Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development

BACKGROUND: Grape berry development is a dynamic process that involves a complex series of molecular genetic and biochemical changes divided into three major phases. During initial berry growth (Phase I), berry size increases along a sigmoidal growth curve due to cell division and subsequent cell expansion, and organic acids (mainly malate and tartrate), tannins, and hydroxycinnamates accumulate to peak levels. The second major phase (Phase II) is defined as a lag phase in which cell expansion ceases and sugars begin to accumulate. Véraison (the onset of ripening) marks the beginning of the third major phase (Phase III) in which berries undergo a second period of sigmoidal growth due to additional mesocarp cell expansion, accumulation of anthocyanin pigments for berry color, accumulation of volatile compounds for aroma, softening, peak accumulation of sugars (mainly glucose and fructose), and a decline in organic acid accumulation. In order to understand the transcriptional network responsible for controlling berry development, mRNA expression profiling was conducted on berries of V. vinifera Cabernet Sauvignon using the Affymetrix GeneChip® Vitis oligonucleotide microarray ver. 1.0 spanning seven stages of berry development from small pea size berries (E-L stages 31 to 33 as defined by the modified E-L system), through véraison (E-L stages 34 and 35), to mature berries (E-L stages 36 and 38). Selected metabolites were profiled in parallel with mRNA expression profiling to understand the effect of transcriptional regulatory processes on specific metabolite production that ultimately influence the organoleptic properties of wine. RESULTS: Over the course of berry development whole fruit tissues were found to express an average of 74.5% of probes represented on the Vitis microarray, which has 14,470 Unigenes. Approximately 60% of the expressed transcripts were differentially expressed between at least two out of the seven stages of berry development (28% of transcripts, 4,151 Unigenes, had pronounced (≥2 fold) differences in mRNA expression) illustrating the dynamic nature of the developmental process. The subset of 4,151 Unigenes was split into twenty well-correlated expression profiles. Expression profile patterns included those with declining or increasing mRNA expression over the course of berry development as well as transient peak or trough patterns across various developmental stages as defined by the modified E-L system. These detailed surveys revealed the expression patterns for genes that play key functional roles in phytohormone biosynthesis and response, calcium sequestration, transport and signaling, cell wall metabolism mediating expansion, ripening, and softening, flavonoid metabolism and transport, organic and amino acid metabolism, hexose sugar and triose phosphate metabolism and transport, starch metabolism, photosynthesis, circadian cycles and pathogen resistance. In particular, mRNA expression patterns of transcription factors, abscisic acid (ABA) biosynthesis, and calcium signaling genes identified candidate factors likely to participate in the progression of key developmental events such as véraison and potential candidate genes associated with such processes as auxin partitioning within berry cells, aroma compound production, and pathway regulation and sequestration of flavonoid compounds. Finally, analysis of sugar metabolism gene expression patterns indicated the existence of an alternative pathway for glucose and triose phosphate production that is invoked from véraison to mature berries. CONCLUSION: These results reveal the first high-resolution picture of the transcriptome dynamics that occur during seven stages of grape berry development. This work also establishes an extensive catalog of gene expression patterns for future investigations aimed at the dissection of the transcriptional regulatory hierarchies that govern berry development in a widely grown cultivar of wine grape. More importantly, this analysis identified a set of previously unknown genes potentially involved in critical steps associated with fruit development that can now be subjected to functional testing.National Science Foundation Plant Genome Project (DBI-0217653); Bioinformatics program (DBI-0136561); National Institute of Health Biomedical Research Infrastructure Network (NIH-NCRR P20 RR16464; National Institute of Health IDeA Network of Biomedical Research Excellence (INBRE, RR-03-008); Nevada Agricultural Experimental Statio

