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  • 1. Abahazi, Emese
    et al.
    Satorhelyi, Peter
    Erdelyi, Balazs
    Vertessy, Beata G.
    Land, Henrik
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Paizs, Csaba
    Berglund, Per
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Poppe, Laszlo
    Covalently immobilized Trp60Cys mutant of omega‰-transaminase from Chromobacterium violaceum for kinetic resolution of racemic amines in batch and continuous-flow modes2018In: Biochemical engineering journal, ISSN 1369-703X, E-ISSN 1873-295X, Vol. 132, p. 270-278Article in journal (Refereed)
    Abstract [en]

    Covalent immobilization of an engineered omega-transaminase mutant Trp60Cys from Chromobacterium violaceum (CvTAW60C) was performed on bisepoxide-activated aminoalkyl resins. Activity of the various CvTAW60C preparations was evaluated in kinetic resolution of four racemic amines (rac-1a–d). The most active EA-G-CvTAW60C preparation (CvTAW60C attached to polymeric resin with ethylamine function activated with glycerol diglycidyl ether—EA-G) could perform the kinetic resolution of racemic 4-phenylbutan-2-amine (rac-1a) over 49% conversion up to 19 consecutive reaction cycles or in media containing up to 50% v/v DMSO as cosolvent in batch mode reactions. The immobilization process of CvTAW60C onto the EA-G resin filled in stainless steel bioreactors was also tested in flow-through mode. Kinetic resolution of three racemic amines containing aromatic moieties (rac-1a-c) was performed in continuous-flow mode resulting in easy-to-separate mixture of the corresponding ketone (2a–c) and the non-converted (R)-amine in high enantiopurity (ee(R)-1a-c ≥ 96%).

  • 2.
    Acevedo Gomez, Yasna
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Applied Electrochemistry.
    Lindbergh, Göran
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Applied Electrochemistry.
    Lagergren, Carina
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Applied Electrochemistry.
    Reformate from biogas used as fuel in a PEM fuel cell2013In: EFC 2013 - Proceedings of the 5th European Fuel Cell Piero Lunghi Conference, 2013, p. 163-164Conference paper (Refereed)
    Abstract [en]

    The performance of a PEM fuel cell can be easily degraded by introducing impurities in the fuel gas. Since reformate of biogas from olive mill wastes will contain at least one third of carbon dioxide, its influence was studied on a PtRu catalyst. A clean reformate gas for the anode (67% H2 and 33% CO2) without any traces of other compounds was used and electrochemical measurements showed that the performance of the fuel cell was hardly affected. However, diluting the hydrogen with higher amounts of CO2 will reduce the performance remarkably.

  • 3.
    Afrasiabi, Roodabeh
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Söderberg, Lovisa
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Jönsson, Håkan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Björk, Per
    Acreo Swedish ICT AB, SE-16440 Kista, Sweden.
    Svahn Andersson, Helene
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Linnros, Jan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Integration of a Droplet-Based Microfluidic System and Silicon Nanoribbon FET Sensor2016In: Micromachines, ISSN 2072-666X, E-ISSN 2072-666X, Micromachines, Vol. 7, no 8, article id 134Article in journal (Refereed)
    Abstract [en]

    We present a novel microfluidic system that integrates droplet microfluidics with a silicon nanoribbon field-effect transistor (SiNR FET), and utilize this integrated system to sense differences in pH. The device allows for selective droplet transfer to a continuous water phase, actuated by dielectrophoresis, and subsequent detection of the pH level in the retrieved droplets by SiNR FETs on an electrical sensor chip. The integrated microfluidic system demonstrates a label-free detection method for droplet microfluidics, presenting an alternative to optical fluorescence detection. In this work, we were able to differentiate between droplet trains of one pH-unit difference. The pH-based detection method in our integrated system has the potential to be utilized in the detection of biochemical reactions that induce a pH-shift in the droplets.

  • 4.
    Agaton, Charlotta
    et al.
    KTH, Superseded Departments, Biotechnology.
    Falk, Ronny
    KTH, Superseded Departments, Biotechnology.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    Hober, Sophia
    KTH, Superseded Departments, Biotechnology.
    Selective enrichment of monospecific polyclonal antibodies for antibody-based proteomics efforts2004In: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1043, p. 33-40Article in journal (Refereed)
    Abstract [en]

    A high stringency protocol, suitable for systematic purification of polyclonal antibodies, is described. The procedure is designed to allow the generation of target protein-specific antibodies suitable for functional annotation of proteins. Antibodies were generated by immunization with recombinantly produced affinity-tagged target proteins. To obtain stringent recovery of the antibodies, a two-step affinity chromatography principle was devised to first deplete the affinity tag-specific antibodies followed by a second step for affinity capture of the target protein-specific antibodies. An analytical dot-blot array system was developed to analyze the cross-reactivity of the affinity-purified antibodies. The results suggest that the protocol can be used in a highly parallel and automated manner to generate mono-specific polyclonal antibodies for large-scale, antibody-based proteomics efforts, i.e. affinity proteomics.

  • 5.
    Agaton, Charlotta
    et al.
    KTH, Superseded Departments, Biotechnology.
    Unneberg, Per
    KTH, Superseded Departments, Biotechnology.
    Sievertzon, Maria
    KTH, Superseded Departments, Biotechnology.
    Holmberg, Anders
    KTH, Superseded Departments, Biotechnology.
    Ehn, Maria
    KTH, Superseded Departments, Biotechnology.
    Larsson, Magnus
    KTH, Superseded Departments, Biotechnology.
    Odeberg, Jacob
    KTH, Superseded Departments, Biotechnology.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Gene expression analysis by signature pyrosequencing2002In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 289, no 1-2, p. 31-39Article in journal (Refereed)
    Abstract [en]

     We describe a novel method for transcript profiling based on high-throughput parallel sequencing of signature tags using a non-gel-based microtiter plate format. The method relies on the identification of cDNA clones by pyrosequencing of the region corresponding to the 3'-end of the mRNA preceding the poly(A) tail. Simultaneously, the method can be used for gene discovery, since tags corresponding to unknown genes can be further characterized by extended sequencing. The protocol was validated using a model system for human atherosclerosis. Two 3'-tagged cDNA libraries, representing macrophages and foam cells, which are key components in the development of atherosclerotic plaques, were constructed using a solid phase approach. The libraries were analyzed by pyrosequencing, giving on average 25 bases. As a control, conventional expressed sequence tag (EST) sequencing using slab gel electrophoresis was performed. Homology searches were used to identify the genes corresponding to each tag. Comparisons with EST sequencing showed identical, unique matches in the majority of cases when the pyrosignature was at least 18 bases. A visualization tool was developed to facilitate differential analysis using a virtual chip format. The analysis resulted in identification of genes with possible relevance for development of atherosclerosis. The use of the method for automated massive parallel signature sequencing is discussed.

  • 6. Agerberth, B
    et al.
    Gunne, H
    Odeberg, Jacob
    KTH, Superseded Departments, Biotechnology.
    Kogner, P
    Boman, H G
    Gudmundsson, G H
    FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis.1995In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 92, no 1, p. 195-9Article in journal (Refereed)
    Abstract [en]

    PR-39, a proline/arginine-rich peptide antibiotic, has been purified from pig intestine and later shown to originate in the bone marrow. Intending to isolate a clone for a human counterpart to PR-39, we synthesized a PCR probe derived from the PR-39 gene. However, when this probe was used to screen a human bone marrow cDNA library, eight clones were obtained with information for another putative human peptide antibiotic, designated FALL-39 after the first four residues. FALL-39 is a 39-residue peptide lacking cysteine and tryptophan. All human peptide antibiotics previously isolated (or predicted) belong to the defensin family and contain three disulfide bridges. The clone for prepro-FALL-39 encodes a cathelin-like precursor protein with 170 amino acid residues. We have postulated a dibasic processing site for the mature FALL-39 and chemically synthesized the putative peptide. In basal medium E, synthetic FALL-39 was highly active against Escherichia coli and Bacillus megaterium. Residues 13-34 in FALL-39 can be predicted to form a perfect amphiphatic helix, and CD spectra showed that medium E induced 30% helix formation in FALL-39. RNA blot analyses disclosed that the gene for FALL-39 is expressed mainly in human bone marrow and testis.

