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Halverson, K., Lönneborg, R. & Petersson, J. (2023). Digitalt stöd till KTH:s forskningsmiljöer: Omvärldsanalys, benchmarkinganalys och rekommendationer för KTH när det gäller stöd kring hantering av forskningsdata, IT-tjänster till och den digitala infrastrukturen för forskningen.. Stockholm: KTH Royal Institute of Technology
Open this publication in new window or tab >>Digitalt stöd till KTH:s forskningsmiljöer: Omvärldsanalys, benchmarkinganalys och rekommendationer för KTH när det gäller stöd kring hantering av forskningsdata, IT-tjänster till och den digitala infrastrukturen för forskningen.
2023 (Swedish)Report (Other (popular science, discussion, etc.))
Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2023. p. 23
National Category
Information Studies
Identifiers
urn:nbn:se:kth:diva-340503 (URN)
Note

QC 20231205

Available from: 2023-12-05 Created: 2023-12-05 Last updated: 2024-03-27Bibliographically approved
Essén, M., Lönneborg, R., Bromark, M. & Hamrin, G. (2021). Digital literacy: – a necessity in digital learning spaces. In: : . Paper presented at Scholarship of Teaching and Learning 2021, Online.
Open this publication in new window or tab >>Digital literacy: – a necessity in digital learning spaces
2021 (English)Conference paper, Oral presentation with published abstract (Refereed)
Abstract [en]

Background and purpose

We assume that, in a possible “post-Covid-19”-scenario, the distance-based teaching at KTH will still be a vital influence onKTH-students' learning experiences and future working lives. This assumption is corroborated by the newly implementedKTH policy on digitalisation, which indicates a higher degree of digital learning activities [1]. By digital literacy we mean the general ability to work productively with digital and technical tools, in particular in blended ordistance-based learning activities. We here use the framework of JISC [2] to define six different elements of digitalcapabilities, whose content can be summarized as: Functional skills, critical use, creative production, participation,development, and self-actualizing. Viewing this framework, we conclude that digital literacy ispart of the general academic skills that students of today need to possess. And as digital literacy is a general academic skill, it is natural to view the library as a promoter of digital literacy. This is in linewith the library already being a learning space for different media literacies [3]. A recent example of this is the “datacarpentry”-activities produced by the KTH Library with collaborators [4]. Hence, our purpose is to investigate how the KTH Library can be both a virtual arena and a physical learning space for digitalliteracy.

Finished work/ongoing work

We made a survey in order to see if, and how, digital literacy is strengthened by learning activities at KTH today. In thesurvey, we frame the questions according to the six JISC-elements. The survey was divided into three parts: a. A directed survey, with follow-up interviews, to KTH Program Directors as well as key administrators of KTH educationalprograms. b. A general survey to students, with emphasis on students in later years of study. c. A directed survey to PhD-candidates, who have participated in KTH Library learning activities recently. From the results of the survey in c. above, we have developed a few workshops on digital literacy, in particular on differentaspects of research data management. The ideas for them also come from needs and requests made by students and teachersin earlier contacts with the KTH Library staff and learning activities. Subjects of these workshops are reflecting the sixelements of the JISC-framework.

Results/observations/lessons learned

The preliminary results of our survey indicate that aspects of digital literacy are covered to some extent by learning activitiestoday, but that the coverage is far from complete at KTH. In our future work, we will explore additional results from thesurvey.

Take-home message

We have mapped how digital literacy is facilitated at KTH today via a survey. We have developed a series of workshopson different aspects of digital literacy for an academic environment. And through our survey and these workshops, we havegained additional insights on how a library can be a natural learning space for fostering digital academic skills. We will in ourtalk highlight some of the achievements, and also briefly discuss some of the challenges for the future.

