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  • 151. Dujon, B
    et al.
    Albermann, K
    Aldea, M
    Alexandraki, D
    Ansorge, W
    Arino, J
    Benes, V
    Bohn, C
    BolotinFukuhara, M
    Bordonne, R
    Boyer, J
    Camasses, A
    Casamayor, A
    Casas, C
    Cheret, G
    Cziepluch, C
    DaignanFornier, B
    Dang, V
    deHaan, M
    Delius, H
    Durand, P
    Fairhead, C
    Feldmann, H
    Gaillon, L
    Galisson, F
    Gamo, J
    Gancedo, C
    Goffeau, A
    Goulding, E
    Grivell, A
    Habbig, B
    Hand, J
    Hani, J
    Hattenhorst, U
    Hebling, U
    Hernando, Y
    Herrero, E
    Heumann, K
    Hiesel, R
    Hilger, F
    Hofmann, B
    Hollenberg, P
    Hughes, B
    Jauniaux, C
    Kalogeropoulos, A
    Katsoulou, C
    Kordes, E
    Lafuente, J
    Landt, O
    Louis, J
    Maarse, C
    Madania, A
    Mannhaupt, G
    Marck, C
    Martin, P
    Mewes, W
    Michaux, G
    Paces, V
    ParleMcDermott, G
    Pearson, M
    Perrin, A
    Pettersson, B
    Poch, O
    Pohl, M
    Poirey, R
    Portetelle, D
    Pujol, A
    Purnelle, B
    Rad, R
    Rechmann, S
    Schwager, C
    Schweizer, M
    Sor, F
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Tarassov, A
    Teodoru, C
    Tettelin, H
    Thierry, A
    Tobiasch, E
    Tzermia, M
    Uhlen, Mathias
    KTH, Superseded Departments, Biotechnology.
    Unseld, M
    Valens, M
    Vandenbol, M
    Vetter, I
    Vicek, C
    Voet, M
    Volckaert, G
    Voss, H
    Wambutt, R
    Wedler, H
    Wiemann, S
    Winsor, B
    Wolfe, H
    Zollner, A
    Zumstein, E
    Kleine, K
    The nucleotide sequence of Saccharomyces cerevisiae chromosome XV1997In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 387, no 6632, p. 98-102Article in journal (Refereed)
    Abstract [en]

    Chromosome XV was one of the last two chromosomes of Saccharomyces cerevisiae to be discovered(1). It is the third-largest yeast chromosome after chromosomes XII and IV, and is very similar in size to chromosome VII. It alone represents 9% of the yeast genome (8% if ribosomal DNA is included). When systematic sequencing of chromosome XV was started, 93 genes or markers were identified, and most of them were mapped(2). However, very little else was known about chromosome XV which, in contrast to shorter chromosomes, had not been the object of comprehensive genetic or molecular analysis. It was therefore decided to start sequencing chromosome XV only in the third phase of the European Yeast Genome Sequencing Programme, after experience was gained on chromosomes III, XI and II (refs 3-5). The sequence of chromosome XV has been determined from a set of partly overlapping cosmid clones derived from a unique yeast strain, and physically mapped at 3.3-kilobase resolution before sequencing. As well as numerous new open reading frames (ORFs) and genes encoding tRNA or small RNA molecules, the sequence of 1,091,283 base pairs confirms the high proportion of orphan genes and reveals a number of ancestral and successive duplications with other yeast chromosomes.

  • 152.
    Dånmark, Staffan
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Finne-Wistrand, Anna
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Schander, K.
    Hakkarainen, Minna
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Arvidson, K.
    Mustafa, K.
    Albertsson, Ann-Christine
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    In vitro and in vivo degradation profile of aliphatic polyesters subjected to electron beam sterilization2011In: ACTA BIOMATERIALIA, ISSN 1742-7061, Vol. 7, no 5, p. 2035-2046Article in journal (Refereed)
    Abstract [en]