  • 7.
    Ahmadian, Afshin
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    AnderssonSvahn, Helene
    KTH, School of Biotechnology (BIO), Nano Biotechnology (closed 20130101). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Massively parallel sequencing platforms using lab on a chip technologies2011In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 11, no 16, p. 2653-2655Article in journal (Refereed)
  • 8.
    Aid, Graham
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Industrial Ecology.
    Brandt, Nils
    KTH, School of Industrial Engineering and Management (ITM), Industrial Ecology.
    Bygg- och rivningsavfall: Action Research vid KTH2010In: Återvinnare För Industrin / [ed] Kjell-Arne Larsson, Stockholm: Rekord Media och Produktion AB , 2010Chapter in book (Other academic)
  • 9.
    Akan, Pelin
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Alexeyenko, Andrey
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Costea, Paul Igor
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hedberg, Lilia
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Werne Solnestam, Beata
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundin, Sverker
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hallman, Jimmie
    Lundberg, Emma
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines2012In: Genome Medicine, ISSN 1756-994X, E-ISSN 1756-994X, Vol. 4, p. 86-Article in journal (Refereed)
    Abstract [en]

    We here present a comparative genome, transcriptome and functional network analysis of three human cancer cell lines (A431, U251MG and U2OS), and investigate their relation to protein expression. Gene copy numbers significantly influenced corresponding transcript levels; their effect on protein levels was less pronounced. We focused on genes with altered mRNA and/or protein levels to identify those active in tumor maintenance. We provide comprehensive information for the three genomes and demonstrate the advantage of integrative analysis for identifying tumor-related genes amidst numerous background mutations by relating genomic variation to expression/protein abundance data and use gene networks to reveal implicated pathways.

  • 10.
    Akan, Pelin
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Stranneheim, Henrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Lexow, Preben
    LingVitae, Oslo.
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Design and assessment of binary DNA for nanopore sequencing2010In: Genome biology, ISSN 1474-760X, Vol. 11, p. P4-Article in journal (Other academic)
  • 11. Aleman, Dionne M.
    et al.
    Glaser, Daniel
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Optimization and Systems Theory.
    Romeijn, H. Edwin
    Dempsey, James F.
    Interior point algorithms: guaranteed optimality for fluence map optimization in IMRT2010In: Physics in Medicine and Biology, ISSN 0031-9155, E-ISSN 1361-6560, Vol. 55, no 18, p. 5467-5482Article in journal (Refereed)
    Abstract [en]

    One of the most widely studied problems of the intensity-modulated radiation therapy (IMRT) treatment planning problem is the fluence map optimization (FMO) problem, the problem of determining the amount of radiation intensity, or fluence, of each beamlet in each beam. For a given set of beams, the fluences of the beamlets can drastically affect the quality of the treatment plan, and thus it is critical to obtain good fluence maps for radiation delivery. Although several approaches have been shown to yield good solutions to the FMO problem, these solutions are not guaranteed to be optimal. This shortcoming can be attributed to either optimization model complexity or properties of the algorithms used to solve the optimization model. We present a convex FMO formulation and an interior point algorithm that yields an optimal treatment plan in seconds, making it a viable option for clinical applications.

  • 12.
    Alm, Tove
    KTH, School of Biotechnology (BIO), Proteomics.
    Interaction engineered three-helix bundle domains for protein recovery and detection2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    HTML clipboard The great advances in DNA technology, e.g. sequencing and recombinant DNA techniques, have given us the genetic information and the tools needed to effectively produce recombinant proteins. Recombinant proteins are valuable means in biotechnological applications and are also emerging as alternatives in therapeutic applications. Traditionally, monoclonal antibodies have been the natural choice for biotechnological and therapeutic applications due to their ability to bind a huge range of different molecules and their natural good affinity. However, the large size of antibodies (150 kDa) limits tissue penetration and the recombinant expression is complicated. Therefore, alternative binders with smaller sizes have been derived from antibodies and alternative scaffolds.

    In this thesis, two structurally similar domains, Zbasic and ABDz1, have been used as purification tags in different contexts. They are both three-helical bundles and derived from bacterial surface domains, but share no sequence homology. Furthermore, by redesign of the scaffold used for ABDz1, a molecule intended for drug targeting with extended in-vivo half-life has been engineered. In Papers I and II, the poly-cationic tag Zbasic is explored and evaluated. Paper I describes the successful investigation of Zbasic as a purification handle under denaturating conditions. Moreover, Zbasic is evaluated as an interaction domain in matrixassisted refolding. Two different proteins were successfully refolded using the same setup without individual optimization. In Paper II, Zbasic is further explored as a purification handle under non-native conditions in a multi-parallel setup. In total, 22 proteins with varying characteristics are successfully purified using a multi-parallel protein purification protocol and a robotic system. Without modifications, the system can purify up to 60 proteins without manual handling. Paper I and II clearly demonstrate that Zbasic can be used as an interaction domain in matrix-assisted refolding and that it offers a good alternative to the commonly used His6-tag under denaturating conditions. In paper III, the small bifunctional ABDz1 is selected from a phage display library. Endowed with two different binding interfaces, ABDz1 is capable of binding both the HSA-sepharose and the protein A-derived MabSelect SuRe-matrix. The bifunctionality of the domain is exploited in an orthogonal affinity setup. Three target proteins are successfully purified using the HSA-matrix and the MabSelect SuRe-matrix. Furthermore, the purity of the target proteins is effectively improved by combining the two chromatographic steps. Thus, paper III shows that the small ABDz1 can be used as an effective purification handle and dual affinity tag without target specific optimization. Paper IV describes the selection and affinity maturation of small bispecific drug-targeting molecules. First generation binders against tumor necrosis factor-α are selected using phage display. Thereafter on-cell surface display and flow cytometry is used to select second-generation binders. The binding to tumor necrosis factor-α is improved up to 30 times as compared to the best first generation binder, and a 6-fold improvement of the binding strength was possible with retained HSA affinity. Paper III and IV clearly demonstrate that dual interaction surfaces can successfully be grafted on a small proteinaceous domain, and that the strategy in paper IV can be used for dual selection of bifunctional binders.

  • 13. Al-Naamani, Laila
    et al.
    Dobretsov, Sergey
    Dutta, Joydeep
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Functional Materials, FNM.
    Chitosan-zinc oxide nanoparticle composite coating for active food packaging applications2016In: Innovative Food Science & Emerging Technologies, ISSN 1466-8564, E-ISSN 1878-5522, Vol. 38, p. 231-237Article in journal (Refereed)
    Abstract [en]

    In this study antimicrobial properties of chitosan and chitosan-zinc oxide (ZnO) nanocomposite coatings on PE films were studied. Oxygen plasma pretreatment of PE films led to increased adhesion by 2% of chitosan and the nanocomposite coating solutions to the packaging films. Scanning Electron Microscopy (SEM) revealed uniform coatings on PE surfaces. Incorporation of ZnO nanoparticles into the chitosan matrix resulted in 42% increase in solubility; swelling decreased by 80% while the water contact angle (WCA) increased from 60 to 95 compared to chitosan coating. PE coated with chitosan-ZnO nanocomposite films completely inactivated and prevented the growth of food pathogens, while chitosan-coated films showed only 10-fold decline in the viable cell counts of Salmonella enterica, Escherichia coli and Staphylococcus aureus after 24-h incubation compared to the control. Industrial relevance: One of the greatest challenges of food industry is microbial contamination. The present study suggests that PE coating with chitosan-ZnO nanocomposite is a promising technique to enhance antimicrobial properties of the films. Chitosan-ZnO nanocomposite coatings improved antibacterial properties of PE by inactivating about 99.9% of viable pathogenic bacteria. Hence, our results show the effectiveness of the nanocomposite coating in the development of active food packaging in order to prolong the shelf life of food products.

