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  • 1.
    Ayoglu, Burcu
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gundberg, Anna
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Khademi, Mohsen
    Karolinska Hosp, Dept Clin Neurosci, Stockholm, Sweden..
    Olsson, Tomas
    Karolinska Hosp, Dept Clin Neurosci, Stockholm, Sweden..
    Uhl, Mathias N
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schwenk, Jochen M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nilsson, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Proteomic profiling of the autoimmunity repertoire in multiple sclerosis2012In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, p. S20-S20Article in journal (Other academic)
  • 2.
    Berglin, Mattias
    RISE, SP – Sveriges Tekniska Forskningsinstitut, SP Kemi Material och Ytor, Material och ytteknik.
    Pellet formation of zygomycetes and immobilization of yeast2013In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 30, no 5, p. 516-522Article in journal (Refereed)
  • 3.
    Berglund, Lars
    et al.
    KTH, School of Biotechnology (BIO).
    Jonasson, K.
    KTH, School of Biotechnology (BIO).
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO). Royal Inst Technol, Sch Biotechnol, Stockholm, Sweden..
    Antibodypedia-towards a user community for antibody validation data2009In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 25, p. S360-S361Article in journal (Other academic)
  • 4.
    Cengic, Ivana
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kaczmarzyk, Danuta
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Yao, Lun
    KTH.
    Hudson, Paul
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    CRISPRi for metabolic engineering and fatty alcohol production in cyanobacteria2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, p. S37-S37Article in journal (Refereed)
  • 5.
    Cerullo, Gabriella
    et al.
    University of Naples “Federico II”, Naples, Italy.
    Varriale, Simona
    University of Naples “Federico II”, Naples, Italy.
    Bozonnet, Sophie
    Université de Toulouse, Toulouse, France.
    Antonopoulou, Io
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Christakopoulos, Paul
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Rova, Ulrika
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Gherbovet, Olga
    Université de Toulouse, Toulouse, France.
    Fauré, Régis
    Université de Toulouse, Toulouse, France.
    Piechot, Alexander
    Taros Chemicals GmbH & Co. KG, Dortmund, Germany.
    Jütten, Peter
    Taros Chemicals GmbH & Co. KG, Dortmund, Germany.
    Brás, Joana L.A.
    NzyTech LDA, Lisbon, Portugal.
    Fontes, Carlos M.G.A.
    NzyTech LDA, Lisbon, Portugal.
    Faraco, Vincenza
    University of Naples “Federico II”, Naples, Italy.
    Directed evolution of the type C feruloyl esterase from Fusarium oxysporum FoFaeC and molecular docking analysis of its improved variants2019In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 51, p. 14-20Article in journal (Refereed)
    Abstract [en]

    The need to develop competitive and eco-friendly processes in the cosmetic industry leads to the search for new enzymes with improved properties for industrial bioconversions in this sector. In the present study, a complete methodology to generate, express and screen diversity for the type C feruloyl esterase from Fusarium oxysporium FoFaeC was set up in a high-throughput fashion. A library of around 30,000 random mutants of FoFaeC was generated by error prone PCR of fofaec cDNA and expressed in Yarrowia lipolytica. Screening for enzymatic activity towards the substrates 5-bromo-4-chloroindol-3-yl and 4-nitrocatechol-1-yl ferulates allowed the selection of 96 enzyme variants endowed with improved enzymatic activity that were then characterized for thermo- and solvent- tolerance. The five best mutants in terms of higher activity, thermo- and solvent- tolerance were selected for analysis of substrate specificity. Variant L432I was shown to be able to hydrolyze all the tested substrates, except methyl sinapate, with higher activity than wild type FoFaeC towards methyl p-coumarate, methyl ferulate and methyl caffeate. Moreover, the E455D variant was found to maintain completely its hydrolytic activity after two hour incubation at 55 °C, whereas the L284Q/V405I variant showed both higher thermo- and solvent- tolerance than wild type FoFaeC. Small molecule docking simulations were applied to the five novel selected variants in order to examine the binding pattern of substrates used for enzyme characterization of wild type FoFaeC and the evolved variants.

  • 6.
    Christakopoulos, Paul
    et al.
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Antonopoulou, Io
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Topakas, Evangelos
    National Technical University of Athens, School of Chemical Engineering, National Technical University of Athens, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens.
    Synthesis of biological active compounds using carbohydrate esterases as biocatalysts2014In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, no Supplement, p. S90-S91Article in journal (Refereed)
    Abstract [en]

    Various fungal and bacterial carbohydrate esterases represent appealing biocatalysts that have the ability not only to deconstruct plant biomass but also to modify compounds with a potential use in food, cosmetic and pharmaceutical industries. Feruloyl esterases (FAEs, E.C. 3.1.1.73) have been proved promising candidates for the enzymatic synthesis of antioxidants allowing more flexible process configurations. Among the advantages they provide are use of lower temperatures (50-60 °C) comparing to the counterpart chemical process (150οC), one step production of one product instead of mixtures and no need of by-product and catalyst residues removal in order to produce clean and high quality substances. Glucuronoyl esterase (GE) synthetic ability needs to be explored towards the production of alkyl branched glucuronic acid derivatives which are non-ionic surfactants and have good surface properties, including biodegradability. In addition, due to their tastelessness, non skin-irritation and non toxicity, these bioactive compounds find diverse uses in the cosmetic and pharmaceutical industries.Aim of this work is the development of competitive and eco-friendly bioconversions based on transesterification reactions catalyzed by FAEs and GEs, for the production of molecules with antioxidant activity, such as phenolic fatty and sugar esters. The synthesis of four biological active compounds (prenyl ferulate, prenyl caffeate, 5-O-(trans-feruloyl)-arabinofuranose, and glyceryl ferulate) was evaluated using recombinant FAEs from Myceliopthora thermophila and Fusarium oxysporum, while the synthesis of benzyl D-glucuronate and prenyl-D-glucuronate was evaluated using recombinant GEs from M. thermophila. All reactions were carried out in ternary systems of n-hexane/alcohol/water forming surfactantless microemulsions.

