title: Circadian expression profiling in grapevine ripening berries

status: Public on Mar 28 2014

summary:
Temperature and solar radiation influence Vitis vinifera L. berry ripening. Both environmental conditions fluctuate cyclically on a daily period basis and the strength of this fluctuation affects grape ripening too. Additionally, a molecular circadian clock regulates daily cyclic expression in a large proportion of the plant transcriptome modulating multiple developmental processes in diverse plant organs and developmental phases. Circadian cycling of fruit transcriptomes has not been characterized in detail despite their putative relevance in the final composition of the fruit. Thus, in this study, gene expression throughout 24 h periods in pre-ripe berries of Tempranillo and Verdejo grapevine cultivars was followed to determine whether different ripening transcriptional programs are activated during certain times of day in different grape tissues and genotypes.
Results: Microarray analyses identified oscillatory transcriptional profiles following circadian variations in the photocycle and the thermocycle. A higher number of expression oscillating transcripts were detected in samples carrying exocarp tissue including biotic stress-responsive transcripts activated around dawn. Thermotolerance-like responses and regulation of circadian clock-related genes were observed in all studied samples. Indeed, homologs of core clock genes were identified in the grapevine genome and, among them, VvREVEILLE1 (VvRVE1), showed a consistent circadian expression rhythm in every grape berry tissue analysed. Light signalling components and terpenoid biosynthetic transcripts were specifically induced during the daytime in Verdejo, a cultivar bearing white-skinned and aromatic berries, whereas transcripts involved in phenylpropanoid biosynthesis were more prominently regulated in Tempranillo, a cultivar bearing black-skinned berries.
Conclusions: The transcriptome of ripening fruits varies in response to daily environmental changes, which might partially be under the control of circadian clock components. Certain cultivar and berry tissue features could rely on specific circadian oscillatory expression profiles. These findings may help to a better understanding of the progress of berry ripening in short term time scales.

overall_design: A total of 54 samples were hybridized. Three different circadian time course series consisted on six time point each. Series corresponded to pericarp of Verdejo grapevine cultivar and berry flesh and skin in separate of Tempranillo cultivar. Three biological replicates were analyzed for each series.


title: Transcript and metabolite analysis of Vitis vinifera cv. Trincadeira berries infected with Botrytis cinerea reveals an activation of a non-sustained plant defense response

status: Public on Mar 31 2014

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

summary: Vitis vinifera berries are sensitive towards infection by the necrothopic pathogen Botrytis cinerea leading to important economic losses worldwide. The combined analysis of the transcriptome and metabolome associated with the infection has not been previously performed in grapes or in another fleshy fruit. In an attempt to identify the molecular and metabolic mechanisms associated with the infection, pepper- corn size fruits (EL 29) were infected in-field and green berries (EL 33) and veraison berries (EL 35) were collected for microarray analysis complemented with metabolic profiling using GC-EI-TOF/MS and headspace GC-EI-MS platforms. The results provide evidence of a reprogramming of carbohydrate and lipid metabolisms towards increased synthesis of secondary metabolites involved in plant defense such as trans-resveratrol and gallic acid. The response is mainly activated in green berries with the putative involvement of jasmonic acid, ethylene, polyamines and auxins whereas salicylic acid does not seem to be involved. At veraison, however, genes encoding protein kinases, MYB and WRKY transcription factors, pathogenesis-related proteins, glutathione S-transferase, stilbene synthase and phenylalanine ammonia-lyase are no longer up-regulated or even down-regulated suggesting that the basal defense response is not active with the onset of ripening. This non-sustained defense response has not been previously reported for necrotrophic, biotrophic, or hemibiotrophic pathogens, and highlights the importance of conducting studies in fruits and not solely in vegetative tissues. Furthermore, this study provided with metabolic biomarkers of infection namely azelaic acid, arabitol and gluconic acid that can be used to monitor infection early in the vineyard.

overall_design: 2 time points in 2011 season at EL 33 and EL 35. 3 biological replicates. Grapes Infected with Botrytis cinerea and control with phosphate buffer

middle: M

first: Patricia

last: Agudelo-Romero


title: The transcriptome of lae1 mutants of Trichoderma reesei cultivated at constant growth rates reveals new targets of LAE1 function

status: Public on Mar 07 2014

city: Debrecen

first: Levente

last: Karaffa

address: Egyetem ter 1.

department: Biochemical Engineering

country: Hungary

institute: University of Debrecen

summary: We used three biological replicas of  T. reesei (QM9414), a Δlae1 mutant and a lae1-overexpressing strain in the chemostat on glucose at two different growth rates (0.075 and 0.020 h-1).

overall_design: Two to four subsequently achieved, independent steady-states were sampled and analysed for each dilution rate and fungal strain.