  • 14. Altai, M.
    et al.
    Tsourma, M.
    Mitran, B.
    Honarvar, H.
    Perols, Anna
    KTH, School of Biotechnology (BIO), Protein Technology.
    Robillard, M.
    Rossin, R.
    ten Hoeve, W.
    Sandstrom, M.
    Orlova, A.
    Karlström, Amelie Eriksson
    KTH, School of Biotechnology (BIO), Protein Technology.
    Tolmachev, V.
    Affibody-based bioorthogonal chemistry-mediated radionuclide pretargeting: proof-of-principle.2015In: European Journal of Nuclear Medicine and Molecular Imaging, ISSN 1619-7070, E-ISSN 1619-7089, Vol. 42, p. S246-S246Article in journal (Refereed)
  • 15.
    Alvfors, Per
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Energy Processes.
    Arnell, Jenny
    IVL.
    Berglin, Niklas
    Innventia.
    Björnsson, Lovisa
    LU.
    Börjesson, Pål
    LU.
    Grahn, Maria
    Chalmers/SP.
    Harvey, Simon
    Chalmers.
    Hoffstedt, Christian
    Innventia.
    Holmgren, Kristina
    IVL.
    Jelse, Kristian
    IVL.
    Klintbom, Patrik
    Kusar, Henrik
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Chemical Technology.
    Lidén, Gunnar
    LU.
    Magnusson, Mimmi
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Energy Processes.
    Pettersson, Karin
    Chalmers.
    Rydberg, Tomas
    IVL.
    Sjöström, Krister
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology.
    Stålbrand, Henrik
    LU.
    Wallberg, Ola
    LU.
    Wetterlund, Elisabeth
    LiU.
    Zacchi, Guido
    LU.
    Öhrman, Olof
    ETC Piteå.
    Research and development challenges for Swedish biofuel actors – three illustrative examples: Improvement potential discussed in the context of Well-to-Tank analyses2010Report (Other academic)
    Abstract [en]

    Currently biofuels have strong political support, both in the EU and Sweden. The EU has, for example, set a target for the use of renewable fuels in the transportation sector stating that all EU member states should use 10% renewable fuels for transport by 2020. Fulfilling this ambition will lead to an enormous market for biofuels during the coming decade. To avoid increasing production of biofuels based on agriculture crops that require considerable use of arable area, focus is now to move towards more advanced second generation (2G) biofuels that can be produced from biomass feedstocks associated with a more efficient land use. Climate benefits and greenhouse gas (GHG) balances are aspects often discussed in conjunction with sustainability and biofuels. The total GHG emissions associated with production and usage of biofuels depend on the entire fuel production chain, mainly the agriculture or forestry feedstock systems and the manufacturing process. To compare different biofuel production pathways it is essential to conduct an environmental assessment using the well-to-tank (WTT) analysis methodology. In Sweden the conditions for biomass production are favourable and we have promising second generation biofuels technologies that are currently in the demonstration phase. In this study we have chosen to focus on cellulose based ethanol, methane from gasification of solid wood as well as DME from gasification of black liquor, with the purpose of identifying research and development potentials that may result in improvements in the WTT emission values. The main objective of this study is thus to identify research and development challenges for Swedish biofuel actors based on literature studies as well as discussions with the the researchers themselves. We have also discussed improvement potentials for the agriculture and forestry part of the WTT chain. The aim of this study is to, in the context of WTT analyses, (i) increase knowledge about the complexity of biofuel production, (ii) identify and discuss improvement potentials, regarding energy efficiency and GHG emissions, for three biofuel production cases, as well as (iii) identify and discuss improvement potentials regarding biomass supply, including agriculture/forestry. The scope of the study is limited to discussing the technologies, system aspects and climate impacts associated with the production stage. Aspects such as the influence on biodiversity and other environmental and social parameters fall beyond the scope of this study. We find that improvement potentials for emissions reductions within the agriculture/forestry part of the WTT chain include changing the use of diesel to low-CO2-emitting fuels, changing to more fuel-efficient tractors, more efficient cultivation and manufacture of fertilizers (commercial nitrogen fertilizer can be produced in plants which have nitrous oxide gas cleaning) as well as improved fertilization strategies (more precise nitrogen application during the cropping season). Furthermore, the cultivation of annual feedstock crops could be avoided on land rich in carbon, such as peat soils and new agriculture systems could be introduced that lower the demand for ploughing and harrowing. Other options for improving the WTT emission values includes introducing new types of crops, such as wheat with higher content of starch or willow with a higher content of cellulose. From the case study on lignocellulosic ethanol we find that 2G ethanol, with co-production of biogas, electricity, heat and/or wood pellet, has a promising role to play in the development of sustainable biofuel production systems. Depending on available raw materials, heat sinks, demand for biogas as vehicle fuel and existing 1G ethanol plants suitable for integration, 2G ethanol production systems may be designed differently to optimize the economic conditions and maximize profitability. However, the complexity connected to the development of the most optimal production systems require improved knowledge and involvement of several actors from different competence areas, such as chemical and biochemical engineering, process design and integration and energy and environmental systems analysis, which may be a potential barrier.

  • 16.
    Andersen, Malin
    KTH, School of Biotechnology (BIO), Gene Technology.
    Computational and experimental approaches to regulatory genetic variation2007Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Genetic variation is a strong risk factor for many human diseases, including diabetes, cancer, cardiovascular disease, depression, autoimmunity and asthma. Most of the disease genes identified so far alter the amino acid sequences of encoded proteins. However, a significant number of genetic variants affecting complex diseases may alter the regulation of gene transcription. The map of the regulatory elements in the human genome is still to a large extent unknown, and it remains a challenge to separate the functional regulatory genetic variations from linked neutral variations.

    The objective of this thesis was to develop methods for the identification of genetic variation with a potential to affect the transcriptional regulation of human genes, and to analyze potential regulatory polymorphisms in the CD36 glycoprotein, a candidate gene for cardiovascular disease.

    An in silico tool for the prediction of regulatory polymorphisms in human genes was implemented and is available at www.cisreg.ca/RAVEN. The tool was evaluated using experimentally verified regulatory single nucleotide polymorphisms (SNPs) collected from the scientific literature, and tested in combination with experimental detection of allele specific expression of target genes (allelic imbalance). Regulatory SNPs were shown to be located in evolutionary conserved regions more often than background SNPs, but predicted transcription factor binding sites were unable to enrich for regulatory SNPs unless additional information linking transcription factors with the target genes were available.

    The in silico tool was applied to the CD36 glycoprotein, a candidate gene for cardiovascular disease. Potential regulatory SNPs in the alternative promoters of this gene were identified and evaluated in vitro and in vivo using a clinical study for coronary artery disease. We observed association to the plasma concentrations of inflammation markers (serum amyloid A protein and C-reactive protein) in myocardial infarction patients, which highlights the need for further analyses of potential regulatory polymorphisms in this gene.

    Taken together, this thesis describes an in silico approach to identify putative regulatory polymorphisms which can be useful for directing limited laboratory resources to the polymorphisms most likely to have a phenotypic effect.

  • 17.
    Anderson, Mattias
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Afewerki, Samson
    Berglund, Per
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Cõrdova, Armando
    Total Synthesis of Capsaicin Analogues from Lignin-Derived Compounds by Combined Heterogeneous Metal, Organocatalytic and Enzymatic Cascades in One Pot2014In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 356, no 9, p. 2113-2118Article in journal (Refereed)
    Abstract [en]

    The total synthesis of capsaicin analogues was performed in one pot, starting from compounds that can be derived from lignin. Heterogeneous palladium nanoparticles were used to oxidise alcohols to aldehydes, which were further converted to amines by an enzyme cascade system, including an amine transaminase. It was shown that the palladium catalyst and the enzyme cascade system could be successfully combined in the same pot for conversion of alcohols to amines without any purification of intermediates. The intermediate vanillyl-amine, prepared with the enzyme cascade system, could be further converted to capsaicin analogues without any purification using either fatty acids and a lipase, or Schotten-Baumann conditions, in the same pot. An aldol compound (a simple lignin model) could also be used as starting material for the synthesis of capsaicin analogues. Using l-alanine as organocatalyst, vanillin could be obtained by a retro-aldol reaction. This could be combined with the enzyme cascade system to convert the aldol compound to vanillylamine in a one-step one-pot reaction.