    Degradation characteristics in response to electron beam sterilization of designed and biodegradable aliphatic polyester scaffolds are relevant for clinically successful synthetic graft tissue regeneration Scaffold degradation in vitro and in vivo were documented and correlated to the macroscopic structure and chemical design of the original polymer The materials tested were of inherently diverse hydrophobicity and crystallinity poly(L-lactide) (poly(LLA)) and random copolymers from L-lactide and epsilon-caprolactone or 1.5-dioxepan-2-one, fabricated into porous and non-porous scaffolds After sterilization, the samples underwent hydrolysis in vitro for up to a year In vivo, scaffolds were surgically implanted into rat calvarial defects and retrieved for analysis after 28 and 91 days In vitro, poly(L-lactide-co-1, 5-dioxepan-2-one) (poly(LLA-co-DXO)) samples degraded most rapidly during hydrolysis, due to the pronounced chain-shortening reaction caused by the sterilization. This was indicated by the rapid decrease in both mass and molecular weight of poly(LLA-co-DXO). Poly(L-lactide-co-epsilon-caprolactone) (poly(LLA-co-CL)) samples were also strongly affected by sterilization, but mass loss was more gradual; molecular weight decreased rapidly during hydrolysis Least affected by sterilization were the poly(LLA) samples, which subsequently showed low mass loss rate and molecular weight decrease during hydrolysis. Mechanical stability varied greatly. poly(LLA-co-CL) withstood mechanical testing for up to 182 days, while poly(LLA) and poly(LLA-co-DXO) samples quickly became too brittle Poly(LLA-co-DXO) samples unexpectedly degraded more rapidly in vitro than in vivo. After sterilization by electron beam irradiation, the three biodegradable polymers present widely diverse degradation profiles, both in vitro and in vivo. Each exhibits the potential to be tailored to meet diverse clinical tissue engineering requirements

  • 153. Ehlén, Åsa
    et al.
    Brennan, Donal J.
    Nodin, Björn
    O'Connor, Darran P.
    Eberhard, Jakob
    Alvarado-Kristensson, Maria
    Jeffrey, Ian B.
    Manjer, Jonas
    Brändstedt, Jenny
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Pontén, Fredrik
    Jirström, Karin
    Expression of the RNA-binding protein RBM3 is associated with a favourable prognosis and cisplatin sensitivity in epithelial ovarian cancer2010In: Journal of Translational Medicine, ISSN 1479-5876, E-ISSN 1479-5876, Vol. 8, p. 78-Article in journal (Refereed)
    Abstract [en]

    Background: We recently demonstrated that increased expression of the RNA-binding protein RBM3 is associated with a favourable prognosis in breast cancer. The aim of this study was to examine the prognostic value of RBM3 mRNA and protein expression in epithelial ovarian cancer (EOC) and the cisplatin response upon RBM3 depletion in a cisplatin-sensitive ovarian cancer cell line. Methods: RBM3 mRNA expression was analysed in tumors from a cohort of 267 EOC cases (Cohort I) and RBM3 protein expression was analysed using immunohistochemistry (IHC) in an independent cohort of 154 prospectively collected EOC cases (Cohort II). Kaplan Meier analysis and Cox proportional hazards modelling were applied to assess the relationship between RBM3 and recurrence free survival (RFS) and overall survival (OS). Immunoblotting and IHC were used to examine the expression of RBM3 in a cisplatin-resistant ovarian cancer cell line A2780-Cp70 and its cisplatin-responsive parental cell line A2780. The impact of RBM3 on cisplatin response in EOC was assessed using siRNA-mediated silencing of RBM3 in A2780 cells followed by cell viability assay and cell cycle analysis. Results: Increased RBM3 mRNA expression was associated with a prolonged RFS (HR = 0.64, 95% CI = 0.47-0.86, p = 0.003) and OS (HR = 0.64, 95% CI = 0.44-0.95, p = 0.024) in Cohort I. Multivariate analysis confirmed that RBM3 mRNA expression was an independent predictor of a prolonged RFS, (HR = 0.61, 95% CI = 0.44-0.84, p = 0.003) and OS (HR = 0.62, 95% CI = 0.41-0.95; p = 0.028) in Cohort I. In Cohort II, RBM3 protein expression was associated with a prolonged OS (HR = 0.53, 95% CI = 0.35-0.79, p = 0.002) confirmed by multivariate analysis (HR = 0.61, 95% CI = 0.40-0.92, p = 0.017). RBM3 mRNA and protein expression levels were significantly higher in the cisplatin sensitive A2780 cell line compared to the cisplatin resistant A2780-Cp70 derivative. siRNA-mediated silencing of RBM3 expression in the A2780 cells resulted in a decreased sensitivity to cisplatin as demonstrated by increased cell viability and reduced proportion of cells arrested in the G2/M-phase. Conclusions: These data demonstrate that RBM3 expression is associated with cisplatin sensitivity in vitro and with a good prognosis in EOC. Taken together these findings suggest that RBM3 may be a useful prognostic and treatment predictive marker in EOC.