title: A novel NAC transcription factor cooperates with bZIP-type transcription factors in dehydration and osmotic stress responses

status: Public on Jan 02 2014

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Multiple transcription factors (TFs) play essential roles in plants under abiotic stress, one of the most challenging conditions of plant survival. However, how these multiple TFs cooperate in abiotic stress responses still remains largely unknown. In this study, we provide evidence that a novel NAC (NAM, ATAF1/2, and CUC2) transcription factor (ANAC096) cooperates with bZIP-type TFs [ABRE-binding factor/ABRE-binding protein (ABF/AREB)] in ensuring survival under dehydration and osmotic stress conditions. Intriguingly, ANAC096 directly interacted with ABF2 and ABF4, but not with ABF3, both in vitro and in vivo. ANAC096 and ABF2 synergistically activated RD29A transcription. The genome-wide gene expression analysis revealed that a major proportion of ABA-responsive genes are under the transcriptional regulation of ANAC096.An Arabidopsis mutant, anac096, was hyposensitive to exogenous abscisic acid (ABA), and showed impaired ABA-induced stomatal closure and increased water loss under dehydration stress conditions. Furthermore, the anac096 abf2 abf4 triple mutant was much more sensitive to dehydration and osmotic stresses than the anac096 single mutant or the abf2 abf4 double-mutant. Based on these results, we propose that ANAC096 is involved in a synergistic relationship with a subset of ABFs for the transcriptional activation of ABA-inducible genes in response to dehydration and osmotic stresses.

overall_design: pTA plants (12-day-old) cultured in liquid medium were treated with 30 uM Dex alone for 1 h (Control) or 30 uM Dex alone for 30 min followed by an additional treatment of 30 min with both 30 uM Dex and 2 uM ABA (ABA). For pTA-ANAC096 plants, 12-day-old seedlings were treated with 30 uM Dex for 1 h (ANAC096) or with 30 uM Dex only for 0.5 h followed by additional 0.5 h incubation with both 2 uM ABA and 30 uM Dex (ANAC096+ABA). Total RNAs were isolated from two biological replicates at each condition and used to measure gene expression level.

first: Inhwan

last: Hwang

first: Daehee


title: The Transcriptomic Regulation of Berry Development is More Important at Night than During the Day

status: Public on Dec 20 2013

city: Montpellier

first: markus

last: rienth

address: 2, Place Pierre Viala

country: France

institute: INRA Montpellier

summary: In order to circumvent environmental changes throughout fruit development, young and ripening berries were sampled simultaneously on continuously flowering microvines acclimated to controlled circadian light and temperature changes.     Gene expression profiles along fruit development were monitored during both day and night with whole genome microarray Nimbelgen® vitis 12x, yielding a total number of 9273 developmentally modulated probesets. All day-detected transcripts were modulated at night, whereas 1755 genes were night-specific. Very similar developmental patterns of gene expression were observed upon independent hierarchical clustering of day and night data, whereas functional categories of allocated transcripts varied according to time of the day. Many transcripts within pathways, known to be upregulated during ripening, in particular those linked to secondary metabolism exhibited a clearer developmental regulation at night than during the day. Functional enrichment analysis also indicated that diurnally modulated genes considerably varied during fruit development, with a shift from cellular organization and photosynthesis in green berries to secondary metabolism and stress-related genes in ripening ones. These results reveal critical changes in gene expression during night development that differ from day development which have not been observed in other transcriptomic studies on fruit development so far.

overall_design: A total of 24 samples were analyzed representing four berry developmental stages (two during green development, two during ripening). Sample were drawn simultaneously in triplicates at day and night on the microvine dwarf (DRCF) GAI mutant.

first: Markus

last: Rienth

first: Laurent

last: Torregrosa

first: Mary

middle: T

last: Kelly

first: Nathalie

last: Luchaire

first: Anne

last: Pellegrino

first: J

last: Grimplet

first: Charles

last: Romieu


title: Global Analysis of Thyroid Receptor Binding Sites Reveals Interaction with the Ddx54 and Thrsp Promoter in Juvenile Mouse Liver

