| 1. |
- Kassa, Eszter, et al.
(författare)
-
Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions
- 2024
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Low affinity and transient protein-protein interactions, such as short linear motif (SLiM)-based interactions, require dedicated experimental tools for discovery and validation. Here, we evaluated and compared biotinylated peptide pulldown and protein interaction screen on peptide matrix (PRISMA) coupled to mass-spectrometry (MS) using a set of peptides containing interaction motifs. Eight different peptide sequences that engage in interactions with three distinct protein domains (KEAP1 Kelch, MDM2 SWIB, and TSG101 UEV) with a wide range of affinities were tested. We found that peptide pulldown can be an effective approach for SLiM validation, however, parameters such as protein abundance and competitive interactions can prevent the capture of known interactors. The use of tandem peptide repeats improved the capture and preservation of some interactions. When testing PRISMA, it failed to provide comparable results for a model peptide that successfully pulled down a known interactor using biotinylated peptide pulldown. Overall, in our hands, we find that albeit more laborious, biotin-peptide pulldown was more successful in terms of validation of known interactions. Our results highlight that the tested affinity-capture MS-based methods for validation of SLiM-based interactions from cell lysates are suboptimal, and we identified parameters for consideration for method development.
|
|
| 2. |
- Kassa, Eszter, et al.
(författare)
-
Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions
- 2023
-
Ingår i: Analytical Biochemistry. - : Elsevier. - 0003-2697 .- 1096-0309. ; 663
-
Tidskriftsartikel (refereegranskat)abstract
- Low affinity and transient protein-protein interactions, such as short linear motif (SLiM)-based interactions, require dedicated experimental tools for discovery and validation. Here, we evaluated and compared biotinylated peptide pulldown and protein interaction screen on peptide matrix (PRISMA) coupled to massspectrometry (MS) using a set of peptides containing interaction motifs. Eight different peptide sequences that engage in interactions with three distinct protein domains (KEAP1 Kelch, MDM2 SWIB, and TSG101 UEV) with a wide range of affinities were tested. We found that peptide pulldown can be an effective approach for SLiM validation, however, parameters such as protein abundance and competitive interactions can prevent the capture of known interactors. The use of tandem peptide repeats improved the capture and preservation of some interactions. When testing PRISMA, it failed to provide comparable results for model peptides that successfully pulled down known interactors using biotinylated peptide pulldown. Overall, in our hands, we find that albeit more laborious, biotin-peptide pulldown was more successful in terms of validation of known interactions. Our results highlight that the tested affinity-capture MS-based methods for validation of SLiM-based interactions from cell lysates are suboptimal, and we identified parameters for consideration for method development.
|
|
| 3. |
- Lind, Anna-Sara, 1977-, et al.
(författare)
-
A New Proportionality Test for Fundamental Rights? : The Joined Cases C-92/09 and C-93/09 Volker und Markus Schecke GbR (C-92/09) and Hartmut Eifert (C-93/09) v. Land Hessen
- 2011
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- In the joined cases C-92/09 and C-93/09 Volker und Markus Schecke GbR (C-92/09) and Hartmut Eifert (C-93/09) v. Land Hessen Judgment of 9 November 2010, not yet published, the Court of Justice of the European Union (Court of Justice) was called upon to balance the right to respect of private life in general, and to the protection of personal data in particular, protected by Articles 7 and 8 of the Charter of Fundamental Rights of the European Union (the Charter), against the principle of transparency stated in Articles 1 and 10 of the Treaty on European Union (TEU) and in Article 15 of the Treaty on the Functioning of the European Union (TFEU). The Court of Justice approached this problem within the context of a reference for a preliminary ruling under Article 267 TFEU. This reference, however, took the form of an indirect challenge to certain EU law provisions that, in the view of the applicants, violated the right to respect of private life and of the protection of personal data. In this analysis the method of the Court of Justice when balancing diverging or even opposing interests protected by EU law will be scrutinised. The authors are critical of the Court’s reasoning, which they consider put too little weight on the fundamental interest of transparency in the case at hand. The analysis is structured as follows. First, in section 1, the arguments of the Applicants and the respondent State respectively will be summarised, followed by the main reasoning of the Court. In section 2, the question of how to balance fundamental rights and general interests will be analysed, taking as the point of departure the question of proportionality as described by the Court. The conclusions are presented in the final section 3.
|
|
| 4. |
- Lind, Anna-Sara, 1977-, et al.