  • 7.
    de Oliveira, Felipe Marques Souza
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mereiter, Stefan
    i3S – Instituto de Investigação e Inovação em Saúde and IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, Portugal.
    Lönn, Peter
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Siart, Benjamin
    Department of Anthropology, University of Vienna, Austria; Department of Behavioral Biology, University of Vienna, Austria .
    Shen, Qiujin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Heldin, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Raykova, Doroteya
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Karlsson, Niclas G.
    Department of Medical Biochemistry and Cell Biology at Institute of Biomedicine, Gothenburg University, Sweden.
    Polom, Karol
    Department of Surgical Oncology, Medical University of Gdansk, Poland; General Surgery and Surgical Oncology Department, Università deli Studi di Siena, Italy..
    Roviello, Franco
    General Surgery and Surgical Oncology Department, Università deli Studi di Siena, Italy..
    Reis, Celso A.
    ) i3S – Instituto de Investigação e Inovação em Saúde and IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Portugal; Faculty of Medicine of the University of Porto, Portugal.
    Kamali-Moghaddam, Masood
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Detection of post-translational modifications using solid-phase proximity ligation assay2018In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 45, p. 51-59Article in journal (Refereed)
    Abstract [en]

    Post-translational modifications (PTMs) regulate protein activities to help orchestrate and fine-tune cellular processes. Dysregulation of PTMs is often related with disorders and malignancies, and may serve as a precise biomarker of disease. Developing sensitive tools to measure and monitor low-abundant PTMs in tissue lysates or serum will be instrumental for opening up new PTM-based diagnostic avenues. Here, we investigate the use of solid-phase proximity ligation assay (SP-PLA) for detection of different PTMs. The assay depends on the recognition of the target protein molecule and its modification by three affinity binders. Using antibodies and lectins, we applied the method for detection of glycosylated CD44 and E-Cadherin, and phosphorylated p53 and EGFR. The assay was found to have superior dynamic range and limit of detection compared to standard ELISAs. In summary, we have established the use of SP-PLA as an appropriate method for sensitive detection of PTMs in lysates and sera, which may provide a basis for future PTM-based diagnostic and prognostic biomarkers

  • 8.
    Dionisi, Hebe
    et al.
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Matos, Marina
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Anselmino, Luciano
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Lozada, Mariana
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Mac Cormack, Walter
    Argentinean Antarctic Inst, Buenos Aires, DF, Argentina / Natl Univ Buenos Aires, Buenos Aires, DF, Argentina.
    Carroll, Jolynn
    Univ Tromsö, N-9001 Tromsö, Norway / Akvaplan Niva AS, FRAM High North Res Ctr Climate & Environm, Tromsö, Norway.
    Lundgren, Leif
    Stockholm University.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Chavarria, Krystle
    Lawrence Berkeley Natl Labs, Berkeley, CA USA.
    Henrissat, Bernard
    Ctr Natl Rech Sci, Marseille, France.
    Jansson, Janet
    Lawrence Berkeley Natl Labs, Berkeley, CA USA.
    Mining alginate lyases in sediment metagenomes from four geographically distant cold coastal environments2014In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, p. S69-S70Article in journal (Refereed)
  • 9. Flanigon, James
    et al.
    Kamali-Moghaddam, Masood
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Burbulis, Ian
    Annink, Carla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Steffen, Martin
    Oeth, Paul
    Brent, Roger
    van den Boom, Dirk
    Landegren, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Cantor, Charles
    Multiplex protein detection with DNA readout via mass spectrometry2013In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 30, no 2, p. 153-158Article in journal (Refereed)
    Abstract [en]

    Multiplex protein quantification has been constrained by issues of assay specificity, sensitivity and throughput. This research presents a novel approach that overcomes these limitations using antibody-oligonucleotide conjugates for immuno-polymerase chain reaction (immuno-PCR) or proximity ligation, coupled with competitive PCR and MALDI-TOF mass spectrometry. Employing these combinations of technologies, we demonstrate multiplex detection and quantification of up to eight proteins, spanning wide dynamic ranges from femtomolar concentrations, using only microliter sample volumes.

  • 10.
    Grimm, Sebastian
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Salahshour, Samaneh
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Nygren, Per-Åke
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Monitored whole gene in vitro evolution of an anti-hRaf-1 affibody molecule towards increased binding affinity2011In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, New biotechnology, ISSN 1876-4347, Vol. 29, no 5, p. 534-542Article in journal (Refereed)
    Abstract [en]

    The use of library technologies for the generation of affinity proteins often includes an affinity maturation step, based on the construction of secondary libraries from which second generation variants with improved affinities are selected. Here, we describe for the first time the affinity maturation of affibody molecules based on step-wise in vitro molecular evolution, involving cycles of error-prone PCR (epPCR) amplification for the introduction of diversity over the entire 58-residue three-helix bundle structure and ribosome display (RD) for the selection of improved variants. The model affibody molecule for the process was Z(RAF322), binding with a 1.9μm equilibrium dissociation constant (K(D)) to human Raf-1 (hRaf-1), a protein kinase of central importance in the MAPK/ERK proliferation pathway. The molecular evolution process was followed on both gene and protein levels via DNA sequencing and a biosensor-based binding analysis of pools of selected variants. After two cycles of diversification and selection, a significant increase in binding response of selected pools was seen. DNA sequencing showed that a dominant alanine to valine substitution had been effectively enriched, and was found in 83% of all selected clones, either alone or in combination with other enriched substitutions. The evolution procedure resulted in variants showing up to 26-fold increases in affinity to the hRaf-1 target. Noteworthy, for the two variants showing the highest affinities, substitutions were also found in affibody framework positions, corresponding to regions of the protein domain not addressed by traditional affibody molecule affinity maturation strategies. Interestingly, thermal melting point (T(m)) analyses showed that an increased affinity could be associated with both higher and lower T(m) values. All investigated variants showed excellent refolding properties and selective binding to hRaf-1, as analysed using a multiplexed bead-based binding assay, making them potentially valuable affinity reagents for cell biology studies.

  • 11.
    Gräslund, Torbjörn
    KTH, School of Biotechnology (BIO), Protein Technology.
    Affibody molecules: therapy and in vivo diagnostic applications2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, p. S48-S48Article in journal (Refereed)
  • 12.
    Gu, Gucci Jijuan
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Friedman, Mikaela
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Jost, Christian
    Johnsson, Kai
    Kamali-Moghaddam, Masood
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Plückthun, Andreas
    Landegren, Ulf
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Söderberg, Ola
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation2013In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 30, no 2, p. 144-152Article in journal (Refereed)
    Abstract [en]

    While antibodies currently play a dominant role as affinity reagents in biological research and for diagnostics, a broad range of recombinant proteins are emerging as promising alternative affinity reagents in detection assays and quantification. DNA-mediated affinity-based assays, such as immuno-PCR and proximity ligation assays (PLA), use oligonucleotides attached to affinity reagents as reporter molecules. Conjugation of oligonucleotides to affinity reagents generally employs chemistries that target primary amines or cysteines. Because of the random nature of these processes neither the number of oligonucleotides conjugated per molecule nor their sites of attachment can be accurately controlled for affinity reagents with several available amines and cysteines. Here, we present a straightforward and convenient approach to functionalize recombinant affinity reagents for PLA by expressing the reagents as fusion partners with SNAP protein tags. This allowed us to conjugate oligonucleotides in a site-specific fashion, yielding precisely one oligonucleotide per affinity reagent. We demonstrate this method using designed ankyrin repeat proteins (DARPins) recognizing the tumor antigen HER2 and we apply the conjugates in different assay formats. We also show that SNAP or CLIP tags expressed as fusion partners of transfected genes, allow oligonucleotide conjugations to be performed in fixed cells, with no need for specific affinity reagents. The approach is used to demonstrate induced interactions between the fusion proteins FKBP and FRB by allowing the in situ conjugated oligonucleotides to direct the production of templates for localized rolling circle amplification reactions.