Keywords
Digital literacy, Global Competence, Course development, Digitally flexible
National Category
Learning Pedagogy
Identifiers
urn:nbn:se:kth:diva-315020 (URN)
Conference
Scholarship of Teaching and Learning 2021, Online
Available from: 2022-06-28 Created: 2022-06-28 Last updated: 2022-06-28
Hamrin, G., Lönneborg, R. & Unger, M. (2016). Teaching information literacy for engineering students in a rapidly changing information landscape. In: Nordic Journal of Information Literacy in Higher Education. Creating Knowledge VIII - Special Issue: . Paper presented at Creating Knowledge VIII - June 2-3, Reykjavik, Iceland. , 8
Open this publication in new window or tab >>Teaching information literacy for engineering students in a rapidly changing information landscape
2016 (English)In: Nordic Journal of Information Literacy in Higher Education. Creating Knowledge VIII - Special Issue, 2016, Vol. 8Conference paper, Oral presentation with published abstract (Refereed)
Abstract [en]

The KTH Library has a long tradition of teaching information searching to technology students. Over the last years teaching information searching has become teaching information literacy, including more evaluation and source criticism. Traditionally, there have been three forms of teaching: independent credit-giving courses, integrated shorter modules in subject-specific courses and support via individual face-to-face supervision.

Although evaluation and source criticism are now important parts of our teaching, much focus is still on search methodology. During this spring we, and our teaching colleagues at the KTH library, will revise and develop the content and pedagogical methodology for the courses and integrated modules in information literacy. In doing so, we need to address important questions on how to face the changing information landscape.

Should the teaching be adapted to the search behaviour observed in our students or should we keep trying to change that behaviour? Do we put our effort into directing students to traditional scientific subject databases or should we put more emphasis on the importance of critically evaluating the search results, regardless of their source? How do we find the balance between these alternatives?

Recently published studies have already covered these questions to some extent. The findings from a systematic literature search, together with insights collected from our development work during Spring 2016, will be used in an analysis of these questions in the context of teaching information literacy for engineering students.

Series
Nordic Journal of Information Literacy in Higher Education
National Category
Information Studies
Identifiers
urn:nbn:se:kth:diva-203770 (URN)10.15845/noril.v8i1.243 (DOI)
Conference
Creating Knowledge VIII - June 2-3, Reykjavik, Iceland
Note

QC 20170405

Available from: 2017-03-16 Created: 2017-03-16 Last updated: 2024-03-18Bibliographically approved
Lerche, M., Dian, C., Round, A., Lönneborg, R., Brzezinski, P. & Leonard, G. A. (2016). The solution configurations of inactive and activated DntR have implications for the sliding dimer mechanism of LysR transcription factors. Scientific Reports, 6, Article ID 19988.
Open this publication in new window or tab >>The solution configurations of inactive and activated DntR have implications for the sliding dimer mechanism of LysR transcription factors
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2016 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 6, article id 19988Article in journal (Refereed) Published
Abstract [en]

LysR Type Transcriptional Regulators (LTTRs) regulate basic metabolic pathways or virulence gene expression in prokaryotes. Evidence suggests that the activation of LTTRs involves a conformational change from an inactive compact apo-configuration that represses transcription to an active, expanded holo-form that promotes it. However, no LTTR has yet been observed to adopt both configurations. Here, we report the results of structural studies of various forms of the LTTR DntR. Crystal structures of apo-DntR and of a partially autoinducing mutant H169T-DntR suggest that active and inactive DntR maintain a compact homotetrameric configuration. However, Small Angle X-ray Scattering (SAXS) studies on solutions of apo-, H169T- and inducer-bound holo-DntR indicate a different behaviour, suggesting that while apo- DntR maintains a compact configuration in solution both H169T- and holo-DntR adopt an expanded conformation. Models of the SAXS-obtained solution conformations of apo- and holo-DntR homotetramers in complex with promoter-operator region DNA are consistent with previous observations of a shifting of LTTR DNA binding sites upon activation and a consequent relaxation in the bend of the promoter-operator region DNA. Our results thus provide clear evidence at the molecular level which strongly supports the 'sliding dimer' hypothesis concerning LTTR activation mechanisms.

