root transcriptome to a pulse of ammonium in a complex soil environment.  This response includes an important role for the mycorrhizal symbiosis in the utilization of an N patch.

overall_design: 9 Total samples were analyzed across 3 treatment groups (3 biological replicates per group). We generated the following pairwise comparisons using JMP Genomics software: Control vs. Low N, Control vs. high N, and low N vs. high N. One way ANOVA was used to determine significantly different expression.  Genes with an FDR≤10% were presented.

first: Daniel

first: Felipe

last: Barrios-Masias

first: Natasha

last: Hausmann

first: Louise

last: Jackson

last: Schachtman


title: Molecular analysis of a tomato OGDH antisense line

status: Public on Sep 01 2012

first: Marc

last: Lohse

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP-Golm

summary: Transgenic tomato (Solanum lycopersicum) plants expressing a fragment of the SlSIOGDH gene encoding subunit E1 of the 2-oxoglutarate dehydrogenase protein complex in the antisense orientation and exhibiting considerable reductions in the activity of this enzyme exhibit a considerably reduced rate of respiration. They were, however, characterised by largely unaltered photosynthetic rates and fruit yield but a restricted leaf, stem and root growth rate. The lines displayed markedly altered metabolic profiles including changes in tricarboxylic acid cycle intermediates and in the majority of the amino acids without alterations in pyridine nucleotide content. Moreover, they displayed a generally accelerated development exhibiting early flowering, accelerated fruit ripening and a markedly earlier onset of leaf senescence. In addition, transcript and selective hormone profiling of gibberellins and ABA revealed changes only in the former coupled to changes in transcripts encoding enzymes of gibberellins biosynthesis. The data obtained are discussed in the context of the importance of this enzyme in both photosynthetic and respiratory metabolism as well as in programs of plant development connected to carbon nitrogen interactions.

overall_design: Three biological replicates per genotype were analysed. Genotypes analyzed were tomato var. M82 wild type plants grown under green house conditions with one 2-oxo-glutarate dehydrogenase antisense line grown under the same conditions.

first: Wagner

middle: L

last: Araújo

first: Adriano

last: Nunes-Nesi

first: Sonia

last: Osorio

first: Ilse

last: Balbo

first: Ina

last: Krahnert

first: Agata

last: Sienkiewicz-Porzucek

first: Bjoern

last: Usadel

first: Alisdair

last: Fernie


title: Gene regulation in parthenocarpic tomato fruit

status: Public on Aug 31 2009

city: Davis

first: Abhaya

middle: M

last: Dandekar

address: One Shields Ave

institute: University of California, Davis

summary:
To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit.

Keywords: genetic modification

overall_design: Wild-type fruit with seeds was compared with transgenic lines INO-IaaM, DefH9-IaaM, INO-RolB, and DefH9-RolB. To find genes with seed-specific expression, we also compared the control with wild-type fruit from which seeds had been manually removed. We had three biological replicates for each treatment and control except DefH9-RolB, for which only two replicates were available. Each CEL file from the microarray represents one plant from each line.

first: Federico

last: Martinelli

first: Russell

last: Reagan

first: Ying

last: Chen

first: Sandra

last: Uratsu


title: Expression data from various tomato plant tissues

status: Public on Feb 01 2010

city: Kisarazu

first: Koh

last: Aoki

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Department of Biotechnology Research

country: Japan

institute: Kazusa DNA Research Institute

summary:
Gene-to-gene coexpression analysis is a powerful approach to infer function of uncharacterized genes. To perform non-targeted coexpression analysis of tomato genes, we collected a developmental gene expression dataset using various tissues of tomato plant. Expression data are collected from 24 different tissue types including root, hypocotyl, cotyledon, leaf at different stages, and fruit tissues at 4 different ripening stages from 4 different Solanum lycopersicum cultivars. Fruits were separated to the flesh and the peel. These two tissue types indeed showed remarkably different gene expression profiles. We also collected data from 4 different ripening stages (mature green, yellow, orange, and red) to detail the changes during ripening. By using this gene expression dataset, we calculated pair-wise Pearson’s correlation coefficients, and performed network-based coexpression analysis. The analysis generated a number of coexpression modules, some of which showed an enrichment of genes associated with specific functional categories. This result will be useful in inferring functions of uncharacterized tomato genes, and in prioritizing genes for further experimental analysis.
We used Affymetrix GeneChip Tomato genome Arrays to detail the global gene expression change using 24 different tomato tissue types (67 hybridizations).