  • 18.
    Andersson, Anders
    KTH, School of Biotechnology (BIO).
    Microarray-based investigation of genome and transcriptome organisation in the archaeon sulfolobus2005Doctoral thesis, comprehensive summary (Other scientific)
  • 19.
    Andersson, Anders
    et al.
    KTH, School of Biotechnology (BIO).
    Bernander, R.
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO).
    Dual-genome primer design for construction of DNA microarrays2005In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 21, no 3, p. 325-332Article in journal (Refereed)
    Abstract [en]

    Motivation: Microarray experiments using probes covering a whole transcriptome are expensive to initiate, and a major part of the costs derives from synthesizing gene-specific PCR primers or hybridization probes. The high costs may force researchers to limit their studies to a single organism, although comparing gene expression in different species would yield valuable information. Results: We have developed a method, implemented in the software DualPrime, that reduces the number of primers required to amplify the genes of two different genomes. The software identifies regions of high sequence similarity, and from these regions selects PCR primers shared between the genomes, such that either one or, preferentially, both primers in a given PCR can be used for amplification from both genomes. To assure high microarray probe specificity, the software selects primer pairs that generate products of low sequence similarity to other genes within the same genome. We used the software to design PCR primers for 2182 and 1960 genes from the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. Primer pairs were shared among 705 pairs of genes, and single primers were shared among 1184 pairs of genes, resulting in a saving of 31% compared to using only unique primers. We also present an alternative primer design method, in which each gene shares primers with two different genes of the other genome, enabling further savings.

  • 20.
    Andersson, Anders
    et al.
    KTH, School of Biotechnology (BIO).
    Eriksson, S.
    Nilsson, P.
    Bernander, R.
    Early replicating ridge-like domains in archaeal chromosomesManuscript (preprint) (Other academic)
  • 21.
    Andersson, Anders
    et al.
    KTH, Superseded Departments, Biotechnology.
    Keskitalo, J.
    Sjödin, A.
    Bhalerao, Rupali
    KTH, Superseded Departments, Biotechnology.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Wissel, K.
    Tandre, K.
    Aspeborg, Henrik
    KTH, Superseded Departments, Biotechnology.
    Moyle, R.
    Ohmiya, Y.
    Brunner, A.
    Gustafsson, P.
    Karlsson, J.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Nilsson, O.
    Sandberg, G.
    Strauss, S.
    Sundberg, B.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    Jansson, S.
    Nilsson, Peter
    KTH, Superseded Departments, Biotechnology.
    A transcriptional timetable of autumn senescence2004In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 5, no 4, p. R24-Article in journal (Refereed)
    Abstract [en]

    Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

  • 22.
    Andersson, Anders
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Lundgren, Magnus
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Eriksson, Stefan
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Rosenlund, Magnus
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.).
    Bernander, Rolf
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Global analysis of mRNA stability in the archaeon Sulfolobus2006In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 7, no 10, p. R99-Article in journal (Refereed)
    Abstract [en]

    Background: Transcript half-lives differ between organisms, and between groups of genes within the same organism. The mechanisms underlying these differences are not clear, nor are the biochemical properties that determine the stability of a transcript. To address these issues, genome-wide mRNA decay studies have been conducted in eukaryotes and bacteria. In contrast, relatively little is known about RNA stability in the third domain of life, Archaea. Here, we present a microarray-based analysis of mRNA half-lives in the hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, constituting the first genome-wide study of RNA decay in archaea. Results: The two transcriptomes displayed similar half-life distributions, with medians of about five minutes. Growth-related genes, such as those involved in transcription, translation and energy production, were over-represented among unstable transcripts, whereas uncharacterized genes were over-represented among the most stable. Half-life was negatively correlated with transcript abundance and, unlike the situation in other organisms, also negatively correlated with transcript length. Conclusion: The mRNA half-life distribution of Sulfolobus species is similar to those of much faster growing bacteria, contrasting with the earlier observation that median mRNA half-life is proportional to the minimal length of the cell cycle. Instead, short half-lives may be a general feature of prokaryotic transcriptomes, possibly related to the absence of a nucleus and/or more limited post-transcriptional regulatory mechanisms. The pattern of growth-related transcripts being among the least stable in Sulfolobus may also indicate that the short half-lives reflect a necessity to rapidly reprogram gene expression upon sudden changes in environmental conditions.

  • 23.
    Andersson, Anders
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Pelve, Erik A.
    Lindeberg, Stefan
    Lundgren, Magnus
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Bernander, Rolf
    Replication-biased genome organisation in the crenarchaeon Sulfolobus2010In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, p. 454-Article in journal (Refereed)
    Abstract [en]

    Background: Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. Results: We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more highly expressed at all three origins. The bias by far exceeds what would be anticipated by gene dosage effects alone. In addition, early replicating regions are denser in archaeal core genes (enriched in essential functions), display lower intergenic distances, and are devoid of mobile genetic elements. Conclusion: The strong replication-biased structuring of the Sulfolobus chromosome implies that the multiple replication origins serve purposes other than simply shortening the time required for replication. The higher-level chromosomal organisation could be of importance for minimizing the impact of DNA damage, and may also be linked to transcriptional regulation.

  • 24. Andersson, K
    et al.
    Gülich, S
    KTH, Superseded Departments (pre-2005), Biochemistry and Biotechnology.
    Hämäläinen, M
    Nygren, P A
    KTH, Superseded Departments (pre-2005), Biochemistry and Biotechnology.
    Hober, Sophia
    KTH, Superseded Departments (pre-2005), Biochemistry and Biotechnology.
    Malmqvist, M
    Kinetic characterization of the interaction of the Z-fragment of protein A with mouse-IgG3 in a volume in chemical space.1999In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 37, no 3Article in journal (Refereed)
    Abstract [en]

    The kinetic rate parameters for the interaction between a single domain analogue of staphylococcal protein A (Z) and a mouse-IgG3 monoclonal antibody (MAb) were measured in Hepes buffer with different chemical additives. Five buffer ingredients (pH, NaCl, DMSO, EDTA, and KSCN) were varied simultaneously in 16 experiments following a statistical experimental plan. The 16 buffers thus spanned a volume in chemical space. A mathematical model, using data from the buffer composition, was developed and used to predict apparent kinetic parameters in five new buffers within the spanned volume. Association and dissociation parameters were measured in the new buffers, and these agreed with the predicted values, indicating that the model was valid within the spanned volume. The pattern of variation of the kinetic parameters in relation to buffer composition was different for association and dissociation, such that pH influenced both association and dissociation and NaCl influenced only dissociation. This indicated that the recognition mechanism (association) and the stability of the formed complex (dissociation) involve different binding forces, which can be further investigated by kinetic studies in systematically varied buffers.

  • 25.
    Andersson, Klara
    KTH, School of Biotechnology (BIO).
    Development of a shake flask method suitable for effective screening of Escherichia coli expression constructs2011Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Screening of expression constructs suitable for protein pharmaceuticals is often done in batch cultivations. But the production of the recombinant protein is made during fed-batch cultivations. The two types of cultivations are different and therefore may good expression constructs that grow poorly in batch cultivations but good in fed-batch cultivations be rejected. Therefore would it be desirable to develop a fed-batch method that can be used in shake flasks. Biosilta has developed a method where starch is broken down into glucose by an enzyme creating fed-batch conditions. This method has been tried out and analyzed during this project. It is shown that the cells grown under these conditions can be glucose limited. However, at a later stage of the cultivation the cells produce a large amount of acetate and pH is not stable. The system builds on a booster tablet which content is unknown. If the booster is not added to the cultivations the cells stop growing, this indicates that there is some other limitation than just glucose. It is also seen that the amount of protein that is produced during this fed-batch mimic cultivation is much lower than that is produced during normal batch cultivations. I would therefore not recommend EnBase as a screening method.

  • 26.
    Andersson, Sofia
    et al.
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Dalhammar, Gunnel
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Land, Carl Johan
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Kuttuva Rajarao, Gunaratna
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Biological nutrient removal by individual and mixed strain biofilmsManuscript (Other academic)
  • 27.
    Andersson, Sofia
    et al.
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Dalhammar, Gunnel
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Land, Carl Johan
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Kuttuva Rajarao, Gunaratna
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Characterization of extracellular polymeric substances from denitrifying organism Comamonas denitrificans2009In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 82, no 3, p. 535-543Article in journal (Refereed)
    Abstract [en]

    Extracellular polymeric substances (EPS) play an important role in the formation and activity of biofilms in wastewater treatment (WWT). The EPS of the denitrifying biomarker Comamonas denitrificans strain 110, produced in different culture media and growth modes, were characterized. The EPS mainly contained protein (3-37%), nucleic acids (9-50%), and carbohydrates (3-21%). The extracellular DNA was found to be important for initial biofilm formation since biofilm, but not planktonic growth, was inhibited in the presence of DNase. The polysaccharide fraction appeared to consist of at least two distinct polymers, one branched fraction (A) made up of glucose and mannose with a molecular weight around 100 kDa. The other fraction (B) was larger and consisted of ribose, mannose, glucose, rhamnose, arabinose, galactose, and N-acetylglucosamine. Fraction B polysaccharides were mainly found in capsular EPS which was the dominant type in biofilms and agar-grown colonies. Fraction A was abundant in the released EPS, the dominant type in planktonic cultures. Biofilm and agar-grown EPS displayed similar overall properties while planktonic EPS showed clear compositional disparity. This study presents results on the physiology of a key WWT organism, which may be useful in the future development of improved biofilm techniques for WWT purposes.