Place, publisher, year, edition, pages
Nature Publishing Group, 2016
National Category
Engineering and Technology
Identifiers
urn:nbn:se:kth:diva-182147 (URN)10.1038/srep19988 (DOI)000368777500001 ()26817994 (PubMedID)2-s2.0-84961344694 (Scopus ID)
Note

QC 20160220

Available from: 2016-02-20 Created: 2016-02-16 Last updated: 2022-09-15Bibliographically approved
Lönneborg, R., Varga, E. & Brzezinski, P. (2012). Directed Evolution of the Transcriptional Regulator DntR: Isolation of Mutants with Improved DNT-Response. PLOS ONE, 7(1), e29994
Open this publication in new window or tab >>Directed Evolution of the Transcriptional Regulator DntR: Isolation of Mutants with Improved DNT-Response
2012 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 7, no 1, p. e29994-Article in journal (Refereed) Published
Abstract [en]

The transcriptional regulator DntR, which previously has been isolated from bacterial strains capable of degrading 2,4dinitrotoluene (DNT), was engineered in order to improve the ability to detect DNT. A directed evolution strategy was employed, where sequence diversity first was created by random mutagenesis in three subsequent rounds, followed by recombination of previously selected mutants. A gfp gene was used as a reporter for transcriptional activity mediated by DntR and cells with higher GFP expression after addition of DNT were sorted out using fluorescence-activated cell sorting (FACS). A DntR mutant, which displayed 10 times higher induction levels than wild-type DntR in response to DNT was isolated. This mutant still maintained low levels of gfp expression in the absence of DNT. The detection limit was,10 mM, a 25-fold improvement compared to wild-type DntR. The functional role of some substitutions found in this clone is discussed in the framework of the structural changes observed when comparing the recently determined structures of DntR with and without bound inducer ligand.

Place, publisher, year, edition, pages
Public Library of Science (PLoS), 2012
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-122687 (URN)10.1371/journal.pone.0029994 (DOI)000301457200026 ()22276138 (PubMedID)2-s2.0-84856020198 (Scopus ID)
Note

QC 20130529

Available from: 2013-05-27 Created: 2013-05-27 Last updated: 2022-06-24Bibliographically approved
Devesse, L., Smirnova, I., Lönneborg, R., Kapp, U., Brzezinski, P., Leonard, G. A. & Dian, C. (2011). Crystal structures of DntR inducer binding domains in complex with salicylate offer insights into the activation of LysR-type transcriptional regulators. Molecular Microbiology, 81(2), 354-367
Open this publication in new window or tab >>Crystal structures of DntR inducer binding domains in complex with salicylate offer insights into the activation of LysR-type transcriptional regulators
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2011 (English)In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 81, no 2, p. 354-367Article in journal (Refereed) Published
Abstract [en]

Activation of LysR-type transcription factors (LTTRs) is thought to result from conformational changes that occur when inducer molecules bind to their Inducer Binding Domains (IBDs). However, the exact nature of these changes remains to be fully elucidated. We present the crystal structures of two truncated constructs of the LTTR DntR in their apo-forms and in complex with its natural inducer molecule, salicylate. These provide a fuller picture of the conformational changes that can occur in LTTR IBDs and offer insights that may be relevant when considering the mechanism of activation of LTTRs. Two of the crystal structures show that DntR IBDs can bind up to two inducer molecules. The full extent of conformational changes observed is achieved only when inducer molecules are bound in both binding sites identified. Point mutations disrupting the putative secondary binding site produce DntR variants with a reduced response to salicylate in a whole cell system, suggesting that this site is functionally relevant.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2011
Keywords
Allosteric Regulation, Binding Sites, Burkholderia, Crystallography, X-Ray, Models, Molecular, Mutant Proteins, Point Mutation, Protein Binding, Protein Conformation, Protein Structure, Tertiary, Salicylates, Transcription Factors
National Category
Other Chemistry Topics
Identifiers
urn:nbn:se:kth:diva-188475 (URN)10.1111/j.1365-2958.2011.07673.x (DOI)000292567200008 ()21692874 (PubMedID)2-s2.0-79960168122 (Scopus ID)
Funder
Swedish Research Council
Note

