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  • 1.
    Ayoglu, Burcu
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Gundberg, Anna
    KTH, Centra, 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, Centra, Science for Life Laboratory, SciLifeLab.
    Schwenk, Jochen M.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Nilsson, Peter
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Proteomic profiling of the autoimmunity repertoire in multiple sclerosis2012Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, s. S20-S20Artikel i tidskrift (Övrigt vetenskapligt)
  • 2.
    Berglund, Lars
    et al.
    KTH, Skolan för bioteknologi (BIO).
    Jonasson, K.
    KTH, Skolan för bioteknologi (BIO).
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO). Royal Inst Technol, Sch Biotechnol, Stockholm, Sweden..
    Antibodypedia-towards a user community for antibody validation data2009Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 25, s. S360-S361Artikel i tidskrift (Övrigt vetenskapligt)
  • 3.
    Bulone, Vincent
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Fiber engineering based on plant cell wall metabolism2009Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 25, s. S247-S247Artikel i tidskrift (Övrigt vetenskapligt)
  • 4.
    Cengic, Ivana
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Kaczmarzyk, Danuta
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Yao, Lun
    KTH.
    Hudson, Paul
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    CRISPRi for metabolic engineering and fatty alcohol production in cyanobacteria2016Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, s. S37-S37Artikel i tidskrift (Refereegranskat)
  • 5.
    Grimm, Sebastian
    et al.
    KTH, Skolan för bioteknologi (BIO), Molekylär Bioteknologi.
    Salahshour, Samaneh
    KTH, Skolan för bioteknologi (BIO), Molekylär Bioteknologi.
    Nygren, Per-Åke
    KTH, Skolan för bioteknologi (BIO), Molekylär Bioteknologi.
    Monitored whole gene in vitro evolution of an anti-hRaf-1 affibody molecule towards increased binding affinity2011Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, New biotechnology, ISSN 1876-4347, Vol. 29, nr 5, s. 534-542Artikel i tidskrift (Refereegranskat)
    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.

  • 6.
    Gräslund, Torbjörn
    KTH, Skolan för bioteknologi (BIO), Proteinteknologi.
    Affibody molecules: therapy and in vivo diagnostic applications2016Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, s. S48-S48Artikel i tidskrift (Refereegranskat)
  • 7.
    Guevara, M.
    KTH.
    Studies on the polymerization of poly (3-hydroxyalkanoate)s produced by Halomonas boliviensis2016Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, s. S152-S153Artikel i tidskrift (Refereegranskat)
  • 8.
    Guevara, Monica
    et al.
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Jarmander, Johan
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Perez-Zabaleta, Mariel
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Quillaguaman, Jorge
    Larsson, Gen
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Production of 3-hydroxybutyrate by E. coli: Application of Nitrogen and Phosphorous limitation to steer fluxes to product formation2014Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, s. S148-S148Artikel i tidskrift (Övrigt vetenskapligt)
  • 9. Gustavsson, Elin
    et al.
    Ek, Sara
    Steen, Johanna
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Kristensson, Malin
    Älgenäs, Cajsa
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Wingren, Christer
    Ottosson, Jenny
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Hober, Sophia
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Borrebaeck, Carl A. K.
    Surrogate antigens as targets for proteome-wide binder selection2011Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 28, nr 4, s. 302-311Artikel i tidskrift (Refereegranskat)
    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.

  • 10.
    Hu, Francis Jingxin
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Rockberg, Johan
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Generation of HER2 monoclonal antibodies using epitopes of a rabbit polyclonal antibody2014Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, nr 1, s. 35-43Artikel i tidskrift (Refereegranskat)
    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.

  • 11.
    Hu, Francis Jingxin
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Volk, Anna-Luisa
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Persson, Helena
    KTH, Skolan för bioteknologi (BIO), Proteinteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab. Lund University, Sweden.
    Säll, Anna
    Borrebaeck, Carl
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Rockberg, Johan
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders2017Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347Artikel i tidskrift (Refereegranskat)
    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.

  • 12.
    Hu, Francis Jingxin
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Volk, Anna-Luisa
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    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, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Rockberg, Johan
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity bindersIngår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347Artikel i tidskrift (Övrigt vetenskapligt)
    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.

  • 13.
    Häggmark, Anna
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Neiman, Maja
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Drobin, Kimi
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Zwahlen, Martin
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Nilsson, Peter
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Schwenk, Jochen M
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Classification of protein profiles from antibody microarrays using heat and detergent treatment.2011Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, nr 5, s. 564-570Artikel i tidskrift (Refereegranskat)
    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.