status: Public on Nov 16 2013

city: Ottawa

first: Martin

last: Paquette

address: 50 Colombine

country: Canada

institute: Health Canada

type: Genome binding/occupancy profiling by genome tiling array

summary: Thyroid hormones (THs) play a critical role in development and throughout adulthood. THs act through the thyroid receptor (TR), which binds to the TH response element (TRE) to regulate the expression of target genes. Although TH action has been studied for decades, surprisingly few TREs have been well validated and characterized. In this study we used chromatin immunoprecipitation followed by microarray analysis (ChIP-chip) to identify TR-binding sites in juvenile (postnatal day 15) mice liver. Microarray analysis revealed twelve TR-binding sites consistent between all analyzed samples. In silico analysis was carried out to search for moderately conserved classic TRE sequences within these novel binding regions, which led to the identification of six candidate TREs within three binding regions. Luciferase reporter assays confirmed the presence of a TRE in the promoter region of DEAD (Asp-Glu-Ala-Asp) box polypeptide 54 (Ddx54) and thyroid hormone responsive SPOT14 (Thrsp). The TR/retinoid X receptor (RXR) heterodimer and RXR homodiner were shown to bind the promoter region of Ddx54 and drive gene expression in the presence of 9-cis-retinoic acid (9cRA). The promoter region of Thrsp was shown to allow binding of the TR/RXR heterodimer, and both T3 and 9cRA were able to significantly increase luciferase activity. The RXR homodimer was also able to bind the response element in the promoter region of Thrsp and increase luciferase activity. Overall, ChIP-chip analysis revealed a relatively limited number of TR-binding sites in juvenile mouse liver despite previous studies showing that numerous genes can be affected by TH disruption at that developmental stage, suggesting that TH action may also be mediated through other intermediates. Collectively the results provide an important step towards characterizing TR-binding sites and identifying the underlying drivers of TR-gene regulation.

overall_design: Three samples were analyzed (total input and immunoprecipitated for each samples).

middle: A

first: Rémi

last: Gagné

first: Hongyan

last: Dong

first: Ella

last: Atlas

first: Mike

middle: G

last: Wade

first: Carole

middle: L

last: Yauk


title: Differential roles of nuclear and cytosolic GI in regulating plant circadian system

status: Public on Sep 01 2013

city: Pohang

first: Seungmin

last: Han

state: Gyeongbuk

address: Hyojadong

department: School of Interdisciplinary Bioscience and Bioengineering

institute: POSTECH

summary: GIGANTEA (GI) is an important modulator of plant circadian system. Recent studies have reported that protein GI is localized in both nucleus and cytosol, and nuclear and cytosolic GI exert differential effect on plant circadian clock. We first generated GI-null mutants and transgenic Arabidopsis plants that expressed GI fused to green fluorescent protein gene (GIpro::GI-GFP) and GI-GFP with a nuclear localization signal (GIpro::GI-GFP-NLS) or with a nuclear export signal (GIpro::GI-GFP-NES) under the control of native promoter in GI-null mutants. To investigate differential roles of nuclear and cytosolic GI in regulating plant circadian clock, we performed genome-wide gene expression profiling for wild-type plants and the GI-transgenic plants at morning and evening, and analyzed complementation patterns of gi-2 lesion by nuclear and cytosolic GI. As a result, we identified four complementation patterns representing genes affected by only nuclear GI (GIN) or cytosolic GI (GIC), those by either GIN or GIC, and those by the action of both GIN and GIC. Furthermore, we compared the transgenic plants expressing GIpro::GI-GFP with WT and the other GI-transgenic plants to confirm whether abnormally expressed genes by the gi-2 mutation can be complemented by restoring protein GI.

overall_design: Wild-type plants (Col), GI-null mutants (gi-2), and the other transgenic gi-2 plants expressing GIpro::GI-GFP (called GI plants), GIpro::GI-GFP-NLS (called GI-NLS plants), and GIpro::GI-GFP-NES (called GI-NES plants) were grown for seven days under conditions of 16 h light and 8 h dark (LD) and harvested at 1h (ZT1) and 16 hr (ZT16) after the light is turned on, representing morning and evening, respectively. mRNA levels were measured from three biological replicates of Col, gi-2, GI-NLS, GI-NES, and GI.

first: Hong

last: Nam


title: miRNA expression profile in rat carotid artery balloon injury model

status: Public on Apr 23 2013

city: Hwasun

first: Nakwon

last: Choe

state: Seoyang-ro 322

address: Baekseo-ro 160

department: Pharmacology

institute: Chonnam Univ. Med. Sch.

