Digital quantitative measurements of gene expression

Mikkilineni, Venugopal; Mitra, Robi D.; Merritt, Joshua; DiTonno, Jason R.; Church, George M.; Ogunnaike, Babatunde A.; Edwards, Jeremy S.

doi:10.1002/bit.20048

Cited by 23 publications

(12 citation statements)

References 23 publications

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“…�orth mentioning are 454-sequencing . �orth mentioning are 454-sequencing technology and digital gene expression (DGE) that have recently been used to study the transcriptome of different organisms and promise to become an efficient and costeffective alternative with high potential in crop research (Mikkilineni et al, 2004;Margulies et al, 2005;Velculescu and Kinzler, 2007;�eber et al, 2007;Torres et al, 2008). Open and closed systems should not be considered as competitors, but rather as complementary technologies to be used depending on the subject to be analyzed and the objectives of the research.…”

Section: Techniques Used For Evaluating Gene Expression In Functionalmentioning

confidence: 99%

Biological Activity of Essential Oils from Leaves and Fruits of Pepper Tree (Schinus molle L.) to Control Rice Weevil (Sitophilus oryzae L.)

Benzi

Stefanazzi

Ferrero

2009

Chilean J. Agric. Res.

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Rice weevil (Sitophilus oryzae L.) is a primary insect pest of stored grain. The development of resistance resulted in the application of synthetic insecticides. In recent years many plant essential oils have provided potential alternatives to currently used insect control agents. The Brazilian pepper tree (Schinus molle L. var. areira (L.) DC.) (Anacardiaceae) ) (Anacardiaceae) has different biological properties such as insecticidal activity. In this study, repellent, fumigant activity, nutritional indices, and feeding deterrent action were evaluated on S. oryzae adults. Filter paper impregnation was used to test fumigant toxicity, whereas treated whole wheat was used to evaluate repellent activity and a flour disk bioassay was done to evaluate feeding deterrent action and nutritional index alteration. Leaf essential oils showed repellent effects at both concentrations (0.04 and 0.4% w/w), while fruit essential oils lacked repellent activity. Both plant oils altered nutritional indices. Fruit essential oils had a strong feeding deterrent action (62%) while leaves had a slight effect (40.6%). With respect to fumigant activity, neither of the essential oils was found to be toxic. Resistance and toxicity problems of the synthetic insecticides have resulted in the necessity of finding more effective and healthier alternatives. Thus, essential oils are the most tested products presently (Papachristos and Stamopoulus, 2002; Umoetok and Gerard, 2003; Zhang et al., 2004; Tapondjou et al., 2005; Ferrero et al., 2006; Sánchez Chopa et al., 2006, Stefanazzi et al., 2006, Wang et al., 2006. Different biological activities of plant derivatives have been demonstrated for the control of stored grain pests (Golob et al., 1999; Rajendran and Sriranjini, 2008).The Brazilian pepper tree (Schinus molle L. var. areira (L.) DC.) is associated with agricultural crops in boundaries, windbreaks, riverbank protection, and watershed conservation. In popular medicine, it is use for its astringent, diuretic, antispasmodic properties among others. In pest control, it is used as a fumigant, repellent, and ovicide (Ruffínengo et al., 2005; Ferrero et al., 2006).The objective of the present study was to evaluate the fumigant, repellent and/or attractant, feeding deterrent activity, and the alterations in the nutritional physiology produced by the essential oils from leaves and fruits of S. molle var. areira on 3-to 4-day-old S. oryzae adults. V. BENZI et al. -BIOLOGICAL ACTIVITY OF ESSENTIAL OILS… MATERIALS AND METHODS InsectsThe insects came from a susceptible colony maintained in the Cátedra de Zoología Agrícola de la Universidad Nacional de Buenos Aires (UBA). They were bred in glass containers, 8 cm in diameter, 13 cm high, sealed with fine netting, maintained at 28 ± 1 ºC, 60-70% HR, a 12:12 photoperiod, and using whole wheat grains as food. Vegetal materialThe vegetal organs (leaves and mature fruits) of the pepper tree were collected during the summer period in Bahía Blanca city, Buenos Aires, Argentina (38°41' S; 62°17' ...