  • 13.
    Guevara, M.
    KTH.
    Studies on the polymerization of poly (3-hydroxyalkanoate)s produced by Halomonas boliviensis2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, p. S152-S153Article in journal (Refereed)
  • 14.
    Guevara, Monica
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Jarmander, Johan
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Perez-Zabaleta, Mariel
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Quillaguaman, Jorge
    Larsson, Gen
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Production of 3-hydroxybutyrate by E. coli: Application of Nitrogen and Phosphorous limitation to steer fluxes to product formation2014In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, p. S148-S148Article in journal (Other academic)
  • 15. Gustavsson, Elin
    et al.
    Ek, Sara
    Steen, Johanna
    KTH, School of Biotechnology (BIO), Proteomics.
    Kristensson, Malin
    Älgenäs, Cajsa
    KTH, School of Biotechnology (BIO), Proteomics.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Wingren, Christer
    Ottosson, Jenny
    KTH, School of Biotechnology (BIO), Proteomics.
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics.
    Borrebaeck, Carl A. K.
    Surrogate antigens as targets for proteome-wide binder selection2011In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 28, no 4, p. 302-311Article in journal (Refereed)
    Abstract [en]

    In the last decade, many initiatives have been taken to develop antibodies for proteome-wide studies, as well as characterization and validation of clinically relevant disease biomarkers. Phage display offers many advantages compared to conventional antibody generation by immunization and hybridoma technology, since it is an unlimited resource of affinity reagents without batch-to-batch variation and is amendable for high throughput. One of the major bottlenecks to proteome-wide binder selection is the limited supply of suitable target antigens representative of the human proteome. Here, we provide proof of principle of using easily accessible, cancer-associated protein epitope signature tags (PrESTs), routinely generated within the Human Protein Atlas project, as surrogate antigens in phage selectionsfor the retrieval of target specific binders. These binders were subsequently tested in western blot, immunohistochemistry and protein microarray application to demonstrate their functionality.

  • 16.
    Hu, Francis Jingxin
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Rockberg, Johan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Generation of HER2 monoclonal antibodies using epitopes of a rabbit polyclonal antibody2014In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, no 1, p. 35-43Article in journal (Refereed)
    Abstract [en]

    One of the issues in using polyclonal antibodies is the limited amount of reagent available from an immunisation, leading to batch-to-batch variation and difficulties in obtaining the same antibody performance when the same antigen is re-immunised into several separate animals. This led to the development of hybridoma technology allowing, at least theoretically, for an unlimited production of a specific binder. Nevertheless, polyclonal antibodies are widely used in research and diagnostics and there exists a need for robust methods to convert a polyclonal antibody with good binding performance into a renewable monoclonal with identical or similar binding specificity. Here we have used precise information regarding the functional recognition sequence (epitope) of a rabbit polyclonal antibody with attractive binding characteristics as the basis for generation of a renewable mouse monoclonal antibody. First, the original protein fragment antigen was used for immunisation and generation of mouse hybridoma, without obtaining binders to the same epitope region. Instead a peptide designed using the functional epitope and structural information was synthesised and used for hybridoma production. Several of the monoclonal antibodies generated were found to have similar binding characteristics to those of the original polyclonal antibody. These monoclonal antibodies detected native HER2 on cell lines and were also able to stain HER2 in immunohistochemistry using xenografted mice, as well as human normal and cancer tissues.

  • 17.
    Hu, Francis Jingxin
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Volk, Anna-Luisa
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Persson, Helena
    KTH, School of Biotechnology (BIO), Protein Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Lund University, Sweden.
    Säll, Anna
    Borrebaeck, Carl
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Rockberg, Johan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders2017In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347Article in journal (Refereed)
    Abstract [en]

    Surface display couples genotype with a surface exposed phenotype and thereby allows screening of gene-encoded protein libraries for desired characteristics. Of the various display systems available, phage display is by far the most popular, mainly thanks to its ability to harbour large size libraries. Here, we describe the first use of a Gram-positive bacterial host for display of a library of human antibody genes which, when combined with phage display, provides ease of use for screening, sorting and ranking by flow cytometry. We demonstrate the utility of this method by identifying low nanomolar affinity scFv fragments towards human epidermal growth factor receptor 2 (HER2). The ranking and performance of the scFv isolated by flow sorting in surface-immobilised form was retained when expressed as soluble scFv and analysed by biolayer interferometry, as well as after expression as full-length antibodies in mammalian cells. We also demonstrate the possibility of using Gram-positive bacterial display to directly improve the affinity of the identified binders via an affinity maturation step using random mutagenesis and flow sorting. This combined approach has the potential for a more complete scan of the antibody repertoire and for affinity maturation of human antibody formats.

  • 18.
    Hu, Francis Jingxin
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Volk, Anna-Luisa
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Persson, Helena
    Department of Immunotechnology, Lund University, Medicon Village (Bldg 406), 223 81 Lund, Sweden..
    Säll, Anna
    Department of Immunotechnology, Lund University, Medicon Village (Bldg 406), 223 81 Lund, Sweden..
    Borrebaeck, Carl
    Department of Immunotechnology, Lund University, Medicon Village (Bldg 406), 223 81 Lund, Sweden..
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Rockberg, Johan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity bindersIn: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347Article in journal (Other academic)
    Abstract [en]

    Surface display couples genotype with a surface exposed phenotype and thereby allows for screening of gene-encoded protein libraries for desired characteristics. Of the various display systems, phage display is by far the most popular, mainly thanks to its ability to harbor large library sizes. Here, we describe the first use of a grampositive host for display of a library of human antibody genes. The method allows for swift generation of binders by combining phage and gram-positive display, for its ease of use for screening, sorting and ranking by flow cytometry. We demonstrate the utility of this method by identifying specific low nanomolar scFv towards human HER2. The ranking and performance of the scFv isolated by flow sorting in surface immobilized form was retained when expressed as soluble scFv and analyzed by biolayer interferometry as well as after expression as full-length antibodies in mammalian cells. We also show the possibility to use gram-positive display to directly improve the affinity of the identified binders via an affinity maturation step using random mutagenesis and flow sorting. We believe this combined approach has the potential for a more complete scan of the antibody repertoire and for swift affinity maturation of human antibody formats.

