Within the skin: Grape berries during the mature stages of ripening

A systems biology approach was used to investigate berry skins of three red- (Cabernet Sauvignon, Merlot, Pinot Noir) and two white-skinned (Chardonnay, Semillon) wine grape cultivars. Identical sample aliquots were analyzed for transcripts by a grapevine whole genome oligonucleotide microarray and RNAseq technologies, proteins by nano-liquid chromatography-mass spectroscopy, and metabolites by gas chromatography-mass spectroscopy and liquid chromatography-mass spectroscopy. Principal components analysis of each of five Omic technologies predicted similar variance between cultivars. Comparison of RNAseq and microarray data revealed a strong Pearson’s correlation (0.80), but concordance of protein with transcript data was low with a Pearson’s correlation of 0.27 and 0.24 for the RNAseq and microarray data, respectively. Integration of metabolite with protein and transcript data produced an expected model of phenylpropanoid biosynthesis, distinguishing red from white grapes, yet, provided detail of individual cultivar differences. The integration of multiple high-throughput Omic datasets revealed complex biochemical variation amongst five cultivars of an ancient and economically important crop species. Grape berry ripening occurs in the late stages of development with increases in sugar, changes in color, and decreases in malate concentration. In the final stages of ripening, fruit flavors and volatile aromas increase to signal readiness for seed dispersal. To identify the common transcriptional changes in the late stages of berry development in multiple grape cultivars, the transcriptomic responses of the berry skins of 7 cultivars of grapes that were grown in the same vineyard were determined using RNAseq at four different °Brix levels (20 to 26 °Brix). The abundance of thousands of transcripts changed significantly in the late stages of berry development. Gene set enrichment analysis of functional Gene Ontology terms provided evidence for a complex interplay of many gene ontology categories including those involved in the circadian clock, postembryonic development, photosynthesis, hormone signaling, reactive oxygen species (ROS), DNA methylation and transcriptional regulation. There were 809 transcription factors (TF) differentially expressed with increasing ˚Brix (~4% of all transcripts and ~32% of all TF), belonging to 81 families, including the C3H, MYB, AP2/ERF and bHLH families. Our analyses indicate that the circadian clock and epigenetic modification are major factors regulating transcription in mature berries.Finally, pathogenesis-related proteins that accumulated in skins of three red-skinned and two white-skinned cultivars: Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay and Semillon, were characterized in silico, using protein and transcript data. Large amounts of identified proteins were classified as pathogenesis-related in berry skins, more so than what was previously observed in shoot tips. Several PR-families had numerous protein members in skins, which maybe a tissue specific occurrence. The transcript abundance was well correlated to the protein abundance in thaumatins of PR-05, but not so in the L-ascorbate peroxidases of PR-09. Haze-forming proteins, while well represented, did not accumulate with more specificity in the white cultivars and were mostly higher in the red cultivar, Pinot Noir. Large accumulations of PR-proteins in skins at harvest provide support for a prolonged and possibly a constitutive defense mechanism that protects a maturing seed within the berry

Abscisic acid transcriptomic signaling varies with grapevine organ

Background: Abscisic acid (ABA) regulates various developmental processes and stress responses over both short (i.e. hours or days) and longer (i.e. months or seasons) time frames. To elucidate the transcriptional regulation of early responses of grapevine (Vitis vinifera) responding to ABA, different organs of grape (berries, shoot tips, leaves, roots and cell cultures) were treated with 10 μM (S)-(+)-ABA for 2 h. NimbleGen whole genome microarrays of Vitis vinifera were used to determine the effects of ABA on organ-specific mRNA expression patterns. Results: Transcriptomic analysis revealed 839 genes whose transcript abundances varied significantly in a specific organ in response to ABA treatment. No single gene exhibited the same changes in transcript abundance across all organs in response to ABA. The biochemical pathways affected by ABA were identified using the Cytoscape program with the BiNGO plug-in software. The results indicated that these 839 genes were involved in several biological processes such as flavonoid metabolism, response to reactive oxygen species, response to light, and response to temperature stimulus. ABA affected ion and water transporters, particularly in the root. The protein amino acid phosphorylation process was significantly overrepresented in shoot tips and roots treated with ABA. ABA affected mRNA abundance of genes (CYP707As, UGTs, and PP2Cs) associated with ABA degradation, conjugation, and the ABA signaling pathway. ABA also significantly affected the expression of several transcription factors (e.g. AP2/ERF, MYC/MYB, and bZIP/AREB). The greatest number of significantly differentially expressed genes was observed in the roots followed by cell cultures, leaves, berries, and shoot tips, respectively. Each organ had a unique set of gene responses to ABA. Conclusions: This study examined the short-term effects of ABA on different organs of grapevine. The responses of each organ were unique indicating that ABA signaling varies with the organ. Understanding the ABA responses in an organ-specific manner is crucial to fully understand hormone action and plant responses to water deficit.Availability of supporting data: All microarray expression data are available at the Gene Expression Omnibus (GEO) database [91] with the accession number GSE78798.Keywords: Abscisic acid signaling, Vitis vinifera L, Organ-specificity, Transcriptomic

Prediction and Optimal Scheduling of Advertisements in Linear Television

Advertising is a crucial component of marketing and an important way for companies to raise awareness of goods and services in the marketplace. Advertising campaigns are designed to convey a marketing image or message to an audience of potential consumers and television commercials can be an effective way of transmitting these messages to a large audience. In order to meet the requirements for a typical advertising order, television content providers must provide advertisers with a predetermined number of impressions in the target demographic. However, because the number of impressions for a given program is not known a priori and because there are a limited number of time slots available for commercials, scheduling advertisements efficiently can be a challenging computational problem. In this case study, we compare a variety of methods for estimating future viewership patterns in a target demographic from past data. We also present a method for using those predictions to generate an optimal advertising schedule that satisfies campaign requirements while maximizing advertising revenue