QC 20160610

Available from: 2016-06-10 Created: 2016-06-10 Last updated: 2022-06-22Bibliographically approved
Lönneborg, R. & Brzezinski, P. (2011). Factors that influence the response of the LysR type transcriptional regulators to aromatic compounds. BMC Biochemistry, 12(49)
Open this publication in new window or tab >>Factors that influence the response of the LysR type transcriptional regulators to aromatic compounds
2011 (English)In: BMC Biochemistry, E-ISSN 1471-2091, Vol. 12, no 49Article in journal (Refereed) Published
Abstract [en]

Background: The transcriptional regulators DntR, NagR and NtdR have a high sequence identity and belong to the large family of LysR type transcriptional regulators (LTTRs). These three regulators are all involved in regulation of genes identified in pathways for degradation of aromatic compounds. They activate the transcription of these genes in the presence of an inducer, but the inducer specificity profiles are different. Results: The results from this study show that NtdR has the broadest inducer specificity, responding to several nitro-aromatic compounds. Mutational studies of residues that differ between DntR, NagR and NtdR suggest that a number of specific residues are involved in the broader inducer specificity of NtdR when compared to DntR and NagR. The inducer response was also investigated as a function of the experimental conditions and a number of parameters such as the growth media, plasmid arrangement of the LTTR-encoding genes, promoter and gfp reporter gene, and the presence of a His(6) tag were shown to affect the inducer response in E. coli DH5 alpha. Furthermore, the response upon addition of both salicylate and 4-nitrobenzoate to the growth media was larger than the sum of responses upon addition of each of the compounds, which suggests the presence of a secondary binding site, as previously reported for other LTTRs. Conclusions: Optimization of the growth conditions and gene arrangement resulted in improved responses to nitro-aromatic inducers. The data also suggests the presence of a previously unknown secondary binding site in DntR, analogous to that of BenM.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2011
Keywords
transcriptional regulator, LysR family, inducer specificity, gfp
National Category
Biochemistry and Molecular Biology
Research subject
Biotechnology
Identifiers
urn:nbn:se:kth:diva-188487 (URN)10.1186/1471-2091-12-49 (DOI)000295222700001 ()21884597 (PubMedID)2-s2.0-80052159033 (Scopus ID)
Note

QC 20160610

Available from: 2016-06-10 Created: 2016-06-10 Last updated: 2024-01-16Bibliographically approved
Nordlund, G., Lönneborg, R. & Brzezinski, P. (2009). Formation of supported lipid bilayers on silica particles studied using flow cytometry.. Langmuir, 25(8), 4601-4606
Open this publication in new window or tab >>Formation of supported lipid bilayers on silica particles studied using flow cytometry.
2009 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 25, no 8, p. 4601-4606Article in journal (Refereed) Published
Abstract [en]

Silica colloidal particles with functionalized surfaces are used, for example, in studies of membrane proteins or for drug delivery, where novel applications are based on the use of particles covered by lipid membrane bilayers. The mechanism by which such supported lipid bilayers are formed on spherical support is not fully understood. Here, we present results from studies of this process using a new method based on now cytometry. The approach enabled us to detect particle populations coated and uncoated with lipids in the same sample according to the vesicle: particle surface area ratio. The data suggest that DOPC lipid vesicles efficiently break upon interaction with the silica colloidal particle surface; only a small fraction of the adsorbed vesicles remain unbroken. Furthermore, the data support earlier observations showing that formation of the lipid bilayer at the surface is a cooperative process, where bilayer formation is catalyzed by previously bound membrane fragments.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2009
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-198493 (URN)10.1021/la8036296 (DOI)000265281700059 ()19265407 (PubMedID)2-s2.0-65249190759 (Scopus ID)
Note

