Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells

BACKGROUND: We previously analyzed human embryonic kidney (HEK) cell lines for the effects that simian virus 40 (SV40) small tumor antigen (ST) has on gene expression using Affymetrix U133 GeneChips. To cross-validate and extend our initial findings, we sought to compare the expression profiles of these cell lines using an alternative microarray platform. METHODS: We have analyzed matched cell lines with and without expression of SV40 ST using an Applied Biosystems (AB) microarray platform that uses single 60-mer oligonucleotides and single-color quantitative chemiluminescence for detection. RESULTS: While we were able to previously identify only 456 genes affected by ST with the Affymetrix platform, we identified 1927 individual genes with the AB platform. Additional technical replicates increased the number of identified genes to 3478 genes and confirmed the changes in 278 (61%) of our original set of 456 genes. Among the 3200 genes newly identified as affected by SV40 ST, we confirmed 20 by QRTPCR including several components of the Wnt, Notch, and Hedgehog signaling pathways, consistent with SV40 ST activation of these developmental pathways. While inhibitors of Notch activation had no effect on cell survival, cyclopamine had a potent killing effect on cells expressing SV40 ST. CONCLUSIONS: These data show that SV40 ST expression alters cell survival pathways to sensitize cells to the killing effect of Hedgehog pathway inhibitors

Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential

BACKGROUND: The acceptance of microarray technology in regulatory decision-making is being challenged by the existence of various platforms and data analysis methods. A recent report (E. Marshall, Science, 306, 630–631, 2004), by extensively citing the study of Tan et al. (Nucleic Acids Res., 31, 5676–5684, 2003), portrays a disturbingly negative picture of the cross-platform comparability, and, hence, the reliability of microarray technology. RESULTS: We reanalyzed Tan's dataset and found that the intra-platform consistency was low, indicating a problem in experimental procedures from which the dataset was generated. Furthermore, by using three gene selection methods (i.e., p-value ranking, fold-change ranking, and Significance Analysis of Microarrays (SAM)) on the same dataset we found that p-value ranking (the method emphasized by Tan et al.) results in much lower cross-platform concordance compared to fold-change ranking or SAM. Therefore, the low cross-platform concordance reported in Tan's study appears to be mainly due to a combination of low intra-platform consistency and a poor choice of data analysis procedures, instead of inherent technical differences among different platforms, as suggested by Tan et al. and Marshall. CONCLUSION: Our results illustrate the importance of establishing calibrated RNA samples and reference datasets to objectively assess the performance of different microarray platforms and the proficiency of individual laboratories as well as the merits of various data analysis procedures. Thus, we are progressively coordinating the MAQC project, a community-wide effort for microarray quality control

Cross platform microarray analysis for robust identification of differentially expressed genes

<p>Abstract</p> <p>Background</p> <p>Microarrays have been widely used for the analysis of gene expression and several commercial platforms are available. The combined use of multiple platforms can overcome the inherent biases of each approach, and may represent an alternative that is complementary to RT-PCR for identification of the more robust changes in gene expression profiles.</p> <p>In this paper, we combined statistical and functional analysis for the cross platform validation of two oligonucleotide-based technologies, Affymetrix (AFFX) and Applied Biosystems (ABI), and for the identification of differentially expressed genes.</p> <p>Results</p> <p>In this study, we analysed differentially expressed genes after treatment of an ovarian carcinoma cell line with a cell cycle inhibitor. Treated versus control RNA was analysed for expression of 16425 genes represented on both platforms.</p> <p>We assessed reproducibility between replicates for each platform using CAT plots, and we found it high for both, with better scores for AFFX. We then applied integrative correlation analysis to assess reproducibility of gene expression patterns across studies, bypassing the need for normalizing expression measurements across platforms. We identified 930 genes as differentially expressed on AFFX and 908 on ABI, with ~80% common to both platforms. Despite the different absolute values, the range of intensities of the differentially expressed genes detected by each platform was similar. ABI showed a slightly higher dynamic range in FC values, which might be associated with its detection system. 62/66 genes identified as differentially expressed by Microarray were confirmed by RT-PCR.</p> <p>Conclusion</p> <p>In this study we present a cross-platform validation of two oligonucleotide-based technologies, AFFX and ABI. We found good reproducibility between replicates, and showed that both platforms can be used to select differentially expressed genes with substantial agreement. Pathway analysis of the affected functions identified themes well in agreement with those expected for a cell cycle inhibitor, suggesting that this procedure is appropriate to facilitate the identification of biologically relevant signatures associated with compound treatment. The high rate of confirmation found for both common and platform-specific genes suggests that the combination of platforms may overcome biases related to probe design and technical features, thereby accelerating the identification of trustworthy differentially expressed genes.</p

Social media and sensemaking patterns in new product development: demystifying the customer sentiment

Artificial intelligence by principle is developed to assist but also support decision making processes. In our study, we explore how information retrieved from social media can assist decision-making processes for new product development (NPD). We focus on consumers’ emotions that are expressed through social media and analyse the variations of their sentiments in all the stages of NPD. We collect data from Twitter that reveal consumers’ appreciation of aspects of the design of a newly launched model of an innovative automotive company. We adopt the sensemaking approach coupled with the use of fuzzy logic for text mining. This combinatory methodological approach enables us to retrieve consensus from the data and to explore the variations of sentiments of the customers about the product and define the polarity of these emotions for each of the NPD stages. The analysis identifies sensemaking patterns in Twitter data and explains the NPD process and the associated steps where the social interactions from customers can have an iterative role. We conclude the paper by outlining an agenda for future research in the NPD process and the role of the customer opinion through sensemaking mechanisms

