| 1. |
- Akan, Pelin, et al.
(författare)
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Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines
- 2012
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Ingår i: Genome Medicine. - : Springer Science and Business Media LLC. - 1756-994X. ; 4, s. 86-
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Tidskriftsartikel (refereegranskat)abstract
- We here present a comparative genome, transcriptome and functional network analysis of three human cancer cell lines (A431, U251MG and U2OS), and investigate their relation to protein expression. Gene copy numbers significantly influenced corresponding transcript levels; their effect on protein levels was less pronounced. We focused on genes with altered mRNA and/or protein levels to identify those active in tumor maintenance. We provide comprehensive information for the three genomes and demonstrate the advantage of integrative analysis for identifying tumor-related genes amidst numerous background mutations by relating genomic variation to expression/protein abundance data and use gene networks to reveal implicated pathways.
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| 2. |
- Andresen, Edith, et al.
(författare)
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Processes in collaborative entrepreneurship : a longitudinal case study of how multiple actors exploit a radically new opportunity
- 2014
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Ingår i: The International Entrepreneurship and Management Journal. - : Springer Science and Business Media LLC. - 1554-7191 .- 1555-1938. ; 10:4, s. 713-726
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Tidskriftsartikel (refereegranskat)abstract
- In this longitudinal case study, the authors integrate the theory on social movement with the entrepreneurship literature on opportunity discovery, evaluation, and exploitation. They construct a model on collaborative entrepreneurial processes in which multiple partners are involved in identifying, forming, and exploiting an opportunity. Three interdependent subprocesses are identified: (1) the opportunity conceptualization dialogue, (2) resource mobilization and, (3) legitimacy building, which significantly contribute to our understanding of how individuals across different organizations become engaged in collaborative entrepreneurial processes. The model of collaborative entrepreneurial processes complements traditional models of the entrepreneurial process, which place the individual entrepreneur at the center of the process and does not consider group mobilization processes in which the actors aim to be creative and innovative in collaborating with actors from other organizations or firms.
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| 3. |
- Bergkvist, Kristina, et al.
(författare)
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Ädelputs
- 2014
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Ingår i: Hantverkslaboratoriets filmkanal på Youtube.
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Filmen berättar om olika typer av ädelputs och vikten av att renovera putsen på rätt sätt. Muraren Bosse J Johanson visar och berättar om husfasader, som t ex på Kungstornen i Stockholm, där man finner ädelputs. I filmen visas och beskrivs också material, verktyg och metoder för att skapa olika typer av ädelputs, muraren Tony Sundkvist demonsterar. Filmen är producerad av Hantverkslaboratoriet 2011. Projektledare ädelputs Kristina Bergkvist, filmsamordnare Anette Lykke Lundberg, foto, klipp och speaker Joakim Jalin.
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| 4. |
- Indén, Tobias, 1977-, et al.
(författare)
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Överprövningar av offentliga upphandlingar : En intervjustudie om skillnader mellan LOU och LUF
- 2014
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Rapport (populärvet., debatt m.m.)abstract
- Syftet med denna studie är att analysera möjliga förklaringar till att upphandlingarsom görs enligt Lagen (2007:1092) om offentlig upphandling inom områdenavatten, energi, transporter och posttjänster (LUF) tycks föranleda en mindre andelöverprövningar än upphandlingar som görs enligt Lagen (2007:1091) om offentligupphandling (LOU). Den senare lagstiftningen är tillämplig på offentliga upphandlingarav tjänster, varor och byggentreprenader som inte faller under de områdensom anges i LUF (se ovan).Tillgänglig statistik visar att överprövning är mer vanligt förekommande blandupphandlingar som regleras av LOU. Detta förhållande kvarstår med hänsyn tagentill att det är mer vanligt att upphandla enligt LOU än LUF. För att belysa möjligaförklaringar till detta har 28 intervjuer genomförts med beställare/upphandlare frånstatliga och kommunala organ samt med företrädare för leverantörer från olikabranscher.Utgångspunkterna för intervjuerna har varit frågor relaterade till upphandlingssituationen(t.ex. organisation och kompetens), juridiska faktorer (t.ex. förhandlingsmöjligheter)samt leverantörernas syn på upphandling (t.ex. överprövningsom affärsstrategi).Intervjuerna ger vid handen att en avgörande anledning till att upphandlingarenligt LUF överprövas i mindre utsträckning än upphandlingar enligt LOU är detmer omfattande förhandlingsutrymme som till skillnad från LOU finns i LUF. Frånupphandlarsidan menar de intervjuade att förhandling förebygger och ger möjlighetatt hantera missförstånd och felaktigheter under upphandlingens gång. Dettaanses minska risken för att en leverantör upplever sig felbehandlad eller upphandlingensom illa genomförd. En annan intressant iakttagelse är att de intervjuadeupphandlarna beskriver att de branscher som upphandlas enligt LOU i högreutsträckning präglas av en ”överprövningskultur”. Av de intervjuade nämner fleraatt LUF-upphandlingar ofta är mer komplexa och att myndigheter som upphandlarunder LUF därför håller sig med upphandlare med hög marknadsspecifikkompetens. En sådan lösning är något som skulle vara mer resurskrävande förkommunala organ, då de ofta förfogar över en i högre grad diversifieradupphandlingsportfölj.
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| 5. |
- Klevebring, Daniel, 1981-, et al.