  • 19.
    Häggmark, Anna
    et al.
    KTH, School of Biotechnology (BIO), Proteomics.
    Neiman, Maja
    KTH, School of Biotechnology (BIO), Proteomics.
    Drobin, Kimi
    KTH, School of Biotechnology (BIO), Proteomics.
    Zwahlen, Martin
    KTH, School of Biotechnology (BIO), Proteomics.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics.
    Schwenk, Jochen M
    KTH, School of Biotechnology (BIO), Proteomics.
    Classification of protein profiles from antibody microarrays using heat and detergent treatment.2011In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, no 5, p. 564-570Article in journal (Refereed)
    Abstract [en]

    Antibody microarrays offer new opportunities for exploring the proteome and to identify biomarker candidates in human serum and plasma. Here, we have investigated the effect of heat and detergents on an antibody-based suspension bead array (SBA) assay using polyclonal antibodies and biotinylated plasma samples. With protein profiles from more than 2300 antibodies generated in 384-plex antibody SBAs, three major classes of heat and detergent susceptibility could be described. The results show that washing of the beads with SDS (rather than Tween) after target binding lowered intensity levels of basically all profiles and that about 50% of the profiles appeared to be lowered to a similar extent by heating of the sample. About 33% of the profiles appeared to be insensitive to heat treatment while another 17% showed a positive influence of heat to yield elevated profiles. The results suggest that the classification of antibodies is driven by the molecular properties of the antibody-antigen interaction and can generally not be predicted based on protein class or Western blot data. The experimental scheme presented here can be used to systematically categorize antibodies and thereby combine antibodies with similar properties into targeted arrays for analysis of plasma and serum.

  • 20.
    Jakobsen, L.
    et al.
    Univ Southern Denmark, Odense, Denmark..
    Vanselow, K.
    Univ Southern Denmark, Odense, Denmark..
    Lundberg, E.
    KTH.
    Poser, I.
    Max Planck Inst, Munich, Germany..
    Hyman, A.
    Max Planck Inst, Munich, Germany..
    Andersen, J.
    Univ Southern Denmark, Odense, Denmark..
    Functional proteomics of the human centrosome2010In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 27, p. S82-S82Article in journal (Other academic)
  • 21.
    Jarmander, Johan
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Guevara, Mónica
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Zabaleta, Mariel Perez
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Sjöberg, Gustav
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Belotserkovsky, Jaroslav
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Quillaguaman, Jorge
    Larsson, Gen
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Production of 3-hydroxybutyrate from waste biomass by metabolically engineered Escherichia coli2014In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, p. S94-S95Article in journal (Other academic)
  • 22. Klingström, Tomas
    et al.
    Soldatova, Larissa
    Stevens, Robert
    Roos, Erik
    Swertz, Morris
    Müller, Kristian
    Kalas, Matus
    Lambrix, Patrick
    Taussig, Michael
    Litton, Jan-Eric
    Landegren, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bongcam-Rudloff, Erik
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Workshop on laboratory protocol standards for the molecular methods database2013In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 30, no 2, p. 109-113Article in journal (Refereed)
    Abstract [en]

    Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.

  • 23.
    Klingström, Tomas
    et al.
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Soldatova, Larissa
    Aberystwyth University, UK.
    Stevens, Robert
    Universtity of Manchester, UK.
    Roos, T. Erik
    University of Groningen, The Netherlands.
    Swertz, Morris A.
    University of Groningen, The Netherlands.
    Müller, Kristian M.
    University of Potsdam, Germany.
    Kalas, Matus
    University of Bergen, Norway.
    Lambrix, Patrick
    Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
    Taussig, Michael J.
    Babraham Bioscience Technologies, Cambridge, UK.
    Litton, Jan-Eric
    Karolinska Institutet, Stockholm, Sweden.
    Landegren, Ulf
    Uppsala University, Sweden.
    Bongcam-Rudloff, Erik
    Swedish University of Agricultural Sciences and Uppsala University, Sweden.
    Workshop on laboratory protocol standards for the molecular methods database2013In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 30, no 2, p. 109-113Article in journal (Refereed)
    Abstract [en]

    Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.

  • 24.
    Landegren, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    AFFINOMICS and the prospects for large-scale protein analyses2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, no 5, p. 491-493Article in journal (Other academic)
  • 25.
    Landegren, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Offshoots of the ESF functional genomics programme2013In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 30, no 3, p. 296-298Article in journal (Refereed)
    Abstract [en]

    After the conclusion of the second five-year period of the European Science Foundation (ESF) programme on functional genomics, it is time to take stock and evaluate its accomplishments. The programme networked leading scientists from a large number of European countries for strategy discussions about the promotion of functional genomics research, and to arrange scientific meetings and exchange programmes. In brief, I believe this programme has punched above its weight, and that it has successfully contributed to the overall organisation of molecular biosciences in Europe. With a modest annual budget the programme has created several interesting new opportunities, some of which may have yet to show their full impact. However, these mini-reviews are intended to provide a personal perspective on this functional genomics effort, and accordingly I focus on my personal experiences from the ESF programme.

  • 26.
    Landegren, Ulf
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Al-Amin, Rasel A.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Björkesten, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    A myopic perspective on the future of protein diagnostics2018In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 45, p. 14-18Article, review/survey (Refereed)
    Abstract [en]

    Plasma proteome analyses of the future promise invaluable insights into states of health, not only by measuring proteins whose role it is to ensure blood homeostasis, but increasingly also as a window into the health of practically any tissue in the body via so-called leakage protein biomarkers. Realizing more of this vast potential will require progress along many lines. Here we discuss the main ones, such as optimal selection of target proteins, affinity reagents, immunoassay formats, samples, and applications, with a view from ongoing work in our laboratory.