Anthocyanidins and anthocyanins: colored pigments as food, pharmaceutical ingredients, and the potential health benefits

Anthocyanins are colored water-soluble pigments belonging to the phenolic group. The pigments are in glycosylated forms. Anthocyanins responsible for the colors, red, purple, and blue, are in fruits and vegetables. Berries, currants, grapes, and some tropical fruits have high anthocyanins content. Red to purplish blue-colored leafy vegetables, grains, roots, and tubers are the edible vegetables that contain a high level of anthocyanins. Among the anthocyanin pigments, cyanidin-3-glucoside is the major anthocyanin found in most of the plants. The colored anthocyanin pigments have been traditionally used as a natural food colorant. The color and stability of these pigments are influenced by pH, light, temperature, and structure. In acidic condition, anthocyanins appear as red but turn blue when the pH increases. Chromatography has been largely applied in extraction, separation, and quantification of anthocyanins. Besides the use of anthocyanidins and anthocyanins as natural dyes, these colored pigments are potential pharmaceutical ingredients that give various beneficial health effects. Scientific studies, such as cell culture studies, animal models, and human clinical trials, show that anthocyanidins and anthocyanins possess antioxidative and antimicrobial activities, improve visual and neurological health, and protect against various non-communicable diseases. These studies confer the health effects of anthocyanidins and anthocyanins, which are due to their potent antioxidant properties. Different mechanisms and pathways are involved in the protective effects, including free-radical scavenging pathway, cyclooxygenase pathway, mitogen-activated protein kinase pathway, and inflammatory cytokines signaling. Therefore, this review focuses on the role of anthocyanidins and anthocyanins as natural food colorants and their nutraceutical properties for health. Abbreviations: CVD: Cardiovascular disease VEGF: Vascular endothelial growth factor

Proportions of nitrogen and sulphur in spring rapeseeds depending on fertilization with these elements

The study was based on a three-year field experiment conducted on degraded black soil, classified as class IIIb soil in the Polish soil valuation system, with neutral pH, high content of phosphorus and potassium, average content of magnesium, and low content of sulphur. The two-factor experiment was carried out in northern Poland (52°73′ N; 18°88′ E), in a split-block design with four replications. The preceding crop each year was sugar beet. The aim of the study was to evaluate the effect of varied levels of nitrogen (first factor – 0, 60, 120 and 180 kg ha-1) and sulphur (second factor – 0, 20 and 60 kg ha-1) applied to the soil and onto the leaves on the content and ratio of these elements in the seeds of the Star cultivar of spring rapeseed. Little variation was noted between growing seasons in the content of nitrogen and sulphur and in their proportions in the seeds. Application of nitrogen alone (without sulphur) and combined application of nitrogen with sulphur caused an increase in the nitrogen content in the seeds and in the N:S ratio. The sulphur content in the seeds of the plants fertilized with nitrogen and sulphur together was significantly higher than in the seeds of the plants fertilized with nitrogen alone and lower than in the plants fertilized with sulphur alone. The highest N:S ratios were obtained in the seeds of plants fertilized with nitrogen alone, and the lowest – following the application of sulphur alone. Application of nitrogen or nitrogen and sulphur caused an increase in the N:S ratio towards optimal values for fodder crops. The method of sulphur application did not significantly affect its content in the rapeseeds or the N:S ratio

Siarka jako czynnik kształtujący efektywność azotu w agrotechnice rzepaku jarego. Część I. Wybrane elementy plonowania

Strict, three-year-long field experiment was performed on degraded Phaeozems, IIIb soil valuation class, with pH ranging from 6.5 to 7.1, of high richness in phosphorus and potassium, medium in magnesium, and low in sulphur. The experiment was carried out in a split-block design with two factors in four repetitions. The aim of the study was to evaluate the effect of various doses of nitrogen (0, 60, 120, and 180 kg·haˉ¹ ) and sulphur (0, 20, and 60 kg·haˉ¹ ), taking into account their different application methods (in-soil and as foliar fertiliser), on the yield components of spring rapeseed cultivar Star. Fertilisation only with nitrogen significantly increased the values of all the studied components, while the sulphur-only fertilisation increased the number of seeds in siliques, as well as the mass of 1000 grains. The number of seeds per silique in none of the research years was significantly affected by the interaction between nitrogen and sulphur. As far as other characteristics are concerned, considering sulphur alongside nitrogen fertilisation, in general, resulted in a significant increase in their values, in comparison with the control plants.Podstawą badań było trzyletnie ścisłe doświadczenie polowe przeprowadzone na czarnej ziemi zdegradowanej, klasy bonitacyjnej IIIb, o obojętnym odczynie, wysokiej zasobności w fosfor i potas oraz niskiej w siarkę. Doświadczenie realizowano w układzie równoważnych bloków z dwoma czynnikami, w czterech powtórzeniach. Celem badań była ocena wpływu zróżnicowanych dawek azotu (0, 60, 120 i 180 kg·haˉ¹ ) i siarki (0, 20 i 60 kg·haˉ¹ ), z uwzględnieniem różnych sposobów jej aplikacji (doglebowo i dolistnie), na elementy plonowania rzepaku jarego odmiany Star. Wyłączne nawożenie azotem istotnie zwiększało wartości wszystkich badanych elementów, wyłączne nawożenie siarką – tylko liczbę nasion w łuszczynach oraz wartość MTN. Tylko liczba nasion w łuszczynach w żadnym z lat badań nie była istotnie kształtowana przez interakcję azotu i siarki. W przypadku pozostałych cech uwzględnienie w nawożeniu siarki obok azotu powodowało na ogół istotny wpływ na kształtowanie ich wartości w porównaniu z kontrolą