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Section: Techniques Used For Evaluating Gene Expression In Functionalmentioning

confidence: 99%

Biological Activity of Essential Oils from Leaves and Fruits of Pepper Tree (Schinus molle L.) to Control Rice Weevil (Sitophilus oryzae L.)

Benzi

Stefanazzi

Ferrero

2009

Chilean J. Agric. Res.

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“…For various well-documented reasons (Dudley et al, 2002;Sebastiani et al, 2003) it is a near- example, (Brenner et al, 2000;Mikkilineni et al, 2004) differential expression determination via standard microarray technology remains an important aspect of gene expression studies.…”

Section: A Theoretical Model Of Differential Expressionmentioning

confidence: 99%

A probabilistic framework for microarray data analysis: Fundamental probability models and statistical inference

Ogunnaike

Gelmi

Edwards

2010

Journal of Theoretical Biology

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A probabilistic framework for microarray data analysis: Fundamental probability models and statistical inference, Journal of Theoretical Biology, doi:10.1016Biology, doi:10. /j.jtbi.2010 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Fundamental probability models and statistical inference 302-831-1048)A c c e p t e d m a n u s c r i p t 2 AbstractGene expression studies generate large quantities of data with the defining characteristic that the number of genes (whose expression profiles are to be determined) exceed the number of available replicates by several orders of magnitude. Standard spot-by-spot analysis still seeks to extract useful information for each gene on the basis of the number of available replicates, and thus plays to the weakness of microarrays. On the other hand, because of the data volume, treating the entire data set as an ensemble, and developing theoretical distributions for these ensembles provides a framework that plays instead to the strength of microarrays. We present theoretical results that under reasonable assumptions, the distribution of microarray intensities follows the Gamma model, with the biological interpretations of the model parameters emerging naturally. We subsequently establish that for each microarray data set, the fractional intensities can be represented as a mixture of Beta densities, and develop a procedure for using these results to draw statistical inference regarding differential gene expression. We illustrate the results with experimental data from gene expression studies on Deinococcus radiodurans following DNA damage using cDNA microarrays.

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“…Gene expression analysis of individual strains was conducted essentially to verify the expression level of the p53 gene as described (Merritt et al 2003;Merritt et al 2005;Mikkilineni et al 2004). The ratio of ADE2:p53 was calculated and the % WT activity for each mutant tested was calculated using a calibration curve (R 2 = 0.93) prepared from the ADE2/p53 ratios of mutants with previously reported activity (Leu330Ala, Leu330His, Gln331Ala and Ile332Ala).…”

Section: Gene Expression Analysismentioning

confidence: 99%

Parallel analysis of tetramerization domain mutants of the human p53 protein using PCR colonies

Merritt

Roberts

Butz

et al. 2007

HUGO J

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A highly-parallel yeast functional assay, capable of screening approximately 100-1,000 mutants in parallel and designed to screen the activity of transcription activator proteins, was utilized to functionally characterize tetramerization domain mutants of the human p53 transcription factor and tumor suppressor protein. A library containing each of the 19 possible single amino acid substitutions (57 mutants) at three positions in the tetramerization domain of the human p53 protein, was functionally screened in Saccharomyces cerevisiae. Amino acids Leu330 and Ile332, whose side chains form a portion of a hydrophobic pocket that stabilizes the active p53 tetramer, were found to tolerate most hydrophobic amino acid substitutions while hydrophilic substitutions resulted in the inactivation of the protein. Amino acid Gln331 tolerated essentially all mutations. Importantly, highly parallel mutagenesis and cloning techniques were utilized which, in conjunction with recently reported highly parallel DNA sequencing methods, would be capable of increasing throughput an additional 2-3 orders of magnitude.

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Digital quantitative measurements of gene expression

Cited by 23 publications

References 23 publications

Biological Activity of Essential Oils from Leaves and Fruits of Pepper Tree (Schinus molle L.) to Control Rice Weevil (Sitophilus oryzae L.)

Biological Activity of Essential Oils from Leaves and Fruits of Pepper Tree (Schinus molle L.) to Control Rice Weevil (Sitophilus oryzae L.)

A probabilistic framework for microarray data analysis: Fundamental probability models and statistical inference

Parallel analysis of tetramerization domain mutants of the human p53 protein using PCR colonies

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