T-REX: software for the processing and analysis of T-RFLP data

Softwar

Swift follow-up observations of candidate gravitational-wave transient events

We present the first multi-wavelength follow-up observations of two candidate gravitational-wave (GW) transient events recorded by LIGO and Virgo in their 2009-2010 science run. The events were selected with low latency by the network of GW detectors and their candidate sky locations were observed by the Swift observatory. Image transient detection was used to analyze the collected electromagnetic data, which were found to be consistent with background. Off-line analysis of the GW data alone has also established that the selected GW events show no evidence of an astrophysical origin; one of them is consistent with background and the other one was a test, part of a "blind injection challenge". With this work we demonstrate the feasibility of rapid follow-ups of GW transients and establish the sensitivity improvement joint electromagnetic and GW observations could bring. This is a first step toward an electromagnetic follow-up program in the regime of routine detections with the advanced GW instruments expected within this decade. In that regime multi-wavelength observations will play a significant role in completing the astrophysical identification of GW sources. We present the methods and results from this first combined analysis and discuss its implications in terms of sensitivity for the present and future instruments.Comment: Submitted for publication 2012 May 25, accepted 2012 October 25, published 2012 November 21, in ApJS, 203, 28 ( http://stacks.iop.org/0067-0049/203/28 ); 14 pages, 3 figures, 6 tables; LIGO-P1100038; Science summary at http://www.ligo.org/science/Publication-S6LVSwift/index.php ; Public access area to figures, tables at https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=p110003

Koolrabi : rassenproef 1e beoordeling stookteelt en 1 beoordeling hetelucht voorjaar 1980

<p><b>Copyright information:</b></p><p>Taken from "Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development"</p><p>http://www.biomedcentral.com/1471-2164/8/429</p><p>BMC Genomics 2007;8():429-429.</p><p>Published online 22 Nov 2007</p><p>PMCID:PMC2220006.</p><p></p>me array and by real-time RT-PCR. Data were from 11 probe sets across seven developmental stages. The difference in the number of PCR cycles required to produce the same amount of product is plotted against the logexpression ratio averaged over the first time point. The linear regression line was constrained to pass through the origin. Grey solid square (1615402_at, TC56083)-ferulate-5-hydroxylase, Apricot solid triangle (1606794_at, TC63891)-osmotin precursor, red solid triangle (1616700_at, TC53526)-sucrose synthase, orange solid diamond (1607760_at, TC51695) flavonoid-3'5'-hydroxylase, light green solid round (1611650_at, TC57228)-WRKY7, dark green open square (1616880_at, TC54034)-cinnamoyl alcohol dehydrogenase, dark blue open triangle (1613896_at, TC62182)-nitrate/chloride transporter), blue open triangle (1615722_s_at, TC51776)-aquaporin PIP1.1, lavender open diamond (1611342_at, TC55943)-serine/threonine kinase, pink open circle (1612132_s_at, TC68311)-protein phosphatase 2C, brown cross (1614931_at, TC61058)-MYB transcription factor

Disruptive viability selection on a black plumage trait associated with dominance.

Traits used in communication, such as colour signals, are expected to have positive consequences for reproductive success, but their associations with survival are little understood. Previous studies have mainly investigated linear relationships between signals and survival, but both hump-shaped and U-shaped relationships can also be predicted, depending on the main costs involved in trait expression. Furthermore, few studies have taken the plasticity of signals into account in viability selection analyses. The relationship between signal expression and survival is of particular interest in melanin-based traits, because their main costs are still debated. Here, we first determined the main factors explaining variability in a melanin-based trait linked to dominance: the bib size of a colonial bird, the sociable weaver Philetairus socius. We then used these analyses to obtain a measure representative of the individual mean expression of bib size. Finally, we used capture-recapture models to study how survival varied in relation to bib size. Variation in bib size was strongly affected by year and moderately affected by age, body condition and colony size. In addition, individuals bearing small and large bibs had higher survival than those with intermediate bibs, and this U-shaped relationship between survival and bib size appeared to be more pronounced in some years than others. These results constitute a rare example of disruptive viability selection, and point towards the potential importance of social costs incurred by the dominance signalling function of badges of status.Our research was funded by the DST-NRF Centre of Excellence at the Percy FitzPatrick Institute (University of Cape Town), the Portuguese Foundation for Science and Technology (FCT, PTDC/BIA-BEC/103818/2008) to RC, the region Languedoc Roussillon, the programme "Chercheur(se)s d’avenir" 2013 and ANR JC 09-JCJC-0050-01JCJC to CD, the Natural Environment Research Council (NERC, UK: NE/G018588/1 and NE/K015257/1) to BJH, and the University of Cape Town and St John’s College, Cambridge (UK) to CNS. This research was also supported by a Marie Curie-IRSES grant (FP7-PEOPLE-2012-IRSES; ‘Cooperation’ 318994) to all and was conducted within the CNRS-CIBIO International Associate Laboratory (LIA) ‘Biodiversity and Evolution’. RC was funded by a ‘Ciência 2008’ fellowship (FCT, Portugal) with further support from FEDER (Operational Programme for Competitiveness Factors – COMPETE, Project “Biodiversity, Ecology and Global Change” co-financed by North Portugal Regional Operational Programme 2007/2013 (ON.2), under the NSRF, ERDF.This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1111/jeb.1271