Prediction and Optimal Scheduling of Advertisements in Linear Television

Advertising is a crucial component of marketing and an important way for companies to raise awareness of goods and services in the marketplace. Advertising campaigns are designed to convey a marketing image or message to an audience of potential consumers and television commercials can be an effective way of transmitting these messages to a large audience. In order to meet the requirements for a typical advertising order, television content providers must provide advertisers with a predetermined number of impressions in the target demographic. However, because the number of impressions for a given program is not known a priori and because there are a limited number of time slots available for commercials, scheduling advertisements efficiently can be a challenging computational problem. In this case study, we compare a variety of methods for estimating future viewership patterns in a target demographic from past data. We also present a method for using those predictions to generate an optimal advertising schedule that satisfies campaign requirements while maximizing advertising revenue

Evaluations of tropospheric aerosol properties simulated by the community earth system model with a sectional aerosol microphysics scheme

A sectional aerosol model (CARMA) has been developed and coupled with the Community Earth System Model (CESM1). Aerosol microphysics, radiative properties, and interactions with clouds are simulated in the size-resolving model. The model described here uses 20 particle size bins for each aerosol component including freshly nucleated sulfate particles, as well as mixed particles containing sulfate, primary organics, black carbon, dust, and sea salt. The model also includes five types of bulk secondary organic aerosols with four volatility bins. The overall cost of CESM1-CARMA is approximately ∼2.6 times as much computer time as the standard three-mode aerosol model in CESM1 (CESM1-MAM3) and twice as much computer time as the seven-mode aerosol model in CESM1 (CESM1-MAM7) using similar gas phase chemistry codes. Aerosol spatial-temporal distributions are simulated and compared with a large set of observations from satellites, ground-based measurements, and airborne field campaigns. Simulated annual average aerosol optical depths are lower than MODIS/MISR satellite observations and AERONET observations by ∼32%. This difference is within the uncertainty of the satellite observations. CESM1/CARMA reproduces sulfate aerosol mass within 8%, organic aerosol mass within 20%, and black carbon aerosol mass within 50% compared with a multiyear average of the IMPROVE/EPA data over United States, but differences vary considerably at individual locations. Other data sets show similar levels of comparison with model simulations. The model suggests that in addition to sulfate, organic aerosols also significantly contribute to aerosol mass in the tropical UTLS, which is consistent with limited data

Transcriptomic analysis of the late stages of grapevine (Vitis vinifera cv. Cabernet Sauvignon) berry ripening reveals significant induction of ethylene signaling and flavor pathways in the skin

Background: Grapevine berry, a nonclimacteric fruit, has three developmental stages; the last one is when berrycolor and sugar increase. Flavors derived from terpenoid and fatty acid metabolism develop at the very end of thisripening stage. The transcriptomic response of pulp and skin of Cabernet Sauvignon berries in the late stages ofripening between 22 and 37 \ub0Brix was assessed using whole-genome micorarrays.Results: The transcript abundance of approximately 18,000 genes changed with \ub0Brix and tissue type. There were alarge number of changes in many gene ontology (GO) categories involving metabolism, signaling and abioticstress. GO categories reflecting tissue differences were overrepresented in photosynthesis, isoprenoid metabolismand pigment biosynthesis. Detailed analysis of the interaction of the skin and pulp with \ub0Brix revealed that therewere statistically significantly higher abundances of transcripts changing with \ub0Brix in the skin that were involved inethylene signaling, isoprenoid and fatty acid metabolism. Many transcripts were peaking around known optimalfruit stages for flavor production. The transcript abundance of approximately two-thirds of the AP2/ERF superfamilyof transcription factors changed during these developmental stages. The transcript abundance of a unique clade ofERF6-type transcription factors had the largest changes in the skin and clustered with genes involved in ethylene,senescence, and fruit flavor production including ACC oxidase, terpene synthases, and lipoxygenases. The transcriptabundance of important transcription factors involved in fruit ripening was also higher in the skin.Conclusions: A detailed analysis of the transcriptome dynamics during late stages of ripening of grapevine berriesrevealed that these berries went through massive transcriptional changes in gene ontology categories involvingchemical signaling and metabolism in both the pulp and skin, particularly in the skin. Changes in the transcriptabundance of genes involved in the ethylene signaling pathway of this nonclimacteric fruit were statisticallysignificant in the late stages of ripening when the production of transcripts for important flavor and aroma compoundswere at their highest. Ethylene transcription factors known to play a role in leaf senescence also appear to play a role infruit senescence. Ethylene may play a bigger role than previously thought in this non-climacteric fruit

Models of time structures of interest rates and their use in valuation of liabilities of life insurance Company

This master thesis aims to describe problematics of the stochastic modeling of time structures of interest rates with Vasicek, CIR and Hull-White models and the use of these models in valuation of liabilities and time value of options and guaranties in life insurance. In the theoretical part of the thesis there are fundamentals of stochastic calculus, stochastic models of interest rates and introduction to problematics of life insurance defined. Furthermore, the last practical part of the thesis demonstrates impact of particular models on the value of liabilities in relation to clients and on the value of TVOG of real European life insurance Company