  • 27.
    Löfdahl, Per-Åke
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology (closed 20130101).
    Nord, Olof
    KTH, School of Biotechnology (BIO), Molecular Biotechnology (closed 20130101).
    Janzon, Lars
    Nygren, Per-Åke
    KTH, School of Biotechnology (BIO), Molecular Biotechnology (closed 20130101).
    Selection of TNF-alpha binding affibody molecules using a beta-lactamase protein fragment complementation assay2009In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 26, no 5, p. 251-259Article in journal (Refereed)
    Abstract [en]

    Protein fragment complementation assays (PCAs) based on different reporter proteins have been described as powerful tools for monitoring dynamic protein-protein interactions in living cells. The present study describes the construction of a PCA system based on genetic splitting of TEM-1 beta-lactamase for the selection of proteins specifically interacting in the periplasm of Escherichia coli bacterial cells, and its application for the selection of affibody molecules binding human tumour necrosis factor-alpha (TNF-alpha) from a combinatorial library. Vectors encoding individual members of a naive 10(9) affibody protein library fused to a C-terminal fragment of the beta-lactamase reporter were distributed via phage infection to a culture of cells harbouring a common construct encoding a fusion protein between a non-membrane anchored version of a human TNF-alpha target and the N-terminal segment of the reporter. An initial binding analysis of 29 library variants derived from surviving colonies using selection plates containing ampicillin and in some cases also the P-lactamase inhibitor tazobactam, indicated a stringent selection for target binding variants. Subsequent analyses showed that the binding affinities (K(D)) for three selected variants studied in more detail were in the range 14-27 nm. The selectivity in binding to TNF-alpha for these variants was further demonstrated in both a cross-target PCA-based challenge and the specific detection of a low nm concentration of TNF-alpha spiked into a complex cell lysate sample. Further, in a biosensor-based competition assay, the binding to TNF-alpha of three investigated affibody variants could be completely blocked by premixing the target with the therapeutic monoclonal antibody adalimumab (Humira (R)), indicating overlapping epitopes between the two classes of reagents. The data indicate that beta-lactamase PICA is a promising methodology for stringent selection of binders from complex naive libraries to yield high affinity reagents with selective target binding characteristics.

  • 28.
    Mandenius, Carl-Fredrik
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, The Institute of Technology.
    Björkman, Mats
    Linköping University, Department of Management and Engineering, Assembly technology. Linköping University, The Institute of Technology.
    Mechatronic design methodology for biotechnology products2009In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 25, no Suppl. 1, p. S190-S190Article in journal (Other academic)
    Abstract [en]

    Biotechnology products can be divided into (1) biologics, which comprise those metabolites, biopolymers, and cell structures that are produced through biological processes, and (2) biotechnical machines, which are apparatuses and devices that transform, change, or analyze ‘biological specimens’ for specific purposes, often by using the biological systems per se. The first category has been thoroughly treated in bioengineering theory and practice while the second has been very scarcely investigated.

    In this presentation is described how the general design science theory can be applied when designing a technical system where biological species or components have the key role in the engineering design solutions. We have named these systems bio-mechatronic systems, since they are combined design achievements between traditional electronic and mechanical sub-systems and the biological systems, and where biological molecules and/or active microbial or cellular components influence the design solutions in a complex way.

    The purpose is to demonstrate that biotechnology and bioengineering related design can utilize and benefit from other commonly used design tools in, for example, mechanical and electric engineering. These tools should result in shorter development times and a reduction of the need for prototype testing and verification.

    Four examples will be presented, all well-known biotechnology products in the pharmaceutical and clinical areas: (1) a protein purification system, (2) a bioreactor system, (3) a biosensor instrument, and (4) an embryonic stem cell manufacturing systems.

  • 29. Mardinoglu, Adil
    et al.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Nielsen, Jens
    The use of Genome-scale metabolic models for drug target and biomarker identification2014In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, p. S49-S49Article in journal (Other academic)
  • 30. McGinn, Steven
    et al.
    Bauer, David
    Brefort, Thomas
    Dong, Liqin
    EI-Sagheer, Afaf
    Elsharawy, Abdou
    Evans, Geraint
    Falk-Sorqvist, Elin
    Forster, Michael
    Fredriksson, Simon
    Freeman, Peter
    Freitag, Camilla
    Fritzsche, Joachim
    Gibson, Spencer
    Gullberg, Mats
    Gut, Marta
    Heath, Simon
    Heath-Brun, Isabelle
    Heron, Andrew J.
    Hohlbein, Johannes
    Ke, Rongqin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). Uppsala University, Sweden.
    Lancaster, Owen
    Le Reste, Ludovic
    Maglia, Giovanni
    Marie, Rodolphe
    Mauger, Florence
    Mertes, Florian
    Mignardi, Marco
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). Uppsala University, Sweden.
    Moens, Lotte
    Oostmeijer, Jelle
    Out, Ruud
    Nyvold Pedersen, Jonas
    Persson, Fredrik
    Picaud, Vincent
    Rotem, Dvir
    Schracke, Nadine
    Sengenes, Jennifer
    Stähler, Peer F.
    Stade, Björn
    Stoddart, David
    Teng, Xia
    Veal, Colin D.
    Zahra, Nathalie
    Bayley, Hagan
    Beier, Markus
    Brown, Tom
    Dekker, Cees
    Ekström, Björn
    Flyvbjerg, Henrik
    Franke, Andre
    Guenther, Simone
    Kapanidis, Achillefs N.
    Kaye, Jane
    Kristensen, Anders
    Lehrach, Hans
    Mangion, Jonathan
    Sauer, Sascha
    Schyns, Emile
    Tost, Jörg
    van Helvoort, Joop M. L. M.
    van der Zaag, Pieter J.
    Tegenfeldt, Jonas O.
    Brookes, Anthony J.
    Mir, Kalim
    Nilsson, Mats
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). Uppsala University, Sweden.
    Willcocks, James P.
    Gut, Ivo G.
    New technologies for DNA analysis - a review of the READNA Project2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, no 3, p. 311-330Article, review/survey (Refereed)
    Abstract [en]

    The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3rd and 4th generation of sequencing methods with nanopores and in situ sequencing, respectively.