  • 154.
    Eisenkolb, I.
    et al.
    Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany.
    Jensch, A.
    Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany.
    Eisenkolb, K.
    Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany.
    Kramer, Andrei
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Buchholz, P. C. F.
    Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany.
    Pleiss, J.
    Institute for Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.
    Spiess, A.
    Institute for Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany.
    Radde, N. E.
    Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany.
    Modeling of biocatalytic reactions: A workflow for model calibration, selection, and validation using Bayesian statistics2019In: AIChE Journal, article id e16866Article in journal (Refereed)
    Abstract [en]

    We present a workflow for kinetic modeling of biocatalytic reactions which combines methods from Bayesian learning and uncertainty quantification for model calibration, model selection, evaluation, and model reduction in a consistent statistical framework. Our workflow is particularly tailored to sparse data settings in which a considerable variability of the parameters remains after the models have been adapted to available data, a ubiquitous problem in many real‐world applications. Our workflow is exemplified on an enzyme‐catalyzed two‐substrate reaction mechanism describing the symmetric carboligation of 3,5‐dimethoxy‐benzaldehyde to (R)‐3,3′,5,5′‐tetramethoxybenzoin catalyzed by benzaldehyde lyase from Pseudomonas fluorescens. Results indicate a substrate‐dependent inactivation of enzyme, which is in accordance with other recent studies.

  • 155.
    Ekblad, Torun
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Chemical Synthesis of Affibody Molecules for Protein Detection and Molecular Imaging2008Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Proteins are essential components in most processes in living organisms. The detection and quantification of specific proteins can be used e.g. as measures of certain physiological conditions, and are therefore of great importance. This thesis focuses on development of affinity-based bioassays for specific protein detection. The use of Affibody molecules for specific molecular recognition has been central in all studies in this thesis. Affibody molecules are affinity proteins developed by combinatorial protein engineering of the 58-residue protein A-derived Z domain scaffold. In the first paper, solid phase peptide synthesis is investigated as a method to generate functional Affibody molecules. Based on the results from this paper, chemical synthesis has been used throughout the following papers to produce Affibody molecules tailored with functional groups for protein detection applications in vitro and in vivo.

     

    In paper I, an orthogonal protection scheme was developed to enable site-specific chemical introduction of three different functional probes into synthetic Affibody molecules. Two of the probes were fluorophores that were used in a FRET-based binding assay to detect unlabeled target proteins. The third probe was biotin, which was used as an affinity handle for immobilization onto a solid support. In paper II, a panel of Affibody molecules carrying different affinity handles were synthesized and evaluated as capture ligands on microarrays. Paper III describes the synthesis of an Affibody molecule that binds to the human epidermal growth factor receptor type 2, (HER2), and the site-specific incorporation of a mercaptoacetyl-glycylglycylglycine (MAG3) chelating site in the peptide sequence to allow for radiolabeling with 99mTc. The derivatized Affibody molecule was found to retain its binding capacity, and the 99mTc-labeling was efficient and resulted in a stable chelate formation. 99mTc-labeled Affibody molecules were evaluated as in vivo HER2-targeting imaging agents in mice. In the following studies, reported in papers IV-VI, the 99mTc-chelating sequence was engineered in order to optimize the pharmacokinetic properties of the radiolabeled Affibody molecules and allow for high-contrast imaging of HER2-expressing tumors and metastatic lesions. The main conclusion from these investigations is that the biodistribution of Affibody molecules can be dramatically modified by amino acid substitutions directed to residues in the MAG3-chelator. Finally, paper VII is a report on the chemical synthesis and chemoselective ligation to generate a cross-linked HER2-binding Affibody molecule with improved thermal stability and tumor targeting capacity.