summary: The proliferation and remodeling of vascular smooth muscle cells (VSMCs) is an important pathological event in atherosclerosis and restenosis. Here we report that microRNA-132 (miR-132) blocks vascular smooth muscle cells (VSMC) proliferation by inhibiting the expression of LRRFIP1 [leucine-rich repeat (in Flightless 1) interacting protein-1]. MicroRNA microarray revealed that miR-132 was upregulated in the rat carotid artery after catheter injury, which was further confirmed by quantitative real-time RT-PCR. Transfection of an miR-132 mimic significantly inhibited the proliferation of VSMCs, whereas transfection of an miR-132 antagomir increased it. Bioinformatics showed that LRRFIP1 is a target candidate of miR-132. miR-132 down-regulated luciferase activity driven by a vector containing the 3’-untranslated region of Lrrfip1 in a sequence-specific manner. LRRFIP1 induced VSMC proliferation. Immunohistochemical analysis revealed that Lrrfip1 was clearly expressed along with the basal laminar area of smooth muscle, and its expression pattern was disrupted 7 days after arterial injury LRRFIP1 mRNA was decreased 14 days after injury. Delivery of miR-132 to rat carotid artery attenuated neointimal proliferation in carotid artery injury models. Our results suggest that miR-132 is a novel regulator of VSMC proliferation that represses neointimal formation by inhibiting LRRFIP1 expression.

overall_design: Balloon injury was induced in the carotid arteries of male Sprague–Dawley rats weighing approximately 250 g. Total RNA were extracted from the arterial sections after 10 days. MicroRNA profile of the sample was compared with non-injured control.

first: Jin-Sook

last: Kwon

first: Ju-Ryung

last: Kim

first: Gwang

middle: H

last: Eom

first: Yongsook

first: Kwang-Il

first: Youngkeun

last: Ahn

first: Hae

middle: J

last: Kee

first: Hyun

last: Kook


title: Systemic analysis of lactose metabolism in Trichoderma reesei identifies a lactose permease that is essential for cellulase induction

status: Public on Jun 30 2013

city: Vienna

first: Christian

middle: P.

last: Kubicek

address: Getreidemarkt 9

country: Austria

institute: TU Vienna

summary: Lactose (1,4-0-ß-d-galactopyranosyl-d-glucose), a by-product from cheese manufacture or  whey processing industries, is known to induce the formation of plant biomass hydrolyzing enzymes needed for the biorefinery industry in the fungus Trichoderma reesei, but the reason for this induction and the underlying mechanism are not fully understood. Here, we used systems analysis of the Trichoderma reesei transcriptome during utilization of lactose. We found that the respective CAZome encoded glycosyl hydrolases specifically tailored for the attack of monocotyledon xyloglucan. In addition, genes for a high number of putative transporters of the major facilitator superfamily were also induced. Systematic knock out of them identified a gene whose knock-out completely impaired lactose utilization and cellulase induction in Trichoderma reesei. These data shed new light on the mechanism by which Trichoderma reesei metabolizes lactose and illuminate the key role of ß-D-galactosides in habitat specificity of this fungus.

overall_design: We used two biological replicas of Trichoderma reesei growing on lactose, glucose and glycerol

middle: P


title: Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose

status: Public on Sep 17 2013

summary: We have examined and compared the transcriptome of T. reesei growing on wheat straw and lactose as carbon sources under otherwise similar conditions.  Gene expression on wheat straw exceeded that on lactose, and 1619 genes were found to be only induced on wheat straw but not on lactose. They comprised 30 % of the CAZome, but were also enriched in genes associated with phospholipid metabolism, DNA synthesis and repair and iron homeostatis. Two thirds of the CAZome was expressed both on wheat straw as well as on lactose, but 60 % of it at least >2-fold higher on the former. Major wheat straw specific genes comprised xylanases, chitinases and ß-mannosidases. Interestingly, the latter two CAZyme families were significantly higher expressed in a strain in which xyr1 encoding the major regulator of cellulase and hemicellulase biosynthesis is non-functional, demonstrating that XYR1 is a repressor of these genes.

overall_design: We used two biological replicas of four T. reesei strains growing on glucose, lactose, and on wheat straw


title: Night heat stress triggered different transcriptomic responses than day stress in green and ripening grapevine (Vitis vinifera) fruits

status: Public on Jan 08 2014

first: markus

last: rienth

summary:
Background: Global climate change, in particular the entailed predicted temperature increase, will noticeably affect plants vegetative and reproductive development. High temperatures alter the composition of the grapevine fruit, one of the most important fruits produced worldwide. This is leading to variable yield and quality, already observed in many growing regions in recent years. However, physiological processes underlying temperature response and tolerance of the grapevine fruit have hardly been investigated. Currently, all studies on fleshy fruits investigating their abiotic stress response on a molecular level were conducted during the day but possible night-specific variations were overlooked. The present study explores the grapevine fruit transcriptomic response at different developmental stages upon heat stress at day and night.
Methodology/Principal Results: Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axis. The recently proposed microvine model was grown in climatic chambers in order to circumvent common constraints and biases introduced in field experiments with perennial vines. Post-véraison berry heterogeneity inside clusters was evaded upon constituting homogenous batches following organic acid and sugar measurements on individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbelGen® 090918 12X microarrays (30K).
Results revealed important differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes within phenylpropanoid metabolism. Precise distinction of post-véraison stages led to a stage-specific detection of anthocyanin-related transcripts repressed by heat. Important modifications in cell wall-related processes as well as indications for a heat-induced delay of ripening and sugar accumulation were observed at véraison and reversed in later stages.
Conclusion: This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity to include different developmental stages and especially different time points in transcriptomic studies.