  • 28.
    Andersson, Sofia
    et al.
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Dalhammar, Gunnel
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Rajarao, Gunaratna Kuttuva
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Persistence and competition of denitrifying biofilms subjected to a natural wastewater floraManuscript (Other academic)
  • 29.
    Andersson, Sofia
    et al.
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Kuttuva Rajarao, Gunaratna
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Land, Carl Johan
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Dalhammar, Gunnel
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Biofilm formation and interactions of bacterial strains found in wastewater treatment systems2008In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 283, no 1, p. 83-90Article in journal (Refereed)
    Abstract [en]

    Biofilm formation and adherence properties of 13 bacterial strains commonly found in wastewater treatment systems were studied in pure and mixed cultures using a crystal violet microtiter plate assay. Four different culture media were used, wastewater, acetate medium, glucose medium and diluted nutrient broth. The medium composition strongly affected biofilm formation. All strains were able to form pure culture biofilms within 24 h in at least one of the tested culture media and three strains were able to form biofilm in all four culture media, namely Acinetobacter calcoaceticus ATCC 23055, Comamonas denitrificans 123 and Pseudomonas aeruginosa MBL 0199. The adherence properties assessed were initial adherence, cell surface hydrophobicity, and production of amyloid fibers and extracellular polymeric substances. The growth of dual-strain biofilms showed that five organisms formed biofilm with all 13 strains while seven formed no or only weak biofilm when cocultured. In dual-strain cultures, strains with different properties were able to complement each other, giving synergistic effects. Strongest biofilm formation was observed when a mixture of all 13 bacteria were grown together. These results on attachment and biofilm formation can serve as a tool for the design of tailored systems for the degradation of municipal and industrial wastewater.

  • 30.
    Andersson, Sofia
    et al.
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Nilsson, Mirja
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Dalhammar, Gunnel
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Kuttuva Rajarao, Gunaratna
    KTH, School of Biotechnology (BIO), Environmental Microbiology.
    Assessment of carrier materials for biofilm formation and denitrification2008In: Vatten, ISSN 0042-2886, Vol. 64, p. 201-207Article in journal (Refereed)
  • 31.
    Andrade, Jorge
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Berglund, Lisa
    KTH, School of Biotechnology (BIO), Gene Technology.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Gene Technology.
    Odeberg, Jacob
    KTH, School of Biotechnology (BIO), Gene Technology.
    Using Grid Technology for Computationally Intensive Applied Bioinformatics Analyses2006In: In Silico Biology, ISSN 1386-6338, Vol. 6, no 6, p. 495-504Article in journal (Refereed)
    Abstract [en]

    For several applications and algorithms used in applied bioinformatics, a bottle neck in terms of computational time may arise when scaled up to facilitate analyses of large datasets and databases. Re-codification, algorithm modification or sacrifices in sensitivity and accuracy may be necessary to accommodate for limited computational capacity of single work stations. Grid computing offers an alternative model for solving massive computational problems by parallel execution of existing algorithms and software implementations. We present the implementation of a Grid-aware model for solving computationally intensive bioinformatic analyses exemplified by a blastp sliding window algorithm for whole proteome sequence similarity analysis, and evaluate the performance in comparison with a local cluster and a single workstation. Our strategy involves temporary installations of the BLAST executable and databases on remote nodes at submission, accommodating for dynamic Grid environments as it avoids the need of predefined runtime environments (preinstalled software and databases at specific Grid-nodes). Importantly, the implementation is generic where the BLAST executable can be replaced by other software tools to facilitate analyses suitable for parallelisation. This model should be of general interest in applied bioinformatics. Scripts and procedures are freely available from the authors.

  • 32.
    Anfelt, Josefine
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Metabolic engineering strategies to increase n-butanol production from cyanobacteria2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The development of sustainable replacements for fossil fuels has been spurred by concerns over global warming effects. Biofuels are typically produced through fermentation of edible crops, or forest or agricultural residues requiring cost-intensive pretreatment. An alternative is to use photosynthetic cyanobacteria to directly convert CO2 and sunlight into fuel. In this thesis, the cyanobacterium Synechocystis sp. PCC 6803 was genetically engineered to produce the biofuel n­-butanol. Several metabolic engineering strategies were explored with the aim to increase butanol titers and tolerance.

    In papers I-II, different driving forces for n-butanol production were evaluated. Expression of a phosphoketolase increased acetyl-CoA levels and subsequently butanol titers. Attempts to increase the NADH pool further improved titers to 100 mg/L in four days.

    In paper III, enzymes were co-localized onto a scaffold to aid intermediate channeling. The scaffold was tested on a farnesene and polyhydroxybutyrate (PHB) pathway in yeast and in E. coli, respectively, and could be extended to cyanobacteria. Enzyme co-localization increased farnesene titers by 120%. Additionally, fusion of scaffold-recognizing proteins to the enzymes improved farnesene and PHB production by 20% and 300%, respectively, even in the absence of scaffold.

    In paper IV, the gene repression technology CRISPRi was implemented in Synechocystis to enable parallel repression of multiple genes. CRISPRi allowed 50-95% repression of four genes simultaneously. The method will be valuable for repression of competing pathways to butanol synthesis.

    Butanol becomes toxic at high concentrations, impeding growth and thus limiting titers. In papers V-VI, butanol tolerance was increased by overexpressing a heat shock protein or a stress-related sigma factor.

    Taken together, this thesis demonstrates several strategies to improve butanol production from cyanobacteria. The strategies could ultimately be combined to increase titers further.

  • 33.
    Anfelt, Josefine
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Kaczmarzyk, Danuta
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Shabestary, Kiyan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Renberg, Björn
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Rockberg, Johan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Nielsen, Jens
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. Tech Univ Denmark.
    Hudson, Elton P.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Genetic and nutrient modulation of acetyl-CoA levels in Synechocystis for n-butanol production2015In: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 14, article id 167Article in journal (Refereed)
    Abstract [en]

    Background: There is a strong interest in using photosynthetic cyanobacteria as production hosts for biofuels and chemicals. Recent work has shown the benefit of pathway engineering, enzyme tolerance, and co-factor usage for improving yields of fermentation products. Results: An n-butanol pathway was inserted into a Synechocystis mutant deficient in polyhydroxybutyrate synthesis. We found that nitrogen starvation increased specific butanol productivity up to threefold, but cessation of cell growth limited total n-butanol titers. Metabolite profiling showed that acetyl-CoA increased twofold during nitrogen starvation. Introduction of a phosphoketolase increased acetyl-CoA levels sixfold at nitrogen replete conditions and increased butanol titers from 22 to 37 mg/L at day 8. Flux balance analysis of photoautotrophic metabolism showed that a Calvin-Benson-Bassham-Phosphoketolase pathway had higher theoretical butanol productivity than CBB-Embden-Meyerhof-Parnas and a reduced butanol ATP demand. Conclusion: These results demonstrate that phosphoketolase overexpression and modulation of nitrogen levels are two attractive routes toward increased production of acetyl-CoA derived products in cyanobacteria and could be implemented with complementary metabolic engineering strategies.

