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Rodrigues M, Lengerer B, Ostermann T, Ladurner P. Molecular biology approaches in bioadhesion research. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2014; 5:983-993. [PMID: 25161834 PMCID: PMC4142862 DOI: 10.3762/bjnano.5.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 06/17/2014] [Indexed: 06/03/2023]
Abstract
The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1) generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2) setting up a BLAST search facility, (3) perform an in situ hybridization screen, and (4) functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives.
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Affiliation(s)
- Marcelo Rodrigues
- University of Innsbruck, Institute of Zoology and Center for Molecular Biosciences Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
| | - Birgit Lengerer
- University of Innsbruck, Institute of Zoology and Center for Molecular Biosciences Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
| | - Thomas Ostermann
- University of Innsbruck, Institute of Zoology and Center for Molecular Biosciences Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
| | - Peter Ladurner
- University of Innsbruck, Institute of Zoology and Center for Molecular Biosciences Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
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Abstract
The molecular anatomy of the vertebrate embryo was systematically analysed through gene expression during early development of the Xenopus frog using whole-mount in situ hybridization. Expression patterns are documented and assembled into the database Axeldb (http://www.dkfz-heidelberg.de/abt0135/axeldb.htm). Synexpression groups representing genes with shared, complex expression pattern that predict molecular pathways involved in patterning and differentiation have been identified. These sets of co-regulated genes show a striking similarity with operons, and may be a key determinant facilitating evolutionary change leading to animal diversity.
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Affiliation(s)
- Nicolas Pollet
- Laboratoire de transgenèse et génétique des amphibiens, CNRS UMR 8080, IBAIC Bât. 447, université Paris-Sud, 91405 Orsay Cedex, France.
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Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, Richards S, Ashburner M, Hartenstein V, Celniker SE, Rubin GM. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol 2002; 3:RESEARCH0088. [PMID: 12537577 PMCID: PMC151190 DOI: 10.1186/gb-2002-3-12-research0088] [Citation(s) in RCA: 474] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2002] [Revised: 11/18/2002] [Accepted: 11/19/2002] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription. RESULTS As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, we examined 2,179 genes by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos. The photomicrographs were annotated using controlled vocabularies for anatomical structures that are organized into a developmental hierarchy. We also generated a detailed time course of gene expression during embryogenesis using microarrays to provide an independent corroboration of the in situ hybridization results. All image, annotation and microarray data are stored in publicly available database. We found that the RNA transcripts of about 1% of genes show clear subcellular localization. Nearly all the annotated expression patterns are distinct. We present an approach for organizing the data by hierarchical clustering of annotation terms that allows us to group tissues that express similar sets of genes as well as genes displaying similar expression patterns. CONCLUSIONS Analyzing gene-expression patterns by in situ hybridization to whole-mount embryos provides an extremely rich dataset that can be used to identify genes involved in developmental processes that have been missed by traditional genetic analysis. Systematic analysis of rigorously annotated patterns of gene expression will complement and extend the types of analyses carried out using expression microarrays.
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Affiliation(s)
- Pavel Tomancak
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720-3200, USA
| | - Amy Beaton
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720-3200, USA
| | - Richard Weiszmann
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elaine Kwan
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720-3200, USA
| | - ShengQiang Shu
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Suzanna E Lewis
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephen Richards
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael Ashburner
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Volker Hartenstein
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Susan E Celniker
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gerald M Rubin
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720-3200, USA
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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