  • 31. McGinn, Steven
    et al.
    Bauer, David
    Brefort, Thomas
    Dong, Liqin
    El-Sagheer, Afaf
    Elsharawy, Abdou
    Evans, Geraint
    Falk-Sörqvist, Elin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Forster, Michael
    Fredriksson, Simon
    Freeman, Peter
    Freitag, Camilla
    Fritzsche, Joachim
    Gibson, Spencer
    Gullberg, Mats
    Gut, Marta
    Heath, Simon
    Heath-Brun, Isabelle
    Heron, Andrew J.
    Hohlbein, Johannes
    Ke, Rongqin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Lancaster, Owen
    Le Reste, Ludovic
    Maglia, Giovanni
    Marie, Rodolphe
    Mauger, Florence
    Mertes, Florian
    Mignardi, Marco
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Moens, Lotte
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Oostmeijer, Jelle
    Out, Ruud
    Pedersen, Jonas Nyvold
    Persson, Fredrik
    Picaud, Vincent
    Rotem, Dvir
    Schracke, Nadine
    Sengenes, Jennifer
    Stähler, Peer F.
    Stade, Björn
    Stoddart, David
    Teng, Xia
    Veal, Colin D.
    Zahra, Nathalie
    Bayley, Hagan
    Beier, Markus
    Brown, Tom
    Dekker, Cees
    Ekström, Björn
    Flyvbjerg, Henrik
    Franke, Andre
    Guenther, Simone
    Kapanidis, Achillefs N.
    Kaye, Jane
    Kristensen, Anders
    Lehrach, Hans
    Mangion, Jonathan
    Sauer, Sascha
    Schyns, Emile
    Tost, Jörg
    van Helvoort, Joop M. L. M.
    van der Zaag, Pieter J.
    Tegenfeldt, Jonas O.
    Brookes, Anthony J.
    Mir, Kalim
    Nilsson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Willcocks, James P.
    Gut, Ivo G.
    New technologies for DNA analysis: a review of the READNA Project2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, no 3, p. 311-330Article, review/survey (Refereed)
  • 32. Mezger, Anja
    et al.
    Kuhnemund, Malte
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Nilsson, Mats
    Herthnek, David
    Highly specific DNA detection employing ligation on suspension bead array readout2015In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 32, no 5, p. 504-510Article in journal (Refereed)
    Abstract [en]

    We show for the first time that monomerized rolling circle amplification (RCA) products can be directly detected with the Luminex suspension bead array readout without the need of PCR amplification. Furthermore, using monomerized RCA products to guide ligation of the detection oligonucleotide (DO) to barcode sequences on the magnetic Luminex beads, combined with efficient washing and increased measurement temperature, yields a higher signal to noise ratio. As a proof-of-principle, we demonstrate detection of pathogenic DNA sequences with high reproducibility, sensitivity and a dynamic range over four orders of magnitude. Using padlock probes in combination with bead suspension arrays opens up the possibility for highly multiplexed DNA targeting and readout.

  • 33.
    Mezger, Anja
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Kuhnemund, Malte
    Nilsson, Mats
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Herthnek, David
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Highly specific DNA detection employing ligation on suspension bead array readout2015In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 32, no 5, p. 504-510Article in journal (Refereed)
    Abstract [en]

    We show for the first time that monomerized rolling circle amplification (RCA) products can be directly detected with the Luminex suspension bead array readout without the need of PCR amplification. Furthermore, using monomerized RCA products to guide ligation of the detection oligonucleotide (DO) to barcode sequences on the magnetic Luminex beads, combined with efficient washing and increased measurement temperature, yields a higher signal to noise ratio. As a proof-of-principle, we demonstrate detection of pathogenic DNA sequences with high reproducibility, sensitivity and a dynamic range over four orders of magnitude. Using padlock probes in combination with bead suspension arrays opens up the possibility for highly multiplexed DNA targeting and readout.

  • 34.
    Moukouli, Maria
    et al.
    National Technical University of Athens.
    Topakas, Evangelos
    National Technical University of Athens.
    Christakopoulos, Paul
    Cloning and optimized expression of a GH-11 xylanase from Fusarium oxysporum in Pichia pastoris2011In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 28, no 4, p. 369-374Article in journal (Refereed)
    Abstract [en]

    The endo-1,4-beta-xylanase gene xyn11a from Fusarium oxysporum, member of the fungal glycosyl hydrolase (GH) family 11, was cloned and expressed in Pichia pastoris. The mature xylanase gene, which generates after the excision of one intron and the secreting signal peptide, was placed under the control of an alcohol oxidase promoter (AOX1) in the plasmid pPICZ alpha C. The final construction was integrated into the genome of the methylotrophic yeast P. pastoris X33 and the ability to produce xylanase activity was evaluated in flask cultures. Recombinant P. pastoris efficiently secreted xylanase into the medium and produced high level of enzymatic activity (110 U/ml) after 216 hours of growth, under methanol induction. To achieve higher enzyme production, the influence of initial pH, methanol concentration, agitation and flask design was evaluated. Under optimum culture conditions, production of the recombinant xylanase increased by 50%, reaching a final yield of 170 U/ml, underpinning aeration as the most important factor in improving enzyme production.

  • 35.
    Neubauer, P.
    et al.
    Tech Univ Berlin, Dept Biotechnol, Berlin, Germany..
    Golson, R.
    BioSilta Oy, Oulu, Finland..
    Neubauer, A.
    BioSilta Oy, Oulu, Finland..
    Ukkonen, K.
    BioSilta Oy, Oulu, Finland..
    Krause, M.
    BioSilta Oy, Oulu, Finland..
    Tegel, Hanna
    KTH, School of Biotechnology (BIO).
    Ottosson, J.
    KTH, School of Biotechnology (BIO).
    Larsen, M. Wittrup
    KTH, School of Biotechnology (BIO).
    Hult, Karl
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Vasala, A.
    BioSilta Oy, Oulu, Finland..
    Using EnBase (TM) to enhance recombinant protein production2009In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 25, p. S190-S190Article in journal (Other academic)
  • 36.
    Neubauer, P.
    et al.
    Tech Univ Berlin, Dept Biotechnol, Berlin, Germany.;BioSilta Oy, FI-90014 Oulu, Finland..
    Siurkus, J.
    Tech Univ Berlin, Dept Biotechnol, Berlin, Germany.;Fermentas UAB, Vilnius, Lithuania..
    Panula-Perala, J.
    Univ Oulu, Dept Proc & Environm Engn, Oulu, Finland..
    Neubauer, A.
    BioSilta Oy, FI-90014 Oulu, Finland..
    Ukkonen, K.
    BioSilta Oy, FI-90014 Oulu, Finland..
    Krause, M.
    BioSilta Oy, FI-90014 Oulu, Finland..
    Meyer, D.
    Brain AG, Zwingenberg, Germany..
    Pelzer, S.
    Brain AG, Zwingenberg, Germany..
    Eck, J.
    Brain AG, Zwingenberg, Germany..
    Tegel, Hanna
    KTH, School of Biotechnology (BIO).
    Ottosson, J.
    KTH, School of Biotechnology (BIO).
    Vasala, A.
    BioSilta Oy, FI-90014 Oulu, Finland..
    EnBase (TM) - MTP based high-cell-density fermentation for high-throughput and high-content screening2009In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 25, p. S161-S161Article in journal (Other academic)
  • 37.
    Nielsen, Jens
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Engineering yeast metabolism for production of fuels and chemicals2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, p. S66-S66Article in journal (Refereed)
  • 38. Nyman, Jonas
    et al.
    Lacintra, Gomes
    Westman, Johan
    University of Borås, School of Engineering.
    Berglin, M
    Lundin, Magnus
    University of Borås, School of Engineering.
    Lennartsson, Patrik
    University of Borås, School of Engineering.
    Taherzadeh, Mohammad
    University of Borås, School of Engineering.
    Pellet formation of zygomycetes and immobilization of yeast2013In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 30, no 5, p. 516-522Article in journal (Refereed)
    Abstract [en]