overall_design: A total of 12 samples were analyzed representing three berry developmental stages (two after the onset of ripening, one during green growth). At each stage, heat stress was applied at day and night. Controls and treated berry samples were drawn in triplicates (two in duplicates) at day and at night on the microvine dwarf (Dwarf Rapid Cycling and Continous Flowering; DRCF) gibberellin-insensitive (GAI) mutant.

first: Markus

last: Rienth

first: Laurent

last: Torregrosa

first: Nathalie

last: Luchaire

first: Rattaphon

last: Chatbanjong

first: Mary

last: Kelly

first: Charles

last: Romieu


title: RHBDD2 silencing and gene expression profiling of breast cancer cells

status: Public on Apr 10 2013

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: In previous studies, we identified a distantly related rhomboid homologue gene known as RHBDD2 (Rhomboid domain containing 2) to be markedly overexpressed in the advanced stages of the breast and colorectal cancer diseases. In order to identify RHBDD2 modulated pathways, we analyzed two breast cancer cell lines (MCF7 and T47D) from control and RHBDD2-siRNA transient gene silencing followed by gene expression profiling analysis using the whole genome Toray 3D-GeneTM Human Oligo Chip. Statistical analysis of the Toray's 3D gene expression profiling data identified 566 commonly differentially expressed genes in association to the RHBDD2 knockdown in both breast cancer cell lines. Among the statistically significant over-represented biological process, we found the apoptosis, cell cycle and response to DNA damage process related genes.  In addition, categories of genes found in the ubiquitin-proteasome and oxidative phosphorylation were also highly enriched related genes in the commonly deregulated gene list. We further used a lentivirus-based system (shRNA-pLKO.1) for stable silencing of RHBDD2 mRNA in the T47D breast cancer cell line. Using a staurosporine-induced apoptosis model, we demonstrate that RHBDD2 abrogation resulted in an apoptosis-resistant phenotype of T47D breast cancer cell line. These data are in line with a recent study, suggesting that RHBDD2 expression could be up-modulated in response to 5FU-induced apoptosis in colorectal cancer cells. Taken together, these data suggest that RHBDD2 could be involved in the modulation of the programmed cell death in cancer cells.

overall_design: In order to analyze differential gene expression profiling of RHBDD2 silencing and control cells, total RNA was isolated from replicate experiments from two breast cancer cell lines (MCF7 and T47D) derived from the negative control-siRNA and the RHBDD2-siRNA treatments in duplicate experiments.

middle: C

first: Ezequiel

last: Lacunza


title: ChIP-on-chip on BMP2 treated C2C12 cells transfected with FLAG tagged Alx3 expression vector

status: Public on Mar 05 2013

city: Shinagawa

first: Atsushi

last: Yamada

state: Tokyo

address: 1-5-8 Hatanodai

department: School of Dentistry

country: Japan

institute: Showa University

summary: FLAG-binding DNA analysis using Agilent Mouse promoter 1M microarray

overall_design: Input vs FLAG-IP


title: Selective defoliation affects plant growth, fruit transcriptional ripening program and flavonoid metabolism in grapevine.

status: Public on Mar 08 2013

city: Bologna

first: Chiara

last: Pastore

address: Viale Fanin, 46

country: Italy

institute: University of Bologna

summary: The purpose of this study was to quantify the effects of basal leaf removal applied in Sangiovese cultivar at two different phonological stages, pre-bloom and veraison, on berry composition. As very few papers were published about the regulation of gene expression induced by vineyard management techniques, we report the first global transcriptomic analysis (integrated with agronomic and biochemical data) aiming to determine the molecular mechanisms that control Sangiovese berry composition. The comparison of gene expression profiles of defoliated vines at pre-bloom and at veraison with the control, revealed a common transcriptional response at the end of veraison in both treated berries, but also a more extensive transcriptome rearrangement in pre-bloom defoliated ones, which could be linked to the strong biochemical changes detected in the berry after pre-bloom veraison.

overall_design: Total RNA recovered from a pool of berries derived from three control plants (C) was compared to total RNA from a pool of berries derived from three defoliated vines at pre-bloom (PB, JD 147,6 basal leaves and  relative laterals removed from each shoot) and three defoliated vines at veraison (V, JD 211,6 basal leaves and  relative laterals removed from each shoot) at beginning of veraison (BV), end of veraison (EV) and harvest (H). For each sampling date microarray analyses were conducted for three different biological replicates for treatment.

