Tim Lewis

University of Newcastle Australia

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Paul C. Dastoor

University of Newcastle Australia

Riku Chowdhury

University of Newcastle Australia

Manish N. Raizada

University of Guelph

Nathan A. Cooling

University of Newcastle Australia

François Fauteux

National Research Council Canada

Trieu N. Trinh

University of Newcastle Australia

Daichao Sheng

University of Technology Sydney

Kristofer L. Thompson

University of Newcastle Australia

Daniel Ashlock

University of Guelph

Alaa Yassin Al-Ahmad

University of Newcastle Australia

Cooperative Institutions

University of Newcastle Australia

Callaghan Innovation

Newcastle University

University of Guelph

University of Basrah

McGill University

Commonwealth Scientific and Industrial Research Organisation

University of Anbar

Lawrence Berkeley National Laboratory

Université Laval

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Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas

BMC Plant Biology (2013)

Christophe Liseron-Monfils Tim Lewis Daniel Ashlock Paul D. McNicholas François Fauteux

Abstract Background The discovery of genetic networks and cis -acting DNA motifs underlying their regulation is a major objective of transcriptome studies. The recent release of the maize genome ( Zea mays L.) has facilitated in silico searches for regulatory motifs. Several algorithms exist to predict cis -acting elements, but none have been adapted for maize. Results A benchmark data set was used to evaluate the accuracy of three motif discovery programs: BioProspector, Weeder and MEME. Analysis showed that each motif discovery tool had limited accuracy and appeared to retrieve a distinct set of motifs. Therefore, using the benchmark, statistical filters were optimized to reduce the false discovery ratio, and then remaining motifs from all programs were combined to improve motif prediction. These principles were integrated into a user-friendly pipeline for motif discovery in maize called Promzea, available at http://www.promzea.org and on the Discovery Environment of the iPlant Collaborative website. Promzea was subsequently expanded to include rice and Arabidopsis. Within Promzea, a user enters cDNA sequences or gene IDs; corresponding upstream sequences are retrieved from the maize genome. Predicted motifs are filtered, combined and ranked. Promzea searches the chosen plant genome for genes containing each candidate motif, providing the user with the gene list and corresponding gene annotations. Promzea was validated in silico using a benchmark data set: the Promzea pipeline showed a 22% increase in nucleotide sensitivity compared to the best standalone program tool, Weeder, with equivalent nucleotide specificity. Promzea was also validated by its ability to retrieve the experimentally defined binding sites of transcription factors that regulate the maize anthocyanin and phlobaphene biosynthetic pathways. Promzea predicted additional promoter motifs, and genome-wide motif searches by Promzea identified 127 non-anthocyanin/phlobaphene genes that each contained all five predicted promoter motifs in their promoters, perhaps uncovering a broader co-regulated gene network. Promzea was also tested against tissue-specific microarray data from maize. Conclusions An online tool customized for promoter motif discovery in plants has been generated called Promzea. Promzea was validated in silico by its ability to retrieve benchmark motifs and experimentally defined motifs and was tested using tissue-specific microarray data. Promzea predicted broader networks of gene regulation associated with the historic anthocyanin and phlobaphene biosynthetic pathways. Promzea is a new bioinformatics tool for understanding transcriptional gene regulation in maize and has been expanded to include rice and Arabidopsis.

Motif (music)

Cis-regulatory module

10.1186/1471-2229-13-42

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Citations (22)

Effects of Equilibria and Kinetics on Contaminant Transport

Elsevier eBooks (2001)

Daichao Sheng Tim Lewis David W. Smith

10.1016/b978-0-08-043981-5.50119-x

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Upscaling laboratory organic electronic sensor devices to roll-to-roll printing: The effect of printable electrodes on device operation

Applied Physics Letters (2024)

Daniel Elkington Nathan A. Cooling Swee Lu Lim Trieu N. Trinh Alaa Yassin Al-Ahmad

The prospect of large-scale production of low-cost electronic devices is a driving factor behind the recent interest in printed organic electronics. However, the upscaling of laboratory organic electronic devices is extremely challenging since it requires the adaptation of materials and fabrication processes optimized for the small scale to industrial manufacturing techniques, such as roll-to-roll printing. Here, we demonstrate the fabrication of all-printed organic biosensors at the pilot production scale for use in the detection of glucose. By translating device architecture and operation, as well as electrode design and ink formulations of previously reported laboratory-scale glucose sensors to industrial printing and coating processes, we demonstrate sub-millimolar sensitivity to glucose in fully printed devices in a process which is now scalable to commercial production quantities. This Letter highlights the significant challenges associated with developing upscaled printed organic electronic biosensors and the approaches needed to address them.

Roll-to-roll processing

Screen printing

Printed Electronics

10.1063/5.0191561

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Citations (1)