Wolbachia Infections Are Virulent and Inhibit the Human Malaria Parasite Plasmodium Falciparum in Anopheles Gambiae

Endosymbiotic Wolbachia bacteria are potent modulators of pathogen infection and transmission in multiple naturally and artificially infected insect species, including important vectors of human pathogens. Anopheles mosquitoes are naturally uninfected with Wolbachia, and stable artificial infections have not yet succeeded in this genus. Recent techniques have enabled establishment of somatic Wolbachia infections in Anopheles. Here, we characterize somatic infections of two diverse Wolbachia strains (wMelPop and wAlbB) in Anopheles gambiae, the major vector of human malaria. After infection, wMelPop disseminates widely in the mosquito, infecting the fat body, head, sensory organs and other tissues but is notably absent from the midgut and ovaries. Wolbachia initially induces the mosquito immune system, coincident with initial clearing of the infection, but then suppresses expression of immune genes, coincident with Wolbachia replication in the mosquito. Both wMelPop and wAlbB significantly inhibit Plasmodium falciparum oocyst levels in the mosquito midgut. Although not virulent in non-bloodfed mosquitoes, wMelPop exhibits a novel phenotype and is extremely virulent for approximately 12–24 hours post-bloodmeal, after which surviving mosquitoes exhibit similar mortality trajectories to control mosquitoes. The data suggest that if stable transinfections act in a similar manner to somatic infections, Wolbachia could potentially be used as part of a strategy to control the Anopheles mosquitoes that transmit malaria

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Performance and Operation of the CMS Electromagnetic Calorimeter

The operation and general performance of the CMS electromagnetic calorimeter using cosmic-ray muons are described. These muons were recorded after the closure of the CMS detector in late 2008. The calorimeter is made of lead tungstate crystals and the overall status of the 75848 channels corresponding to the barrel and endcap detectors is reported. The stability of crucial operational parameters, such as high voltage, temperature and electronic noise, is summarised and the performance of the light monitoring system is presented

Assessing sustainability in housing LED urban regeneration : insights from a housing association in Northern England

How far do current assessment methods allow the thorough evaluation of sustainable urban regeneration? Would it be useful, to approach the evaluation of the environmental and social impacts of housing regeneration schemes, by making both hidden pitfalls and potentials explicit, and budgeting costs and benefits in the stakeholders’ perspective? The paper aims at answering these questions, by focusing on a case study located in the Manchester area, the City West Housing Trust, a nonprofit housing association. Drawing from extensive fieldwork and including several interviews with key experts from this housing association, the paper first attempts to monetize the environmental and social value of two extant projects – a high-rise housing estate and an environmentally-led program. It then discusses whether and how a stakeholder-oriented approach would allow more engagement of both current and potential funders in the projects at hand. Findings from both the literature and the empirical data that was gathered show how in current housing regeneration processes, room for significant improvements in terms of assessment methods still exist. Findings additionally show that the environmental and social spillovers are largely disregarded because of a gap in the evaluation tools. This may also hinder the potential contributions of further funders in the achievements of higher impacts in terms of sustainability