| 1. |
- Klevebring, Daniel, 1981-, et al.
(författare)
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Automation of cDNA Synthesis and Labelling Improves Reproducibility
- 2009
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Ingår i: Journal of Biomedicine and Biotechnology. - : Hindawi Limited. - 1110-7243 .- 1110-7251. ; 2009, s. 396808-
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Tidskriftsartikel (refereegranskat)abstract
- Background. Several technologies, such as in-depth sequencing and microarrays, enable large-scale interrogation of genomes and transcriptomes. In this study, we asses reproducibility and throughput by moving all laboratory procedures to a robotic workstation, capable of handling superparamagnetic beads. Here, we describe a fully automated procedure for cDNA synthesis and labelling for microarrays, where the purification steps prior to and after labelling are based on precipitation of DNA on carboxylic acid-coated paramagnetic beads. Results. The fully automated procedure allows for samples arrayed on a microtiter plate to be processed in parallel without manual intervention and ensuring high reproducibility. We compare our results to a manual sample preparation procedure and, in addition, use a comprehensive reference dataset to show that the protocol described performs better than similar manual procedures. Conclusions. We demonstrate, in an automated gene expression microarray experiment, a reduced variance between replicates, resulting in an increase in the statistical power to detect differentially expressed genes, thus allowing smaller differences between samples to be identified. This protocol can with minor modifications be used to create cDNA libraries for other applications such as in-depth analysis using next-generation sequencing technologies.
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| 2. |
- Lubovac, Zelmina
(författare)
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Investigating Topological and Functional Features of Multimodular Proteins
- 2009
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Ingår i: Journal of Biomedicine and Biotechnology. - : Hindawi Publishing Corporation. - 1110-7243 .- 1110-7251. ; , s. Article Number: 472415-
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Tidskriftsartikel (refereegranskat)abstract
- To generate functional modules as functionally and structurally cohesive formations in protein interaction networks (PINs) constitutes an important step towards understanding how modules communicate on a higher level of the PIN organisation that underlies cell functionality. However, we need to understand how individual modules communicate and are organized into the higher-order structure(s) of the PIN organization that underlies cell functionality. In an attempt to contribute to this understanding, we make an assumption that the proteins reappearing in several modules, termed here as multimodular proteins (MMPs), may be useful in building higher-order structure(s) as they may constitute communication points between different modules. In this paper, we investigate common properties shared by these proteins and compare them with the properties of so called single-modular proteins (SMPs) by analyzing three aspects: functional aspect, that is, annotation of the proteins, topological aspect that is betweenness centrality of the proteins, and lethality. Furthermore, we investigate the interconnectivity role of some proteins that are identified as functionally and topologically important.
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