  • 34.
    Anfelt, Josefine
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Shabestary, Kiyan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Hudson, Elton P.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Complementary effects of ATP, acetyl-CoA and NADH driving forces increase butanol production in Synechocystis sp. PCC 6803Manuscript (preprint) (Other academic)
  • 35.
    Angleby, Helen
    KTH, School of Biotechnology (BIO).
    Analysis of domestic dog mitochondrial DNA sequence variation for forensic investigations2005Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    The first method for DNA analysis in forensics was presented in 1985. Since then, the introduction of the polymerase chain reaction (PCR) has rendered possible the analysis of small amounts of DNA and automated sequencing and fragment analysis techniques have facilitated the analyses. In most cases short tandemly repeated regions (STRs) of nuclear DNA are analysed in forensic investigations, but all samples cannot be successfully analysed using this method. For samples containing minute amounts of DNA or degraded DNA, such as shed hairs, analysis of mitochondrial DNA (mtDNA) is generally more successful due to the presence of thousands of copies of mtDNA molecules per cell.

    In Sweden, ~40 % of all households have cats or dogs. With ~9 million humans shedding ~100 scalp hairs per day, and ~1.6 million cats and ~1 million dogs shedding hairs it is not surprising that shed hairs are one of the most common biological evidence found at crime scenes. However, the match probability for domestic dog mtDNA analysis has only been investigated in a few minor studies. Furthermore, although breed –sequence correlations of the noncoding mtDNA control region (CR) have been analysed in a few studies, showing limited correlations, no largescale studies have been performed previously. Thus, there have not been any comprehensive studies of forensic informativity of dog mtDNA. In the two papers presented in this thesis we have tried to lay a foundation for forensic use of analysis of domestic dog mtDNA. In the first paper, CR sequences were analysed and the exclusion capacity was investigated for a number of different populations. This is also the first comprehensive study of the correlation between mtDNA CR type and breed, type, and geographic origin of domestic dogs. Since the exclusion capacity for analysis of domestic dog CR sequences is relatively low, it was investigated in the second paper to what extent the discrimination power is improved by analysis of coding sequence. The exclusion capacity improved considerably when 3,000 base pairs of coding sequences where analysed in addition to CR sequences. This study will hopefully work as a basis for future development of analysis of dog mtDNA for forensic purposes.

  • 36.
    Angleby, Helen
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Oskarsson, Mattias
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pang, Junfeng
    Zhang, Ya-ping
    Leitner, Thomas
    Braham, Caitlyn
    Arvestad, Lars
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Webb, Kristen M.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Forensic Informativity of similar to 3000bp of Coding Sequence of Domestic Dog mtDNA2014In: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 59, no 4, p. 898-908Article in journal (Refereed)
    Abstract [en]

    The discriminatory power of the noncoding control region (CR) of domestic dog mitochondrial DNA alone is relatively low. The extent to which the discriminatory power could be increased by analyzing additional highly variable coding regions of the mitochondrial genome (mtGenome) was therefore investigated. Genetic variability across the mtGenome was evaluated by phylogenetic analysis, and the three most variable similar to 1kb coding regions identified. We then sampled 100 Swedish dogs to represent breeds in accordance with their frequency in the Swedish population. A previously published dataset of 59 dog mtGenomes collected in the United States was also analyzed. Inclusion of the three coding regions increased the exclusion capacity considerably for the Swedish sample, from 0.920 for the CR alone to 0.964 for all four regions. The number of mtDNA types among all 159 dogs increased from 41 to 72, the four most frequent CR haplotypes being resolved into 22 different haplotypes.

  • 37.
    Angleby, Helen
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Savolainen, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Forensic informativity of domestic dog mtDNA control region sequences2005In: Forensic Science International, ISSN 0379-0738, E-ISSN 1872-6283, Vol. 154, no 03-feb, p. 99-110Article in journal (Refereed)
    Abstract [en]

    We have analysed the genetic information to be obtained from analysis of mitochondrial DNA (mtDNA) in domestic dogs studying the exclusion capacity in different populations and the correlation between mtDNA types and breeds or types of dogs. The exclusion capacities for a 573 bp sequence of the mitochondrial control region was between 0.86 and 0.95 for dogs in Sweden, the UK, Germany, Japan and China. The direct correlation between mtDNA type and breed, type of dog, and geographical origin of breed was generally low, but in some cases certain mtDNA types were overrepresented in one breed, and for wider groupings such as morphologically similar breeds, some mtDNA types were in many cases found in a distinct group of breeds, often originating from the same geographic region. This type of information may be used as an indication of the breed and, with some degree of probability, to include or exclude certain breeds from being the source of evidence materials.

  • 38.
    Arnau, Laurent
    KTH, School of Chemical Science and Engineering (CHE).
    Techno-Economic Feasibility Study for the Production of Microalgae Based Plant Biostimulant2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Microalgae are considered as a potential feedstock for many promising applications. Some active substances in microalgae have plant biostimulation effects potentially useful in agriculture. However, to produce such a microalgal biomass, specific microalgae cultivation and post-treatment processes must be designed to preserve active substances. A particular focus is provided on cultivation (tubular photobioreactor) and different plausible post-treatment scenarios for microalgae separation (flocculation and centrifugation) and preservation (sterilization and drying). For each step, yield and energy consumption are modeled using data taken from literature or lab and pilot scale experiments. Industrial equipment for scale-up process is also studied by comparing existing systems. These models enable to make an economic evaluation of the whole process and to study its profitability for each scenario. The breakeven price is calculated as a function of the production rate. Several parameters are suggested to improve system efficiency and profitability at the end of this study. However, a better microalgae characterization and more experiments on potential post-treatment systems are required to improve the accuracy of the model.

  • 39.
    Atat, Rachad
    et al.
    KTH, School of Information and Communication Technology (ICT), Communication Systems, CoS, Radio Systems Laboratory (RS Lab).
    Yaacoub, E.
    Alouini, M. -S
    Abu-Dayya, A.
    Peer-to-peer content sharing techniques for energy efficiency in wireless networks with fast channel variations2013In: Green Networking and Communications: ICT for Sustainability, CRC Press , 2013, p. 3-28Chapter in book (Other academic)
    Abstract [en]

    According to the International Telecommunication Union, information and communication technology (ICT) was emitting 0.83 GtCO2e (gigatons of carbon dioxide equivalent), contributing to around 2%-2.5% of global greenhouse gas (GHG) emissions in 2007 [1]. With the continuous growth of ICT, especially in developing countries, the GHG emissions are expected to grow at double the rate over the next 10 years [1]. The Global e-Sustainability Initiative research is estimating a 72% increase in ICT energy usage from 2007 to 2020 with around 1.43 GtCO2e emissions in 2020 [1]. In addition, the telecommunications industry is witnessing an explosive increase in data traffic especially with the introduction of wireless modems and smart phones and with the presence of more than one billion wireless subscribers today. The data traffic volume is increasing by a factor of 10 every 5 years, leading to an increase of 16%-20% in energy consumption every 5 years [2]. For instance, in India, the mobile telecom industry is considered the fastest-growing sector with 584.3 million subscribers in 2010-2011 with an annual growth rate of 49.15%. It is estimated that the energy consumption of the Indian Mobile Telecom Industry was 163 PJ (petajoules) with 52.66 million tons emissions of carbon dioxide (CO2) in 2010-2011 [3]. A user who travels a distance of 25 km using public transport such as car or train can result in 1.22 kg of CO2 emissions, compared to 0.11 kg of CO2 emissions for 1 hour of video conferencing with two laptops [4]. A talk of 2 minutes per day on the phone can produce 47 kg CO2e (equivalent) per year, with a total of 125 million tons of CO2e produced by mobile phones in 1 year [5]. 

  • 40.
    Ayoglu, Burcu
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nilsson, Peter
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schwenk, Jochen M.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Multiplexed antigen bead arrays for the assessment of antibody selectivity and epitope mapping2018In: Epitope Mapping Protocols, Humana Press Inc. , 2018, p. 239-248Chapter in book (Refereed)
    Abstract [en]

    With the increasing number of binding reagents for affinity-based investigations of the human proteome, high-throughput tools for the characterization of the used reagents become essential. For the analysis of binding selectivity, bead-based antigen arrays offer a miniaturized and parallelized assay platform to meet such needs, as they enable two-dimensional multiplexing to analyze up to 384 samples against up to 500 analytes in a single round of analysis. In this chapter, we describe our protocols for the generation of multiplex bead arrays built on immobilized protein fragments, as well as biotinylated peptides. Combined together, these two versions of antigen arrays offer a versatile approach for multiplexed characterization of antibody binding selectivity, off-target interactions, as well as mapping for the amino acids of epitopes involved in antibody binding.

