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Nilsson, Olle
Publications (3 of 3) Show all publications
Freyhult, E., Cui, Y., Nilsson, O. & Ardell, D. H. (2007). New computational methods reveal tRNA identity element divergence between Proteobacteria and Cyanobacteria. Biochimie, 89(10), 1276-1288
Open this publication in new window or tab >>New computational methods reveal tRNA identity element divergence between Proteobacteria and Cyanobacteria
2007 (English)In: Biochimie, ISSN 0300-9084, E-ISSN 1638-6183, Vol. 89, no 10, p. 1276-1288Article in journal (Refereed) Published
Abstract [en]

There are at least 21 subfunctional classes of tRNAs in most cells that, despite a very highly conserved and compact common structure, must interact specifically with different cliques of proteins or cause grave organismal consequences. Protein recognition of specific tRNA substrates is achieved in part through class-restricted tRNA features called tRNA identity determinants. In earlier work we used TFAM, a statistical classifier of tRNA function, to show evidence of unexpectedly large diversity among bacteria in tRNA identity determinants. We also created a data reduction technique called function logos to visualize identity determinants for a given taxon. Here we show evidence that determinants for lysylated isoleucine tRNAs are not the same in Proteobacteria as in other bacterial groups including the Cyanobacteria. Consistent with this, the lysylating biosynthetic enzyme TilS lacks a C-terminal domain in Cyanobacteria that is present in Proteobacteria. We present here, using function logos, a map estimating all potential identity determinants generally operational in Cyanobacteria and Proteobacteria. To further isolate the differences in potential tRNA identity determinants between Proteobacteria and Cyanobacteria, we created two new data reduction visualizations to contrast sequence and function logos between two taxa. One, called Information Difference logos (ID logos), shows the evolutionary gain or retention of functional information associated to features in one lineage. The other, Kullback–Leibler divergence Difference logos (KLD logos), shows recruitments or shifts in the functional associations of features, especially those informative in both lineages. We used these new logos to specifically isolate and visualize the differences in potential tRNA identity determinants between Proteobacteria and Cyanobacteria. Our graphical results point to numerous differences in potential tRNA identity determinants between these groups. Although more differences in general are explained by shifts in functional association rather than gains or losses, the apparent identity differences in lysylated isoleucine tRNAs appear to have evolved through both mechanisms.

Keywords
tRNA identity, Function logos, tRNA identity determinants, Lysylated isoleucine tRNA, TilS, Aminoacyl-tRNA synthetase, Proteobacteria, Cyanobacteria, Kullback–Leibler Divergence
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-96429 (URN)10.1016/j.biochi.2007.07.013 (DOI)000250613600015 ()17889982 (PubMedID)
Available from: 2007-11-13 Created: 2007-11-13 Last updated: 2017-12-14Bibliographically approved
Björklund, H., Nilsson, O., Svensson, O. & Vorobyov, S. (2004). Controlled Linear Programming: Boundedness and Duality.
Open this publication in new window or tab >>Controlled Linear Programming: Boundedness and Duality
2004 (English)Report (Other scientific)
Abstract [en]

Computer supported work is often stressful and inadequate computer sys-tems and poor usability contribute to the problem. Still the work situation, and work environment of users are seldom considered when developing computer systems, and it is difficult to incorporate the ideas of User Centred Systems Design (UCSD) in practice. Hence, this research addresses the dif-ficulty in integrating usability, UCSD and occupational health issues in IT systems development in order to improve the resulting work situation and well-being of users. How do basic values and perspectives of stakeholders in systems development projects affect the work with UCSD, usability and users’ health issues in the organisations studied?

This research aims at influencing systems development in practice; hence, research is carried out in real life settings with an action research approach. Data is gathered and analysed with a qualitative research approach with in-terview studies, meetings with stakeholders, analysis of documentation, ob-servations and field studies. The theoretical framework adheres to situated action, participatory design, and UCSD that stresses the importance of in-volving users in the design process.

This research shows that several basic values and perspectives affect sys-tems development and hinder the usability work, for example, the perspec-tive on user representatives, the value of rationality and objectivity, and the perspective underpinning descriptions and discourse on work. Moreover, this research indicates that the strong business values of automation, efficiency and customer satisfaction shape the development of new technology, and ultimately the tasks and work practices of the civil servants. In short, the studies show that there are some contradictions in business values and the implementation of user-centred systems design, usability and health issues in systems development.

Attitudes and perspectives are not easily changed, and change comes gradually. In these organisations, we continuously discuss the integration of health issues in systems development, and by introducing and changing the models of systems development these will hopefully enable communication and change forwards of new perspectives and values. However, a focus on models alone is insufficient and therefore we need to develop a systematic approach to include reflection and new perspectives. Perhaps the reflection itself would help us see our values and perspectives and to alter them?

Series
DIMACS Technical Report ; 2004-56
National Category
Other Computer and Information Science
Identifiers
urn:nbn:se:uu:diva-18872 (URN)
Available from: 2007-01-04 Created: 2007-01-04 Last updated: 2018-01-12
Björklund, H., Nilsson, O., Svensson, O. & Vorobyov, S. (2004). The Controlled Linear Programming Problem.
Open this publication in new window or tab >>The Controlled Linear Programming Problem
2004 (English)Report (Other scientific)
Series
DIMACS Technical Report ; 2004-41
Identifiers
urn:nbn:se:uu:diva-18875 (URN)
Available from: 2007-01-04 Created: 2007-01-04
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