    Pelleted growth provides many advantages for filamentous fungi, including decreased broth viscosity, improved aeration, stirring, and heat transfer. Thus, the factors influencing the probability of pellet formation of Rhizopus sp. in a defined medium was investigated using a multifactorial experimental design. Temperature, agitation intensity, Ca2+-concentration, pH, and solid cellulose particles, each had a significant effect on pelletization. Tween 80, spore concentration, and liquid volume were not found to have a significant effect. All of the effects were additive; no interactions were significant. The results were used to create a simple defined medium inducing pelletization, which was used for immobilization of a flocculating strain of Saccharomyces cerevisiae in the zygomycetes pellets. A flor-forming S. cerevisiae strain was also immobilized, while a non-flocculating strain colonized the pellets but was not immobilized. No adverse effects were detected as a result of the close proximity between the filamentous fungus and the yeast, which potentially allows for co-fermentation with S. cerevisiae immobilized in pellets of zygomycetes

  • 39.
    Perez-Zabaleta, Mariel
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    (R)-3-Hydroxybutyrate production in a metabolically engineered Escherichia coli2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, p. S117-S117Article in journal (Refereed)
  • 40.
    Perez-Zabaleta, Mariel
    et al.
    KTH, School of Biotechnology (BIO).
    Jarmander, Johan
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Guevara, Monica
    KTH, School of Biotechnology (BIO).
    Quillaguaman, Jorge
    Larsson, Gen
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Design and flux modelling for recombinant production of 3-Hydroxybutyrate in Escherichia coli2014In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, p. S167-S167Article in journal (Other academic)
  • 41.
    Rockberg, Johan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Split-GFP and droplet microfluidics allows high-throughput screening of mammalian cell factories2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, p. S51-S51Article in journal (Refereed)
  • 42.
    Sjöberg, Ronald
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mattsson, Cecilia
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson, Eni
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hellström, Cecilia
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ayoglu, Burcu
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Exploration of high-density protein microarrays for antibody validation and autoimmunity profiling2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, no 5, p. 582-592Article in journal (Refereed)
    Abstract [en]

    High-density protein microarrays of recombinant human protein fragments, representing 12,412 unique Ensembl Gene IDs, have here been produced and explored. These protein microarrays were used to analyse antibody off-target interactions, as well as for profiling the human autoantibody repertoire in plasma against the antigens represented by the protein fragments. Affinity-purified polyclonal antibodies produced within the Human Protein Atlas (HPA) were analysed on microarrays of three different sizes, ranging from 384 antigens to 21,120 antigens, for evaluation of the antibody validation criteria in the HPA. Plasma samples from secondary progressive multiple sclerosis patients were also screened in order to explore the feasibility of these arrays for broad-scale profiling of autoantibody reactivity. Furthermore, analysis on these near proteome-wide microarrays was complemented with analysis on HuProt (TM) Human Proteome protein microarrays. The HPA recombinant protein microarray with 21,120 antigens and the HuProt (TM) Human Proteome protein microarray are currently the largest protein microarray platforms available to date. The results on these arrays show that the Human Protein Atlas antibodies have few off-target interactions if the antibody validation criteria are kept stringent and demonstrate that the HPA-produced high-density recombinant protein fragment microarrays allow for a high-throughput analysis of plasma for identification of possible autoantibody targets in the context of various autoimmune conditions.

  • 43.
    Sjöberg, Ronald
    et al.
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Sundberg, Mårten
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Gundberg, Anna
    KTH, School of Biotechnology (BIO).
    Sivertsson, Åsa
    KTH, School of Biotechnology (BIO).
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO).
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Validation of affinity reagents using antigen microarrays2011In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, no 5, p. 555-563Article in journal (Refereed)
    Abstract [en]

    There is a need for standardised validation of affinity reagents to determine their binding selectivity and specificity. This is of particular importance for systematic efforts that aim to cover the human proteome with different types of binding reagents. One such international program is the SH2-consortium, which was formed to generate a complete set of renewable affinity reagents to the SH2-domain containing human proteins. Here, we describe a microarray strategy to validate various affinity reagents, such as recombinant single-chain antibodies, mouse monoclonal antibodies and antigen-purified polyclonal antibodies using a highly multiplexed approach. An SH2-specific antigen microarray was designed and generated, containing more than 6000 spots displayed by 14 identical subarrays each with 406 antigens, where 105 of them represented SH2-domain containing proteins. Approximately 400 different affinity reagents of various types were analysed on these antigen microarrays carrying antigens of different types. The microarrays revealed not only very detailed specificity profiles for all the binders, but also showed that overlapping target sequences of spotted antigens were detected by off-target interactions. The presented study illustrates the feasibility of using antigen microarrays for integrative, high-throughput validation of various types of binders and antigens.

  • 44.
    Sjöberg, Ronald
    et al.
    KTH, Proteomik.
    Sundberg, Mårten
    KTH, Proteomik.
    Gundberg, Anna
    KTH, Skolan för bioteknologi (BIO).
    Sivertsson, Åsa
    KTH, Skolan för bioteknologi (BIO).
    Schwenk, Jochen M.
    KTH, Skolan för bioteknologi (BIO).
    Uhlén, Mathias
    KTH, Proteomik.
    Nilsson, Peter
    KTH, Proteomik.
    Validation of affinity reagents using antigen microarrays2011In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, no 5, p. 555-563Article in journal (Other academic)
    Abstract [en]

    There is a need for standardised validation of affinity reagents to determine their binding selectivity and specificity. This is of particular importance for systematic efforts that aim to cover the human proteome with different types of binding reagents. One such international program is the SH2-consortium, which was formed to generate a complete set of renewable affinity reagents to the SH2-domain containing human proteins. Here, we describe a microarray strategy to validate various affinity reagents, such as recombinant single-chain antibodies, mouse monoclonal antibodies and antigen-purified polyclonal antibodies using a highly multiplexed approach. An SH2-specific antigen microarray was designed and generated, containing more than 6000 spots displayed by 14 identical subarrays each with 406 antigens, where 105 of them represented SH2-domain containing proteins. Approximately 400 different affinity reagents of various types were analysed on these antigen microarrays carrying antigens of different types. The microarrays revealed not only very detailed specificity profiles for all the binders, but also showed that overlapping target sequences of spotted antigens were detected by off-target interactions. The presented study illustrates the feasibility of using antigen microarrays for integrative, high-throughput validation of various types of binders and antigens.