  • 14.
    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 centrosome2010Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 27, s. S82-S82Artikel i tidskrift (Övrigt vetenskapligt)
  • 15.
    Jarmander, Johan
    et al.
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Guevara, Mónica
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Zabaleta, Mariel Perez
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Sjöberg, Gustav
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Belotserkovsky, Jaroslav
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Quillaguaman, Jorge
    Larsson, Gen
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Production of 3-hydroxybutyrate from waste biomass by metabolically engineered Escherichia coli2014Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, s. S94-S95Artikel i tidskrift (Övrigt vetenskapligt)
  • 16.
    Larsen, M. W.
    et al.
    KTH, Skolan för bioteknologi (BIO), Biokemi (stängd 20130101).
    Zielinska, Dorota
    KTH, Skolan för bioteknologi (BIO), Biokemi (stängd 20130101).
    Martinelle, Mats
    KTH, Skolan för bioteknologi (BIO), Biokemi (stängd 20130101).
    Hildalgo, A.
    UAM CSIC, Ctr Biol Mol Severo Ochoa, Madrid, Spain..
    Jensen, L. J.
    Bornscheuer, U. T.
    Ernst Moritz Arndt Univ Greifswald, Inst Biochem, Dept Biotechnol & Enzyme Catalysis, D-17487 Greifswald, Germany..
    Hult, Karl
    KTH, Skolan för bioteknologi (BIO), Biokemi (stängd 20130101).
    Suppression of water as a nucleophile in Pseudozyma (Candida) antarctica lipase B catalysis2009Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 25, s. S127-S127Artikel i tidskrift (Övrigt vetenskapligt)
  • 17.
    Löfdahl, Per-Åke
    et al.
    KTH, Skolan för bioteknologi (BIO), Molekylär Bioteknologi (stängd 20130101).
    Nord, Olof
    KTH, Skolan för bioteknologi (BIO), Molekylär Bioteknologi (stängd 20130101).
    Janzon, Lars
    Nygren, Per-Åke
    KTH, Skolan för bioteknologi (BIO), Molekylär Bioteknologi (stängd 20130101).
    Selection of TNF-alpha binding affibody molecules using a beta-lactamase protein fragment complementation assay2009Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 26, nr 5, s. 251-259Artikel i tidskrift (Refereegranskat)
    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.

  • 18. Mardinoglu, Adil
    et al.
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Nielsen, Jens
    The use of Genome-scale metabolic models for drug target and biomarker identification2014Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, s. S49-S49Artikel i tidskrift (Övrigt vetenskapligt)
  • 19.
    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, Skolan för bioteknologi (BIO).
    Ottosson, J.
    KTH, Skolan för bioteknologi (BIO).
    Larsen, M. Wittrup
    KTH, Skolan för bioteknologi (BIO).
    Hult, Karl
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Industriell bioteknologi.
    Vasala, A.
    BioSilta Oy, Oulu, Finland..
    Using EnBase (TM) to enhance recombinant protein production2009Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 25, s. S190-S190Artikel i tidskrift (Övrigt vetenskapligt)
  • 20.
    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, Skolan för bioteknologi (BIO).
    Ottosson, J.
    KTH, Skolan för bioteknologi (BIO).
    Vasala, A.
    BioSilta Oy, FI-90014 Oulu, Finland..
    EnBase (TM) - MTP based high-cell-density fermentation for high-throughput and high-content screening2009Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 25, s. S161-S161Artikel i tidskrift (Övrigt vetenskapligt)
  • 21.
    Nielsen, Jens
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Engineering yeast metabolism for production of fuels and chemicals2016Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, s. S66-S66Artikel i tidskrift (Refereegranskat)
  • 22.
    Perez-Zabaleta, Mariel
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    (R)-3-Hydroxybutyrate production in a metabolically engineered Escherichia coli2016Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, s. S117-S117Artikel i tidskrift (Refereegranskat)
  • 23.
    Perez-Zabaleta, Mariel
    et al.
    KTH, Skolan för bioteknologi (BIO).
    Jarmander, Johan
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Guevara, Monica
    KTH, Skolan för bioteknologi (BIO).
    Quillaguaman, Jorge
    Larsson, Gen
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Design and flux modelling for recombinant production of 3-Hydroxybutyrate in Escherichia coli2014Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, s. S167-S167Artikel i tidskrift (Övrigt vetenskapligt)
  • 24.
    Rockberg, Johan
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Split-GFP and droplet microfluidics allows high-throughput screening of mammalian cell factories2016Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, s. S51-S51Artikel i tidskrift (Refereegranskat)
  • 25.
    Rockberg, Johan
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Split-GFP and droplet microfluidics allows high-throughput screening of mammalian cell factories2016Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, s. S34-S34Artikel i tidskrift (Övrigt vetenskapligt)
  • 26.
    Sjöberg, Ronald
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Mattsson, Cecilia
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Andersson, Eni
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Hellström, Cecilia
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Schwenk, Jochen M.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ayoglu, Burcu
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Nilsson, Peter
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Exploration of high-density protein microarrays for antibody validation and autoimmunity profiling2016Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, nr 5, s. 582-592Artikel i tidskrift (Refereegranskat)
    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.

  • 27.
    Sjöberg, Ronald
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik (stängd 20130101).
    Sundberg, Mårten
    KTH, Skolan för bioteknologi (BIO), Proteomik (stängd 20130101).
    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, Skolan för bioteknologi (BIO), Proteomik (stängd 20130101).
    Nilsson, Peter
    KTH, Skolan för bioteknologi (BIO), Proteomik (stängd 20130101).
    Validation of affinity reagents using antigen microarrays2011Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, nr 5, s. 555-563Artikel i tidskrift (Refereegranskat)
    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.

  • 28. Säll, A.
    et al.
    Persson, Helena
    KTH, Skolan för bioteknologi (BIO), Proteinteknologi. KTH, Centra, 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 approach2016Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 33, nr 5, s. 503-513Artikel i tidskrift (Refereegranskat)
    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.

  • 29.
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Centra, 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 disease2012Ingår i: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 29, s. S34-S34Artikel i tidskrift (Övrigt vetenskapligt)
1 - 29 av 29
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