first: Sara

last: Zenoni


title: Sauvignon blanc berry developmental

status: Public on Dec 31 2012

city: Stellenbosch

first: Daniel

last: Jacobson

address: Victoria Street

country: South Africa

institute: Stellenbosch University

summary: Berries were sample at three developmental stages (green, veraison and ripe) and flash frozen in the field in liquid nitrogen. The frozen tissue was subsequently ground in liquid nitrogen and stored at  80°C. At least three independent berry samples were collected (with n≥50 berries per sample) at three time points: at pre-véraison/green stage (Eichhorn-Lorenz (E-L) system stage 31), at véraison (E-L stage 34) and at ripe/harvest stage (E-L stage 38)

overall_design: Ground tissues for each developmental stage were pooled.  Replicates: Separate RNA extractions were performed on aliquots of the ground tissue from each developmental stage, labeled and hybiridized to the microarrays


title: Co-evolution between Grapevine rupestris stem pitting-associated virus and Vitis vinifera L. induces a decrease in defence responses and physiological performance associated with an increase in photosynthesis-related gene transcription

status: Public on Oct 05 2012

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

institute: University of Verona

summary: Grapevine rupestris stem pitting-associated virus (GRSPaV) is a widespread virus affecting Vitis spp. Although it has established a compatible viral interaction in Vitis vinifera L. without the development of phenotypic alterations, it can occur as distinct variants that show different symptoms in diverse Vitis species. We investigated the changes induced by GRSPaV in V. vinifera cv Bosco, an Italian white grape variety, by combining agronomic, physiological, and molecular approaches, in order to provide comprehensive information about the global effects of GRSPaV. In two consecutive years, this virus caused a moderate decrease in physiological efficiency, yield performance, and sugar content in berries associated with several transcriptomic alterations. Transcript profiles were analysed by microarray techniques in petiole, leaf, and berry samples collected at véraison and by quantitative real-time RT-PCR (qRT-PCR) in a time course carried out at five relevant grapevine developmental stages. Global gene expression analyses showed that transcriptomic changes were highly variable among the different organs and the different phenological phases. GRSPaV triggers some unique responses in the grapevine at véraison, never reported before for other plant-virus interactions, such as an increase in transcripts involved in photosynthesis and CO2 fixation, associated with a moderate reduction in the photosynthesis rate and some defence mechanisms, and to an overlap with responses to water and salinity stresses. We hypothesise that the long co-existence between grapevine and GRSPaV has resulted in the evolution of a form of mutual adaptation between the virus and its host. This study contributes to elucidating alternative mechanisms used by infected plants to contend with viruses.

overall_design: The study was carried out in a vineyard planted in 2002 in Albenga (Liguria), North-West Italy, where a row was established with the white grape cultivar Bosco (V. vinifera L.). Microarray analysis was carried out on leaves, petioles, and berries collected at véraison (E-L35) in 2010. For each of the six GRSPaV-free and six GRSPaV-infected vines selected for the physiological and agronomical parameters evaluation, we collected 6 leaves (3 basal and 3 apical) with the related petioles and 12 berries from 3 different bunches. Samples from each organ were arbitrary pooled in 3 independent biological replicates and total RNA was extracted according to the method described by Gambino et al. (2008).

first: Giorgio

last: Gambino

first: Danila

last: Cuozzo

last: Pagliarani

first: Marco

last: Vitali

first: Paolo

last: Boccacci

first: Mario

last: Pezzotti

first: Franco

last: Mannini


title: Increasing the source/sink ratio in Vitis vinifera (cv Sangiovese) induces extensive transcriptome reprogramming and modifies berry ripening

status: Public on Mar 05 2012

summary:
Background: Cluster thinning is an agronomic practice in which a proportion of berry clusters are removed from the vine to increase the source/sink ratio and improve the quality of the remaining berries. Until now no transcriptomic data have been reported describing the mechanisms that underlie the agronomic and biochemical effects of thinning.
Results: We profiled the transcriptome of Vitis vinifera cv. Sangiovese berries before and after thinning at veraison using a genome-wide microarray representing all grapevine genes listed in the latest V1 gene prediction. Thinning increased the source/sink ratio from 0.6 to 1.2 m2 leaf area per kg of berries and boosted the sugar and anthocyanin content at harvest. Extensive transcriptome remodeling was observed in thinned vines 2 weeks after thinning and at ripening. This included the enhanced modulation of genes that are normally regulated during berry development and the induction of a large set of genes that are not usually expressed.
Conclusion: Cluster thinning has a profound effect on several important cellular processes and metabolic pathways including carbohydrate metabolism and the synthesis and transport of secondary products. The integrated agronomic, biochemical and transcriptomic data revealed that the positive impact of cluster thinning on final berry composition reflects a much more complex outcome than simply enhancing the normal ripening process.