overall_design: We collected gene expression data from 24 different tomato tissue types using 67 hybridizations. Root, hypocotyl, cotyledon, and leaf were sampled from 3-week-old or 5-week–old plant of Solanum lycopersicum cultivar Micro-Tom. Fruit tissues were sampled from S. lycopersicum cultivars Micro-Tom, Anthocyanin fruit (Aft, LA1996), Line27859, and Momotaro 8 (Takii, Japan). From Micro-Tom fruit, the peel and the flesh were separately sampled from 4 different ripening stages: mature green (MG, approximately 30 day after anthesis), yellow (Y, approximately 35 days after anthesis), orange (O, approximately 38-40 days after anthesis), and red (R, approximately 45-48 days after anthesis). From fruits of Aft and Line27859, the peel and the flesh were sampled at mature green (MG, approximately 40 days after anthesis) and red (R, approximately 50-55 days after anthesis) stages. From Momotaro 8, the peel and the flesh were sampled at red (R, 50- approximately 50-55 days after anthesis) stages. For each tissue type, 2-4 biological replicates were made in RNA preparation.

first: Soichi

last: Ozaki

first: Yoshiyuki

last: Ogata

first: Kunihiro

last: Suda

first: Tatsuya

last: Suzuki

first: Naoki

last: Yamamoto

first: Atsushi

last: Kurabayashi

first: Taneaki

last: Tsugane

first: Takashi

last: Fujii

first: Chiaki

last: Konishi

first: Shuji

last: Inai

first: Daisuke

last: Shibata


title: Expression data of tomato fruit responses to Botrytis cinerea

status: Public on May 22 2009

first: Dario

last: Cantu

institute: UC Davis

summary:
Tomato fruit ripening is associated with a dramatic increase in susceptibility to the fungal pathogen Botrytis cinerea, the causal agent of gray mold. Mature green fruit, prior to ripening, are largely resistant to B. cinerea, whereas red fruit, at the end of ripening, are susceptible to B. cinerea infection.
We used microarrays to detail the gene expression changes that are induced by B. cinerea when tomato fruit at unripe and ripe stages are infected.

Keywords: plant responses to pathogens

overall_design: Tomato fruit at mature green and red ripe stages were wound inoculated with a water suspension of B. cinerea conidia. Twenty four hours post inoculation fruit pericarp and epicarp tissue around and including the inoculation sites was collected and the total RNA extracted. Total RNA was also collected from healthy and mock inoculated fruit.

first: Ann

last: Powell


title: Tomato wild type, vector control and transgenic lines expressing InsP 5-ptase: mature fruits, root tips, and leaves

status: Public on Nov 15 2008

city: Raleigh

first: Mariya

last: Khodakovskaya

state: NC

address: 4218 Gardner Hall

department: Plant Biology

institute: North Carolina State University

summary:
To reduce the level of major second messenger inositol-1,4,5-triphosphate (InsP3), we generated transgenic tomato plants (cv. Micro-Tom) that are expressing InsP 5-ptase gene.  To understand effects of transgene (InsP 5-ptase) on gene expression we carried out microarray analysis from different parts of transgenic and control (wild type, empty vector control) tomato plants
Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in transgenic tomato plants expressing InsP 5-ptase gene
Keywords: genetic modification

overall_design:
Ripe fruits of wild type, vector control and two transgenic tomato lines expressing InsP 5-ptase gene  were selected for RNA extraction and hybridization on Affymetrix microarrays
First two leaves of 10 day old light grown in vitro seedlings of wild type, vector control and two transgenic tomato lines expressing InsP 5-ptase gene  were selected for RNA extraction and hybridization on Affymetrix microarrays
10 day old etiolated root tips of wild type, vector control and two transgenic tomato lines expressing InsP 5-ptase gene  were selected for RNA extraction and hybridization on Affymetrix microarrays

first: Heike

middle: W

last: Sederoff


title: tomato salt response

status: Public on Jun 01 2010

city: Beijing

first: Wei

last: Sun

address: 20 Nan Xin Cun

country: China

institute: Institute of Botany, Chinese Academy of Sciences

summary:
Wild halophytic tomato has long been considered as an ideal gene donor for improving salt tolerance in tomato cultivars. Here, a wild tomato genotype, Solanum pimpinellifolium ‘PI365967’ is significantly more salt-tolerant than a cultivar, Solanum lycopersicom ‘moneymaker’. Affymetrix Tomato Genome Arrays was used to compare the transcriptome change of PI365967 and Moneymaker by salt treatment.After treatment with 200 mM NaCl for 5 h, PI365967 showed relatively fewer responsive genes compared to Moneymaker. Salt Overly Sensitive (SOS) pathway was found to be more active in PI365967 than in Moneymaker, coinciding with relatively less accumulation of Na+ in shoots of PI365967. A gene encoding salicylic acid-binding protein 2 (SABP2) was induced by salinity only in PI365967, suggesting a possible role of salicylic acid signaling in salt response of PI365967. The fact that two genes encoding lactoylglutathione lyase were salt-inducible only in PI365967, together with much higher basal expression of several glutathione S-transferase genes, suggested a more effective detoxification system in PI365967.
Key words: salt tolerance, transcriptomic profiling, wild tomato, ion homeostasis, SABP2.