(författare)
-
EU-rättsliga frågor kring arbetsmodellerna till ny yttrandefrihetsgrundlag
- 2010
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Rapporten tillämpar främst EU-rättslig metod och presenterar risker. I de fall risker noterats finns förslag till åtgärder. Lissabonfördraget öppnar nya möjligheter att aktivt värna om den svenska grundlagsskyddade yttrandefriheten. Det finns en risk för konflikt mellan modellerna och EU:s dataskyddsdirektiv. Möjligen behövs en ny hänvisning till PuL i grundlagen för de fall då yttranden inte med stöd i dataskyddsdirektivets artikel 9 kan undantas från direktivets tillämpningsområde. Ansvarsmodellens krav på ansvarig utgivare med svenskt hemvist riskerar att stå i strid med EU-rättens krav på fri rörlighet för varor och tjänster. Vi föreslår därför en komplettering till ansvarsmodellen. Det är inte möjligt att nå trygg förvissning om att en viss grundlagsreglering av yttrandefriheten är förenlig med EU-rätten. Vid en eventuell konflikt bör svenska domstolar inhämta förhandsavgörande, men bör då också ställa sina frågor till EU-domstolen på ett sätt som värnar den svenska grundlagen. Domstolarna har också ur svensk synvinkel möjlighet att med hänvisning till svensk grundlag frångå den handlingslinje som följer av ett givet förhandsavgörande.
|
|
| 5. |
- Valarcher, Jean-Francois, et al.
(författare)
-
Single-Shot Vaccines against Bovine Respiratory Syncytial Virus (BRSV) : Comparative Evaluation of Long-Term Protection after Immunization in the Presence of BRSV-Specific Maternal Antibodies
- 2021
-
Ingår i: Vaccines. - : MDPI. - 2076-393X. ; 9:3
-
Tidskriftsartikel (refereegranskat)abstract
- The induction of long-lasting clinical and virological protection is needed for a successful vaccination program against the bovine respiratory syncytial virus (BRSV). In this study, calves with BRSV-specific maternally derived antibodies were vaccinated once, either with (i) a BRSV pre-fusion protein (PreF) and Montanide(TM) ISA61 VG (ISA61, n = 6), (ii) BRSV lacking the SH gene (Delta SHrBRSV, n = 6), (iii) a commercial vaccine (CV, n = 6), or were injected with ISA61 alone (n = 6). All calves were challenged with BRSV 92 days later and were euthanized 13 days post-infection. Based on clinical, pathological, and proteomic data, all vaccines appeared safe. Compared to the controls, PreF induced the most significant clinical and virological protection post-challenge, followed by Delta SHrBRSV and CV, whereas the protection of PreF-vaccinated calves was correlated with BRSV-specific serum immunoglobulin (Ig)G antibody responses 84 days post-vaccination, and the IgG antibody titers of Delta SHrBRSV- and CV-vaccinated calves did not differ from the controls on this day. Nevertheless, strong anamnestic BRSV- and PreF-specific IgG responses occurred in calves vaccinated with either of the vaccines, following a BRSV challenge. In conclusion, PreF and Delta SHrBRSV are two efficient one-shot candidate vaccines. By inducing a protection for at least three months, they could potentially improve the control of BRSV in calves.
|
|
| 6. |
|
|
| 7. |
- Arvidsson, Per I., et al.
(författare)
-
Öppenheten förstör chansen till patent
- 2015
-
Ingår i: Svenska dagbladet. - Stockholm : Svenska Dagbladet AB & Co.. - 2001-3868.
-
Tidskriftsartikel (populärvet., debatt m.m.)
|
|
| 8. |
|
|
| 9. |
- Cedernaes, Jonathan, et al.
(författare)
-
Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans
- 2018
-
Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 4:8
-
Tidskriftsartikel (refereegranskat)abstract
- Curtailed sleep promotes weight gain and loss of lean mass in humans, although the underlying molecular mechanisms are poorly understood. We investigated the genomic and physiological impact of acute sleep loss in peripheral tissues by obtaining adipose tissue and skeletal muscle after one night of sleep loss and after one full night of sleep. We find that acute sleep loss alters genome-wide DNA methylation in adipose tissue, and unbiased transcriptome-, protein-, and metabolite-level analyses also reveal highly tissue-specific changes that are partially reflected by altered metabolite levels in blood. We observe transcriptomic signatures of inflammation in both tissues following acute sleep loss, but changes involving the circadian clock are evident only in skeletal muscle, and we uncover molecular signatures suggestive of muscle breakdown that contrast with an anabolic adipose tissue signature. Our findings provide insight into how disruption of sleep and circadian rhythms may promote weight gain and sarcopenia.
|
|
| 10. |
- Chen, Moashan, et al.
(författare)
-
Data on the expression of cellular lncRNAs in human adenovirus infected cells
- 2016
-
Ingår i: Data in Brief. - Elsevier : Elsevier BV. - 2352-3409. ; 8, s. 1263-1279
-
Tidskriftsartikel (refereegranskat)abstract
- Expression of cellular long non-coding RNAs (lncRNAs) in human primary lung fibroblasts (IMR-90) during the course of adenovirus type 2 (Ad2) infection was studied by strand-specific whole transcriptome sequencing. In total, 645 cellular lncRNAs were expressed at a significant level and 398 of them were changed more than 2-fold. The changes in expression followed a distinct temporal pattern. Significantly, 80% of the changes occurred at the late phase and 80% of the de-regulated lncRNAs were up-regulated. The three largest groups of deregulated lncRNAs were 125 antisense RNAs, 111 pseudogenes and 85 long intergenic non-coding RNAs (lincRNAs). Lastly, more than 36% of lncRNAs have been shown to interact with RNA binding proteins.
|
|