(författare)
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Analysis of transcript and protein overlap in a human osteosarcoma cell line
- 2010
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11:1, s. 684-
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Tidskriftsartikel (refereegranskat)abstract
- Background: An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins. In this study, we used massive transcriptome sequencing (RNA-seq) to investigate the transcriptome of a human osteosarcoma cell line and compared the expression levels with in situ protein data obtained in-situ from antibody-based immunohistochemistry (IHC) and immunofluorescence microscopy (IF). Results: A large-scale analysis based on 2749 genes was performed, corresponding to approximately 13% of the protein coding genes in the human genome. We found the presence of both RNA and proteins to a large fraction of the analyzed genes with 60% of the analyzed human genes detected by all three methods. Only 34 genes (1.2%) were not detected on the transcriptional or protein level with any method. Our data suggest that the majority of the human genes are expressed at detectable transcript or protein levels in this cell line. Since the reliability of antibodies depends on possible cross-reactivity, we compared the RNA and protein data using antibodies with different reliability scores based on various criteria, including Western blot analysis. Gene products detected in all three platforms generally have good antibody validation scores, while those detected only by antibodies, but not by RNA sequencing, generally consist of more low-scoring antibodies. Conclusion: This suggests that some antibodies are staining the cells in an unspecific manner, and that assessment of transcript presence by RNA-seq can provide guidance for validation of the corresponding antibodies.
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| 6. |
- Lundberg, Emma, et al.
(författare)
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Defining the transcriptome and proteome in three functionally different human cell lines
- 2010
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Ingår i: Molecular Systems Biology. - : EMBO. - 1744-4292 .- 1744-4292. ; 6, s. 450-
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Tidskriftsartikel (refereegranskat)abstract
- An essential question in human biology is how cells and tissues differ in gene and protein expression and how these differences delineate specific biological function. Here, we have performed a global analysis of both mRNA and protein levels based on sequence-based transcriptome analysis (RNA-seq), SILAC-based mass spectrometry analysis and antibody-based confocal microscopy. The study was performed in three functionally different human cell lines and based on the global analysis, we estimated the fractions of mRNA and protein that are cell specific or expressed at similar/different levels in the cell lines. A highly ubiquitous RNA expression was found with > 60% of the gene products detected in all cells. The changes of mRNA and protein levels in the cell lines using SILAC and RNA ratios show high correlations, even though the genome-wide dynamic range is substantially higher for the proteins as compared with the transcripts. Large general differences in abundance for proteins from various functional classes are observed and, in general, the cell-type specific proteins are low abundant and highly enriched for cell-surface proteins. Thus, this study shows a path to characterize the transcriptome and proteome in human cells from different origins.
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| 7. |
- Lykke Lundberg, Anette, et al.
(författare)
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Det är berget som bestämmer
- 2014
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Ingår i: Hantverkslaboratoriets filmkanal på Youtube.
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Sigvard Nyström, stenarbetare och ägare av Glava skifferbrott, visar hur man spränger, bryter, klyver och hugger takskiffer. En film av Anette Lykke Lundberg och Joakim Jalin. Filmen är inspelad i Glava, Värmland, 2011 och producerad av Hantverkslaboratoriet.
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| 8. |
- Rollenhagen, Carl, et al.
(författare)
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The context and habits of accident investigation practices : A study of 108 Swedish investigators
- 2010
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Ingår i: Safety Science. - : Elsevier BV. - 0925-7535 .- 1879-1042. ; 48:7, s. 859-867
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Tidskriftsartikel (refereegranskat)abstract
- The context and habits of accident investigation practices were explored by means of questionnaire data obtained from accident investigators in the healthcare, transportation, nuclear and rescue sectors in Sweden. Issues explored included; resources, training, time spent in different phases of an investigation, methods and procedures, beliefs about causes to accidents, communication issues, etc. Examples of findings were: differences in the extent to which the 'human factor' was perceived as a dominant cause to accidents; manning resources to support investigations were perceived as rather scarce; underutilization of data from safety related processes such as risk analysis and auditing data; the phase of suggesting remedial actions (recommendations) were comparatively brief and generally not well supported. A majority of the investigators thought that the investigations were free from pressures to follow a specific direction; the investigators also thought that performing an investigation in itself (regardless of the specific results) had positive influences on safety. A majority of the investigators thought that upper management had a relatively strong influence on safety in the organizations. The results are discussed in terms of suggestions for strategies to strengthen investigation practices - particularly those conducted as part-time work in organizations.
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| 9. |
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| 10. |
- Werne Solnestam, Beata, et al.
(författare)
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Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs
- 2012
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 13:1, s. 574-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The majority of published gene-expression studies have used RNA isolated from whole cells, overlooking the potential impact of including nuclear transcriptome in the analyses. In this study, mRNA fractions from the cytoplasm and from whole cells (total RNA) were prepared from three human cell lines and sequenced using massive parallel sequencing. Results: For all three cell lines, of about 15000 detected genes approximately 400 to 1400 genes were detected in different amounts in the cytoplasmic and total RNA fractions. Transcripts detected at higher levels in the total RNA fraction had longer coding sequences and higher number of miRNA target sites. Transcripts detected at higher levels in the cytoplasmic fraction were shorter or contained shorter untranslated regions. Nuclear retention of transcripts and mRNA degradation via miRNA pathway might contribute to this differential detection of genes. The consequence of the differential detection was further investigated by comparison to proteomics data. Interestingly, the expression profiles of cytoplasmic and total RNA correlated equally well with protein abundance levels indicating regulation at a higher level. Conclusions: We conclude that expression levels derived from the total RNA fraction be regarded as an appropriate estimate of the amount of mRNAs present in a given cell population, independent of the coding sequence length or UTRs.
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