overall_design: In one treatment, 9 six-leaf-old plants of one tomato genotype (PI365967 or Moneymaker) were divided into three biological replicates and treated hydroponically under sterile condition with (or without) 200 mM NaCl for 5 h. RNA isolated from pooled three individual plants was used in hybridization to one chip, resulting in 12 chips in total.

first: Xinna

last: Xu

first: Aihua

last: Liu

first: Huishan

last: Zhu

first: Xuejun

last: Hua


title: Expression data from PSARK::IPT Nicotiana and wildtype plants

status: Public on Jan 09 2010

first: Zvi

last: Peleg

address: P.O.Box 12

department: Inst. of Plant Sciences

institute: Hebrew University

summary:
Stress-induced leaf senescence could be delayed in transgenic plants expressing isopentenyltransferase (IPT), an enzyme that catalyzes the rate-limiting step in CK synthesis under the control of SARK, a maturation- and stress-inducible promoter (Rivero et al., 2007). Increased CK production resulted in enhanced drought tolerance of the transgenic PSARK::IPT plants, with minimal yield loss (Rivero et al., 2007). We have used a large-scale expression profiling approach to investigate the effects of PSARK::IPT on gene expression to elucidate the molecular events associated with the CK-induced drought tolerance displayed by the PSARK::IPT plants.
We used tomato genechips to capture the differential transcriptional responses of WT and PSARK::IPT plants under control and water stress conditions

overall_design: Leaf samples from well watered (1000 mL per day) and water stressed (300 mL per day) plants were collected for RNA extraction and hybridization on Affymetrix microarrays after 45 days of stress.

first: Eduardo

last: Blumwald

first: Rosa

last: Rivero


title: Trafficking of mRNA from tomato to dodder

status: Public on Feb 01 2007

city: Blacksburg

first: James

last: Westwood

state: VA

address: 401 Latham Hall

department: Plant Pathol. Physiol. Weed Sci.

institute: Virginia Tech

summary:
An intriguing new paradigm in plant biology is that systemically-mobile mRNAs play a role in coordinating development.  In this process, specific mRNAs are loaded into the phloem transport stream for translocation to distant tissues, where they may impact developmental processes.  However, despite its potential significance for plant growth regulation, mRNA trafficking remains poorly understood and challenging to study.  Here we show that phloem-mobile mRNAs can also traffic between widely divergent species from a host to the plant parasite, lespedeza dodder (Cuscuta pentagona Engelm.).  Reverse transcriptase PCR (RT-PCR) and microarray analysis were used to detect specific tomato transcripts in dodder grown on tomato (Lycopersicon esculentum Mill.) that were not present in control dodder grown on other host species.  The foreign transcripts included LeGAI, which has been previously shown to be translocated in the phloem, as well as nine other transcripts not reported to be mobile.  Dodders are parasitic plants that obtain resources by drawing from the phloem of a host plant, and have joint plasmodesmata with host cortical cells.  Although viruses are known to move between dodder and its hosts, translocation of endogenous plant mRNA has not been reported.  These results point to a potentially new level of interspecies communication, and raise questions about the ability of parasites to recognize, use, and respond to transcripts acquired from their hosts.
Keywords: mRNA trafficking, parasitism, parasitic plant

sample_organism:
Solanum lycopersicum
Cuscuta pentagona

overall_design: In order to identify potential tomato transcripts in dodder, microarray analysis was performed on RNA from dodder and hosts.  Total RNA was extracted from the tomato host and from dodder grown on tomato, Arabidopsis, tobacco, or pumpkin.  The host tomato RNA was included to verify that any transcripts detected in the parasite were in fact expressed in the host.  The dodder samples grown on tobacco, Arabidopsis, and pumpkin served as controls for dodder genes that may cross-hybridize with tomato array probes, with three different host species used to minimize any host-specific effects on dodder gene expression.  Samples were analyzed using the Affymetrix GeneChip Tomato Array and transcripts scored for presence or absence in each sample.  Considering that host transcripts present in dodder would be at low levels and diluted with dodder transcripts, a P-value of 0.06 in at least two of three biological replicates was used as the threshold for scoring a transcript as being present.

first: Jeannine

last: Roney