  • 45. Säll, A.
    et al.
    Persson, Helena
    KTH, School of Biotechnology (BIO), Protein Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Lund University, Sverige.
    Öhlin, M.
    Borrebaeck, C. A. K.
    Wingren, C.
    Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach2016In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, no 5, p. 503-513Article in journal (Refereed)
    Abstract [en]

    Increasing the understanding of a proteome and how its protein composition is affected by for example different diseases, such as cancer, has the potential to improve strategies for early diagnosis and therapeutics. The Global Proteome Survey or GPS is a method that combines mass spectrometry and affinity enrichment with the use of antibodies. The technology enables profiling of complex proteomes in a species independent manner. The sensitivity of GPS, and other methods relying on affinity enrichment, is largely affected by the activity of the exploited affinity reagent. We here present an improvement of the GPS platform by utilizing an antibody immobilization approach which ensures a controlled immobilization process of the antibody to the magnetic bead support. More specifically, we make use of an antibody format that enables site-directed biotinylation and use this in combination with streptavidin coated magnetic beads. The performance of the expanded GPS platform was evaluated by profiling yeast proteome samples. We demonstrate that the oriented antibody immobilization strategy increases the ability of the GPS platform and results in larger fraction of functional antibodies. Additionally, we show that this new antibody format enabled in-solution capture, i.e. immobilization of the antibodies after sample incubation. A workflow has been established that permit the use of an oriented immobilization strategy for the GPS platform.

  • 46.
    Taherzadeh, Mohammad J.
    et al.
    University of Borås, School of Engineering.
    Edebo, L.
    Exploring zygomycetes fungi for industrial applications2009In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 25, no 1, p. 83-Article in journal (Refereed)
  • 47.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. Royal Inst Technol KTH, Albanova Univ Ctr, Stockholm, Sweden..
    A Human Protein Atlas to study human biology and disease2012In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, p. S34-S34Article in journal (Other academic)
  • 48.
    Weibrecht, Irene
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Gavrilovic, Milan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lindbom, Lena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Landegren, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wählby, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Söderberg, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Visualising individual sequence-specific protein-DNA interactions in situ2012In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, no 5, p. 589-598Article in journal (Refereed)
    Abstract [en]

    Gene expression-a key feature for modulating cell fate-is regulated in part by histone modifications, which modulate accessibility of the chromatin to transcription factors. Until now, protein-DNA interactions (PDIs) have mostly been studied in bulk without retrieving spatial information from the sample or with poor sequence resolution. New tools are needed to reveal proteins interacting with specific DNA sequences in situ for further understanding of the orchestration of transcriptional control within the nucleus. We present herein an approach to visualise individual PDIs within cells, based on the in situ proximity ligation assay (PLA). This assay, previously used for the detection of protein-protein interactions in situ, was adapted for analysis of target PDIs, using padlock probes to identify unique DNA sequences in complex genomes. As a proof-of-principle we detected histone H3 interacting with a 26bp consensus sequence of the Alu-repeat abundantly expressed in the human genome, but absent in mice. However, the mouse genome contains a highly similar sequence, providing a model system to analyse the selectivity of the developed methods. Although efficiency of detection currently is limiting, we conclude that in situ PLA can be used to achieve a highly selective analysis of PDIs in single cells.

  • 49.
    Zerva, Anastasia
    et al.
    Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
    Koutroufini, Efthymia
    Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
    Kostopoulou, Ioanna
    Laboratory of Organic Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
    Detsi, Anastasia
    Laboratory of Organic Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
    Topakas, Evangelos
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    A novel thermophilic laccase-like multicopper oxidase from Thermothelomyces thermophila and its application in the oxidative cyclization of 2′,3,4-trihydroxychalcone2019In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 49, p. 10-18Article in journal (Refereed)
    Abstract [en]

    Laccase-like multicopper oxidases (LMCOs) are a heterogeneous group of oxidases, acting mainly on phenolic compounds and which are widespread among many microorganisms, including Basidiomycetes and Ascomycetes. Here, we report the cloning, heterologous expression, purification and characterization of a novel LMCO from the thermophilic fungus Thermothelomyces thermophila. The 1953 bp lmco gene sequence comprises of 3 exons interrupted by 2 introns and according to the LccED database the translated sequence belongs to superfamily 6 of multicopper oxidases. After removal of the introns, the gene was transformed into Pichia pastoris, under the control of the alcohol oxidase (AOX1) promoter. The heterologous enzyme was purified with an apparent molecular weight of 80 kDa. TtLMCO1 displayed optimum activity at pH 4 and 50 °C and appeared thermostable up to 50 °C. A variety of phenolic compounds were oxidized by TtLMCO1, including standard laccase substrates such as ABTS and 2,6 dimethoxyphenol. The UV/Vis spectrum of purified TtLMCO1 indicates that it belongs to yellow laccase-like oxidases. The enzyme was used for the bioconversion of 2′,3,4-trihydroxychalcone to 3′,4′-dihydroxy-aurone, a bioactive aurone recently shown to possess inhibitory activity against several isoforms of the histone deacetylase complex (HDAC). Overall, the thermophilic yellow LMCO TtLMCO1 presents a number of superior properties with potential use in industrial biocatalysis.

  • 50.
    Zieba, Agata
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology.
    Grannas, Karin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Söderberg, Ola
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Gullberg, Mats
    Nilsson, Mats
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools.
    Landegren, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular tools. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Molecular tools for companion diagnostics2012In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, no 6, p. 634-640Article, review/survey (Refereed)
    Abstract [en]

    The heterogeneous nature of cancer results in highly variable therapeutic responses even among patients with identical stages and grades of a malignancy. The move towards personalised medicine in cancer therapy has therefore been motivated by a need to customise therapy according to molecular features of individual tumours. Companion diagnostics serves to support early drug development, it can provide surrogate markers in clinical trials, and also guide selection of individual therapies and monitoring of responses in routine clinical care. The era of companion diagnostics can be said to have begun with the introduction of the HercepTest - a first-of-a-kind diagnostic tool developed by DakoCytomation in 1998 to select patients for therapy with the anticancer drug Herceptin (trastuzumab). Herceptin and the paired test proved that companion diagnostics can help guide patient-tailored therapies. We will discuss herein technologies to analyse companion diagnostics markers at the level of DNA, RNA or protein, focusing on a series of methods developed in our laboratory that can facilitate drug development and help stratify patients for therapy.

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