overall_design: Total RNA recovered from a pool of berries derived from three control plants (C) was compared to total RNA from a pool of berries derived from three cluster thinned vines (50% of cluster removed) at beginning of véraison (BV), end of véraison (EV) and harvest (H). For each sampling date microarray analyses were conducted for three different biological replicates for treatment.


title: Transcriptome during shift of Trichoderma reesei from mycelial growth to asexual sporulation

status: Public on Dec 08 2011

first: Christian

last: Kubicek

summary: The asexual spore or conidium plays a critical role in the life cycle of many filamentous fungi, being the primary means for dispersion in the environment. To investigate the transcriptional changes taking place during the sporulation phase in T. reesei, which culminates with the production of the conidiospores, microarray experiments were performed. Among the 1,994 distinct genes displaying >90 % confidence , a total of 900 were classified as differentially expressed, relative to time zero of sporulation, at at least one of the time points analyzed. The main functional categories (FunCat) overrepresented among upregulated genes were those involving solute transport, metabolism, transcriptional regulation, secondary metabolite synthesis, lipases, proteases and particularly cellulases and hemicellulases. Categories overrepresented among downregulated genes were especially those associated with ribosomal and mitochondrial functions. The upregulation of cellulase and hemicellulase genes was depending on the function of the positive transcriptional regulator XYR1, but the latter exerted no influence on sporulation itself.  At least 20 % of the significantly regulated genes occured non-randomly distributed within the T. reesei genome suggesting an epigenetic component in the regulation of conidiation. The significant upregulation of cellulases and hemicellulases during conidiation, and thus cellulase and hemicelulase content in the spores of T. reesei lend to hypothesize that the ability to hydrolyse plant biomass is a major trait of this fungus to break dormancy and reinitiate vegetative growth after a period of facing unfavorable conditions

overall_design: One control and three sample points, checked by a marker enzyme for sporulation and by microscopy, were done in two biologicvao replicas

first: Benjamin

last: Metz

first: Verena

last: Seidl-Seiboth

first: Thomas

last: Haarmann

first: Alexeij

last: Kopchinskiy

first: Patrick

last: Lorenz

first: Bernhard

last: Seiboth


title: Various genetic interactions of GIGANTEA and EARLY FLOWERING 4 by a functional dominance during a day in Arabidopsis

status: Public on Jul 01 2012

first: Hee Jung

last: Koo

address: Hyojadong San 31

institute: Pohang University of Science and Technology

summary: Plants use their endogenous clock to regulate many physiological processes related to their survival and adaptability. GIGANTEA (GI), one of the clock proteins, contributes to the maintenance of circadian period length and amplitude and also regulates flowering time and hypocotyl growth in response to day length. In addition to GI, EARLY FLOWERING 4 (ELF4), another clock regulator, also contributes to these processes. However, little is known about the overall interactions between GI and ELF4 in Arabidopsis. In this study, we investigated the genetic interactions between GI and ELF4 in circadian output regulation. The results show that GI is dominant to ELF4 in flowering time determination, but ELF4 is dominant to GI in hypocotyl growth regulation. Moreover, GI and ELF4 have a synergistic effect on endogenous clock regulation. Further, gene expression profiling of gi-2, elf4, and gi-2 elf4 mutants confirmed that GI and ELF4 had differential dominant effects on circadian physiological outputs at dawn and dusk, respectively. This differential dominance of GI and ELF4 provides a potential means to achieve the diversity in the regulation of circadian physiological outputs including flowering time and hypocotyl growth.

overall_design: The genetic interactions between GI and ELF4 could be time-dependent functional dominance along a day, called temporal dominance hereafter. To test this hypothesis, we performed gene expression profiling of WT, gi-2, elf4 and gi elf4 plants at dawn (ZT1) and dusk (ZT16).

first: Hong

last: Nam

first: Daehee

last: Hwang


title: Gene expression profiling of liver from dairy cows subjected to intra-mammary LPS treatment: time course

status: Public on Nov 03 2008

city: Tjele

first: Peter

last: Sørensen

address: Blichers Alle 1

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary:
Liver plays a profound role in the acute phase response (APR) observed in the early phase of acute bovine mastitis caused by Escherichia coli (E. coli). To gain an insight into the genes and pathways involved in hepatic APR of dairy cows we performed a global gene expression analysis of liver tissue sampled at different time points before and after intra-mammary (IM) exposure to E. coli lipopolysaccharide (LPS) treatment.
Keywords: Time course