  • 41. Balzani, D.
    et al.
    Holzapfel, Gerhard
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.), Biomechanics. Graz University of Technology, Institute of Biomechanics, Center of Biomedical Engineering.
    Brinkhues, S.
    Modeling of damage in soft biological tissues and application to arterial walls2011In: Computational Plasticity XI - Fundamentals and Applications, 2011, p. 764-775Conference paper (Refereed)
    Abstract [en]

    A new material model is proposed for the description of stress-softening observed in cyclic tension tests performed on soft biological tissues. The modeling framework is based on the concept of internal variables introducing a scalar-valued variable for the representation of fiber damage. Remanent strains in fiber direction can be represented as a result of microscopic damage of the fiber crosslinks. Particular internal variables are defined able to capture the nature of soft biological tissues that no damage occurs in the physiological loading domain. A specific model is adjusted to experimental data taking into account the supra-physiological loading regime. For the description of the physiological domain polyconvex functions are used which also take into account fiber dispersion in a phenomenological approach. The applicability of the model in numerical simulations is shown by a representative example where the damage distribution in an arterial cross-section is analyzed.

  • 42.
    Bandmann, Nina
    KTH, School of Biotechnology (BIO).
    Rational and combinatorial genetic engineering approaches for improved recombinant protein production and purification2007Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    The bacterium Escherichia coli (E. coli) is in many situations an ideal host for production of recombinant proteins, since it generally provides a rapid and economical means to achieve sufficiently high product quantities. However, there are several factors that may limit this host’s ability to produce large amounts of heterologous proteins in a soluble and native form. For many applications a high purity of the recombinant protein is demanded, which implies a purification strategy where the product efficiently can be isolated from the complex milieu of host cell contaminants. In this thesis, different strategies based on both rational and combinatorial genetic engineering principles have been investigated, aiming at improving and facilitating recombinant E. coli protein production and purification.

    One objective was to improve the PEG/salt aqueous two-phase system (ATPS) purification process of the lipase cutinase, by increasing the selectivity of the protein for the system top-phase. Peptide tags, with varying properties, were designed and genetically fused to the C-terminal end of ZZ-cutinase. Greatly increased partitioning values were observed for purified protein variants fused to tryptophan containing peptide tags, particularly a (WP)4 peptide. The partitioning properties of the ZZ-cutinase-(WP)4 protein were also retained when added to the ATPS directly from an E. coli total cell disintegrate, emphasizing the applicability of this genetic engineering strategy for primary protein purification in ATPSs.

    Further on, a combinatorial library approach using phage display technology was investigated as a tool for identification of peptide tags capable of improving partitioning properties of ZZ-cutinase in an ATPS. Repeated ATPS-based partitioning-selection cycles of a large phagemid (pVIII) peptide library, resulted in isolation of phage particles preferentially decorated with peptides rich in tyrosine and proline residues. Both a peptide corresponding to a phage library derived peptide sequence as well as peptides designed based on information of amino acid appearance frequencies in later selection rounds, were shown to improve partitioning several-fold when genetically fused to the C-terminal end of ZZ-cutinase. From the two- to four–fold increased production yields observed for these fusion proteins compared to ZZ-cutinase-(WP)4, it was concluded that the selection system used allowed for selection of desired peptide properties related to both partitioning and E. coli protein production parameters.

    Bacterial protein production is affected by several different mRNA and protein sequence-related features. Attempts to address single parameters in this respect are difficult due to the inter-dependence of many features, for example between codon optimization and mRNA secondary structure effects. Two combinatorial expression vector libraries (ExLib1 and ExLib2) were constructed using a randomization strategy that potentially could lead to variations in many of these sequence-related features and which would allow a pragmatic search of vector variants showing positive net effects on the level of soluble protein production. ExLib1 was constructed to encode all possible synonymous codons of an eight amino acid N-terminal extension of protein Z, fused to the N-terminal of an enhanced green fluorescent reporter protein (EGFP). In ExLib2, the same eight positions were randomized using an (NNG/T) degeneracy code, which could lead to various effects on both the nucleotide and protein level, through the introduction of nucleotide sequences functional as e.g. alternative ribosome binding or translation initiation sites or as translated codons for an Nterminal extension of the target protein by a peptide sequence. Flow cytometric analyses and sorting of library cell cultures resulted in isolation of clones displaying several-fold increases in whole cell fluorescence compared to a reference clone. SDS-PAGE and western blot analyses verified that this was a result of increases (up to 24-fold) in soluble intracellular ZEGFP product protein content. Both position specific codon bias effects and the appearance of new ribosomal binding sites in the library sequences were concluded to have influenced the protein production.

    To explore the possibility of applying the same combinatorial library strategy for improving soluble intracellular production of heterologous proteins proven difficult to express in E. coli, three proteins with either bacterial (a transcriptional regulator (DntR)) or human (progesterone receptor ligand binding domain (PRLBD) and 11-β Hydroxysteroid dehydrogenase type I (11-β)) origin, were cloned into the ExLib2 library. Flow cytometric sorting of libraries resulted in isolation of DntR library clones showing increased soluble protein production levels and PR-LBD library clones with up to ten-fold increases in whole cell fluorescence, although the product under these conditions co-separated with the insoluble cell material.

  • 43.
    Bandmann, Nina
    et al.
    KTH, Superseded Departments, Biotechnology.
    Collet, Eric
    KTH, Superseded Departments, Biotechnology.
    Leijen, J
    Uhlén, M
    Veide, Andres
    KTH, Superseded Departments, Biotechnology.
    Nygren, Per-Åke
    KTH, Superseded Departments, Biotechnology.
    Genetic engineering of the Fusarium solani pisi lipase cutinase for enhanced partitioning in PEG-phosphate aqueous two-phase systems2000In: Journal of Biotechnology, ISSN 0168-1656, E-ISSN 1873-4863, Vol. 79, no 2, p. 161-172Article in journal (Refereed)
    Abstract [en]

    The Fusarium solani pisi lipase cutinase has been genetically engineered to investigate the influence of C-terminal peptide extensions on the partitioning of the enzyme in PEG-salt based aqueous two-phase bioseparation systems. Seven different cutinase lipase variants were constructed containing various C-terminal peptide extensions including tryptophan rich peptide tags ((WP)(2) and (WP)(4)), positively ((RP)(4)) and negatively ((DP)(4)) charged tags as well as combined tags with tryptophan together with either positively ((WPR)(4)) or negatively ((WPD)(4)) charged amino acids. The modified cutinase variants were stably produced in Escherichia coli as secreted to the periplasm from which they were efficiently purified by IgG-affinity chromatography employing an introduced N-terminal IgG-binding ZZ affinity fusion partner present in all variants. Partitioning experiments performed in a PEG 4000/sodium phosphate aqueous two-phase system showed that for variants containing either (WP)(2) or (WP)(4) peptide extensions, 10- to 70-fold increases in the partitioning to the PEG rich top-phase were obtained, when compared to the wild type enzyme. An increased partitioning was also seen for cutinase variants tagged with both tryptophans and charged amino acids, whereas the effect of solely charged peptide extensions was relatively small. In addition, when performing partitioning experiments from cell disintegrates, the (WP)(4)-tagged cutinase showed a similarly high PEG-phase partitioning, indicating that the effect from the peptide tag was unaffected by the background of the host proteins. Taken together, the results show that the partitioning of the recombinantly produced cutinase model enzyme could be significantly improved by relatively minor genetic engineering and that the effects observed for purified proteins are retained also in an authentic whole cell disintegrate system. The results presented should be of general interest also for the improvement of the partitioning properties of other industrially interesting proteins including bulk enzymes.