QC 20170112

Available from: 2016-12-16 Created: 2016-12-16 Last updated: 2022-06-27Bibliographically approved
Lönneborg, R., Smirnova, I., Dian, C., Leonard, G. A. & Brzezinski, P. (2007). In vivo and in vitro investigation of transcriptional regulation by DntR.. Journal of Molecular Biology, 372(3), 571-82
Open this publication in new window or tab >>In vivo and in vitro investigation of transcriptional regulation by DntR.
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2007 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 372, no 3, p. 571-82Article in journal (Refereed) Published
Abstract [en]

DntR is a bacterial transcription factor that has been isolated from Burkholderia species that are able to degrade the nitro-aromatic compound 2,4-dinitrotoluene. We recently solved the X-ray crystal structure of DntR, which suggested a putative location of an inducer-binding cavity (IBC). In this study, we constructed mutants of DntR in which residues lining the proposed IBC were modified in order to identify the structural elements involved in inducer binding, to modulate the inducer binding specificity, and to investigate the mechanism of transcriptional regulation by DntR. The transcriptional activation of the reporter gene gfp induced by the wild-type and mutant DntRs was monitored by analysing whole-cell fluorescence using flow-cytometry after addition of a number of potential inducer compounds. Three of the mutant proteins (F111L; F111V/H169V and Y110S/F111V) were purified and the binding constants for several of the potential inducers to these mutants were estimated. Furthermore, crystal structures of the F111L and Y110S/F111V mutant proteins were solved and used to explain changes in the inducer binding specificity at an atomic level. A comparison of the inducing capability in the whole-cell system and binding constants for a number of potential inducers suggests a mechanism where binding of an inducer molecule is not the sole requirement for transcriptional activation. In addition, specific interactions between DntR and the inducer molecule resulting in a conformational change of the protein are needed.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-104682 (URN)10.1016/j.jmb.2007.06.076 (DOI)000249494800002 ()17681542 (PubMedID)2-s2.0-34548189428 (Scopus ID)
Note

QC 20130513

Available from: 2007-10-23 Created: 2012-11-09 Last updated: 2022-06-24Bibliographically approved
Hedhammar, M., Stenvall, M., Lönneborg, R., Nord, O., Sjölin, O., Brismar, H., . . . Hober, S. (2005). A Novel flow cytometry-based method for analysis of expression levels in Escherichia coli, giving information about precipitated and soluble protein. Journal of Biotechnology, 119(2), 133-146
Open this publication in new window or tab >>A Novel flow cytometry-based method for analysis of expression levels in Escherichia coli, giving information about precipitated and soluble protein
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2005 (English)In: Journal of Biotechnology, ISSN 0168-1656, E-ISSN 1873-4863, Vol. 119, no 2, p. 133-146Article in journal (Refereed) Published
Abstract [en]

A high throughput method for screening of protein expression is described. By using a flow cytometer, levels of both soluble and precipitated protein can simultaneously be assessed in vivo. Protein fragments were fused to the N-terminus of enhanced GFP and the cell samples were analysed using a flow cytometer. Data concerning whole cell fluorescence and light scattering was collected. The whole cell fluorescence is probing intracellular concentrations of soluble fusion proteins. Concurrently, forward scattered light gives data about inclusion body formation, valuable information in process optimisation. To evaluate the method, the cells were disrupted, separated into soluble and non-soluble fractions and analysed by gel electrophoresis. A clear correlation between fluorescence and soluble target protein was shown. Interestingly, the distribution of the cells regarding forward scatter (standard deviation) correlates with the amount of inclusion bodies formed. Finally, the newly developed method was used to evaluate two different purification tags, His(6) and Z(basic), and their effect on the expression pattern.

Place, publisher, year, edition, pages
Elsevier BV, 2005
Keywords
protein production levels; inclusion bodies; green fluorescent protein (GFP); flow cytometry; Z(basic); His(6)
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-8273 (URN)10.1016/j.jbiotec.2005.03.024 (DOI)000232042900003 ()15996784 (PubMedID)2-s2.0-24044436165 (Scopus ID)
Note

QC 20100824

Available from: 2005-11-02 Created: 2005-11-02 Last updated: 2022-06-26Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-7679-1369

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