overall_design: Eight healthy, high yielding Holstein-Friesian dairy cows in their first lactation (9 to 12 weeks after calving) were chosen for this study. At time 0 the right front quarter was infused with 200 μg E. coli LPS dissolved in 10 ml 0.9% NaCl solution, the left front quarter serving as control was infused with 10 ml 0.9% NaCl solution. Liver biopsies were taken at –22, 3, 6, 9, 12 and 48 hours relative to LPS infusion in 4 cows, and also at –22, 9 and 48 hours in the remaining 4 cows. RNA from liver biopsies was isolated and biotin labeled cRNA was loaded onto the Affymetric GeneChip Bovine Genome Array. A control study using cows infused with 0.9% NaCl showed that there was no effect of taking the biopsy, neither in the clinical measurement nor in the expression of a selected subset of genes. Therefore, only samples taken from the LPS treated cows were measured for the gene expression using microarrays.

first: Li

last: Jiang

first: Christine

last: Røntved

first: Lotte

last: Nielsen

first: Klaus

last: Ingvartsen


title: Expression analysis of Hypocrea jecorina CBS999.97(MAT1-2) wild-type and delta-env1 strains in four different light and darkness conditions

city: Taipei

first: Ting-Fang

last: Wang

address: Academia Sinica. 128 Sec. 2, Academia Rd

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: Investigation of whole genome gene expression level changes in response to different light conditions of the H. jecorina CBS999.97(MAT1-2) parental strain (W) and the deletion strain delta-env1 (E). These two strains were grown on malt extract agar(Merck) at 25℃ in four different conditions: (1) 24L: constant light illumination (24L); (2) 12L12D: in a 12h light/dark cycle and then 6h light illumination; (3) 12D12L: in a 12h dark/light cycle and then 6h constant darknes;  (4) 24D:  constant darkness. The wild-type strain is potent for sexual development in 12D12L, 12L12D and 24D, whereas the delta-env1 mutant undergo sexual development only in 24D. By contrast, the wild-type strain is female sterile in 24L, and  the delta-env1 mutant is female sterile in 12D12L, 12L12D and 24D. Our results reveal that  conidation-specific genes, mating locus gene, h-type maitng pheromone genes, and genes invovled in processing and secretion of h-type mating pheromone are significantly upregulated in all four female sterile conditions (W-24L, E-12L12D, E-12D12L and E-24L).

overall_design: We used two biological replicates of two H. jecorina CBS999.97 (MAT1-2) strains, wild-type (W) and delta-env(E) on the cellophane-covered malt extract agar (MEA) plate at 25℃ for 7.25 days.

first: Chia-Ling

last: Chen

first: Hsio-Che

last: Kuo

first: Chih-Li

first: Doris

last: Tisch

first: Monika

last: Schmoll

first: Ruey-Shyang


title: Genetic analysis of the genome wide role of G-proteins in rice metabolism

status: Public on Dec 01 2010

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

country: India

institute: Guru Gobind Singh Indraprastha University

summary: The current study reports a genome-wide transcriptional profiling of the only known Gα mutants in rice (RGA1).

overall_design: Total RNA was isolated from the leaves of 25 day old rice d1 (Gα) mutant (HO-541) and its corresponding wild type (Nipponbare) grown on B-5 agar media.Total RNAs from the rice Gα mutant and wild type were first converted into cDNAs, from which labeled cRNAs were generated with Cy3 and Cy5 dyes and hybridized with 44K 60-mer whole genome rice microarrays on glass slides.The slides were washed and scanned on an Agilent scanner (G2565B) at 100 % laser power and data extracted with Agilent Feature Extraction software (version 9.1). The experiment was repeated with a biological-cum-technical replicate, where total RNA samples from a fresh batch of rice (mutant and WT) plants were labeled with opposite dyes (dye-swap) and used for microarray analysis.

first: Ravi

last: Pathak

first: Nanadula


title: isd-starch-Initiation synthesis and degradation : an integrated approach toward the understanding of starch metabolism and formation in plants

status: Public on May 12 2011

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

institute: INRA

summary:
gnp06-02_starch - isd-starch - What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves. - comparison between several mutant of the starch biosynthesis and the WT, at the end of the day and at the end of the night

Keywords: gene knock out

overall_design: 48 dye-swap - CATMA arrays

first: Sandra

last: Pelletier

first: Jean-Pierre

last: Renou

first: Maria-cecilia

middle: c

last: Arias

first: Marie-Laure

last: Martin-Magniette


title: ISD-starch (initiation, synthesis, and degradation): an integrated approach toward the understanding of starch metabolism and formation in plants

status: Public on Mar 01 2011

city: BEAUCOUZE

address: 42, rue Georges Morel - BP 60057