  • 44.
    Bandmann, Nina
    et al.
    KTH, School of Biotechnology (BIO).
    Löfdahl, Per-Åke
    KTH, School of Biotechnology (BIO).
    Lönneborg, Rosa
    KTH, School of Biotechnology (BIO).
    Älgenäs, Cajsa
    KTH, School of Biotechnology (BIO).
    Nygren, Per-Åke
    KTH, School of Biotechnology (BIO).
    Exploring the use of a combinatorial expression vector library for facilitated soluble recombinant protein productionManuscript (Other academic)
  • 45.
    Bandmann, Nina
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Nygren, Per-Åke
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Combinatorial expression vector engineering for tuning of recombinant protein production in Escherichi coli2007In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 35, no 5Article in journal (Refereed)
    Abstract [en]

    The complex and integrated nature of both genetic and protein level factors influencing recombinant protein production in Escherichia coli makes it difficult to predict the optimal expression strategy for a given protein. Here, two combinatorial library strategies were evaluated for their capability of tuning recombinant protein production in the cytoplasm of E. coli. Large expression vector libraries were constructed through either conservative (ExLib1) or free (ExLib2) randomization of a seven-amino-acid window strategically located between a degenerated start codon and a sequence encoding a fluorescently tagged target protein. Flow cytometric sorting and analyses of libraries, subpopulations or individual clones were followed by SDS-PAGE, western blotting, mass spectrometry and DNA sequencing analyses. For ExLib1, intracellular accumulation of soluble protein was shown to be affected by codon specific effects at some positions of the common N-terminal extension. Interestingly, for ExLib2 where the same sequence window was randomized via seven consecutive NN(G/T) tri-nucleotide repeats, high product levels (up to 24-fold higher than a reference clone) were associated with a preferential appearance of novel SID-like sequences. Possible mechanisms behind the observed effects are discussed.

  • 46.
    Bandmann, Nina
    et al.
    KTH, Superseded Departments, Biotechnology.
    van Alstine, James
    KTH, Superseded Departments, Biotechnology.
    Veide, Andres
    KTH, Superseded Departments, Biotechnology.
    Nygren, Per-Åke
    KTH, Superseded Departments, Biotechnology.
    Functional selection of phage displayed peptides for facilitated design of fusion tags improving aqueous two-phase partitioning of recombinant proteins2002In: Journal of Biotechnology, ISSN 0168-1656, E-ISSN 1873-4863, Vol. 93, no 1, p. 1-14Article in journal (Refereed)
    Abstract [en]

    Aqueous two-phase systems allow for the unequal distribution of proteins and other molecules in water-rich solutions containing phase separating polymers or surfactants. One approach to improve the partitioning properties of recombinant proteins is to produce the proteins as fused to certain peptide tags. However, the rational design of such tags has proven difficult since it involves a compromise between multivariate parameters such as partitioning properties, solvent accessibility and production/secretion efficiency. In this work, a novel approach for the identification of suitable peptide tag extensions has been investigated, Using the principles of selection, rather than design, peptide sequences contributing to an improved partitioning have been identified using phage display technology. A 40 million member phagemid library of random nona-peptides, displayed as fusion to the major coat protein pVIII of the filamentous phage M 13, was employed in the selection of top-phase partitioning phage particles in a PEG/sodium phosphate system. After multiple cycles of selection by partitioning, peptides with high frequencies of both tyrosine and proline residues were found to be over represented in selected clones. The identified peptide sequences, or derivatives thereof, were subsequently individually analyzed for their partitioning behavior as displayed on phage, as free synthetic peptides and as genetically fused to a recombinant model target protein. The results showed that novel peptide sequences capable of enhancing top-phase partitioning without interfering with protein production and secretion indeed could be identified for the aqueous two-phase system investigated.

  • 47.
    Banerjee, Indradumna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Russom, Aman
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Lab-on-DVD: Optical Disk Drive-Based Platforms for Point-of-Care Diagnostics2018In: Frugal Innovation in Bioengineering for the Detection of Infectious Diseases / [ed] AK Chavali, R Ramji, Switzerland: Springer, 2018, 2, p. 23-38Chapter in book (Refereed)
    Abstract [en]

    There is a growing demand for simple, affordable, reliable and quality-assured point-of-care (POC) diagnostics for use in resource-limited settings. Among the top ten leading causes of death worldwide, three are infectious diseases, namely, respiratory infections, HIV/AIDS and diarrheal diseases (World Health Organization 2012). Although high-quality diagnostic tests are available, these are often not available to patients in developing countries. While recent development in microfluidics and “lab-on-a-chip” devices has the potential to spur the development of protocols and affordable instruments for diagnosis of infectious disease at POC, integration of complex sample preparation and detection into automated molecular and cellular systems remain a bottleneck for implementation of these systems at resource-limited settings. Towards this, we describe here how low-cost optical drives can, with minor modifications, be turned into POC diagnostic platforms. A DVD drive is essentially a highly advanced and low-cost optical laser-scanning microscope, with the capability to deliver high-resolution images for biological applications. Furthermore, the inherent centrifugal force on rotational discs is elegantly used for sample preparation and integration. Hence, the merging of low-cost optical disc drives with centrifugal microfluidics is feasible concept for POC diagnostics, specifically designed to meet the needs at resource-limited settings.

  • 48.
    Barbe, Laurent
    et al.
    KTH, School of Biotechnology (BIO).
    Lundberg, Emma
    KTH, School of Biotechnology (BIO), Proteomics.
    Oksvold, Per
    KTH, School of Biotechnology (BIO), Proteomics.
    Stenius, Anna
    KTH, School of Biotechnology (BIO).
    Lewin, Erland
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Björling, Erik
    KTH, School of Biotechnology (BIO).
    Asplund, Anna
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University.
    Pontén, Fredrik
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Andersson-Svahn, Helene
    KTH, School of Biotechnology (BIO), Proteomics.
    Toward a confocal subcellular atlas of the human proteome2008In: Molecular and cellular proteomics, ISSN 1535-9476, Vol. 7, no 3, p. 499-508Article in journal (Refereed)
    Abstract [en]

    Information on protein localization on the subcellular level is important to map and characterize the proteome and to better understand cellular functions of proteins. Here we report on a pilot study of 466 proteins in three human cell lines aimed to allow large scale confocal microscopy analysis using protein-specific antibodies. Approximately 3000 high resolution images were generated, and more than 80% of the analyzed proteins could be classified in one or multiple subcellular compartment(s). The localizations of the proteins showed, in many cases, good agreement with the Gene Ontology localization prediction model. This is the first large scale antibody-based study to localize proteins into subcellular compartments using antibodies and confocal microscopy. The results suggest that this approach might be a valuable tool in conjunction with predictive models for protein localization.

  • 49.
    Basselet, Pascal
    et al.
    KTH, School of Biotechnology (BIO), Bioprocess Technology.
    Wegrzyn, Grzegorz
    Enfors, Sven-Olof
    KTH, School of Biotechnology (BIO), Bioprocess Technology.
    Gabig-Ciminska, Magdalena
    KTH, School of Biotechnology (BIO), Bioprocess Technology.
    Sample processing for DNA chip array-based analysis of enterohemorrhagic Escherichia coli (EHEC)2008In: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 7Article in journal (Refereed)
    Abstract [en]

    Background: Exploitation of DNA-based analyses of microbial pathogens, and especially simultaneous typing of several virulence-related genes in bacteria is becoming an important objective of public health these days. Results: A procedure for sample processing for a confirmative analysis of enterohemorrhagic Escherichia coli (EHEC) on a single colony with DNA chip array was developed and is reported here. The protocol includes application of fragmented genomic DNA from ultrasonicated colonies. The sample processing comprises first 2.5 min of ultrasonic treatment, DNA extraction (2x), and afterwards additional 5 min ultrasonication. Thus, the total sample preparation time for a confirmative analysis of EHEC is nearly 10 min. Additionally, bioinformatic revisions were performed in order to design PCR primers and array probes specific to most conservative regions of the EHEC-associated genes. Six strains with distinct pathogenic properties were selected for this study. At last, the EHEC chip array for a parallel and simultaneous detection of genes etpC-stx1-stx2-eae was designed and examined. This should permit to sense all currently accessible variants of the selected sequences in EHEC types and subtypes. Conclusion: In order to implement the DNA chip array-based analysis for direct EHEC detection the sample processing was established in course of this work. However, this sample preparation mode may also be applied to other types of EHEC DNA-based sensing systems.

  • 50.
    Baumann, Martin J.
    et al.
    KTH, School of Biotechnology (BIO).
    Eklöf, Jens
    KTH, School of Biotechnology (BIO).
    Michel, G.
    Kallas, Åsa
    KTH.
    Teeri, Tuula
    KTH, School of Biotechnology (BIO).
    Czjzek, Mirjam
    KTH.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Structural analysis of nasturtium NXG reveals the evolution of GH16 xyloglucanase activity from XETs: biological implications for cell wall metabolismManuscript (Other academic)
1234567 1 - 50 of 743
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