     

    Taken together, the studies presented in this thesis illustrate how peptide synthesis can be used for production and modification of small affinity proteins, such as Affibody molecules for protein detection applications.

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    FULLTEXT02
  • 156. Ekman, M.
    et al.
    Björlenius, Berndt
    Stockholm Water Co.
    Andersson, M.
    Control of the aeration volume in an activated sludge process using supervisory control strategies2006In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 40, no 8, p. 1668-1676Article in journal (Refereed)
    Abstract [en]

    In this paper, a simulation benchmark of a pre-denitrifying activated sludge process is utilized in order to evaluate a supervisory aeration volume control strategy. The aeration volume control strategy has also been evaluated in a pilot plant at Hammarby Sjostad in Stockholm, Sweden. The main idea has been to let the dissolved oxygen (DO) concentration in some of the aerated compartments be determined by a higher level controller driven by the DO concentration in other compartments. In this way, only sensors for measuring the DO concentrations are needed for the decision of time varying DO set-points. The high reliability of such sensors implies robust input values for the proposed control strategy. Moreover, it is known that the respiration rate is affected by the content of substrate and nitrogen in the compartments; therefore, the suggested manipulations of the DO set-points are indirectly determined by the current load into the plant. Compared to constant DO control and a supervisory DO set-point control strategy based on ammonium measurements in the last aerobic compartment, the suggested aeration volume control strategy could reduce the effluent nitrate and ammonium concentrations significantly without increasing the aeration energy.

  • 157.
    Elmlund, Dominika
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Towards unbiased 3D reconstruction: in single-particle cryo-electron microscopy2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Cryo-electron microscopy of freestanding molecules (single-particles) plays a pivotal role in the difficult and pressing challenge of determining the structures of large macromolecular complexes. Molecular volumes are generated by aligning large sets of randomly oriented two-dimensional (2D) projection images in three dimensions (3D) before reconstruction is performed using tomographic techniques. The increasing popularity of the single-particle method is highly correlated with technical advances in instrumentation and computation. This thesis introduces new computational methods for 3D structure determination from electron microscopic projection images of single molecules. The algorithms have been developed to fill a gap in the single particle methodology – the lack of methods for ab initio 3D reconstruction of asymmetrical or low-symmetry molecules co-existing in different functional states. The proposed approach does not rely on a priori information about the structure or the character of the sample heterogeneity, which minimizes template dependence and makes the methods applicable to a wide range of single molecules. The presented algorithms constitute the basis of a new open source software package - SIMPLE (Single-particle IMage Processing Linux Engine). SIMPLE is an efficient and easy-to-use image processing system for semi-automated ab initio 3D reconstruction from challenging single-particle data sets (asymmetrical particles, significant degree of heterogeneity).

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    FULLTEXT01
  • 158. El-Seedi, H. R.
    et al.
    Khalifa, S. A. M.
    Taher, Eman A.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Farag, M. A.
    Saeed, A.
    Gamal, M.
    Hegazy, M. -EF.
    Youssef, D.
    Musharraf, S. G.
    Alajlani, M. M.
    Xiao, J.
    Efferth, T.
    Cardenolides: Insights from chemical structure and pharmacological utility2019In: Pharmacological Research, ISSN 1043-6618, E-ISSN 1096-1186, Vol. 141, p. 123-175Article in journal (Refereed)
    Abstract [en]

    Cardiac glycosides (CGs) are a class of naturally occurring steroid-like compounds, and members of this class have been in clinical use for more than 1500 years. They have been used in folk medicine as arrow poisons, abortifacients, heart tonics, emetics, and diuretics as well as in other applications. The major use of CGs today is based on their ability to inhibit the membrane-bound Na + /K + -ATPase enzyme, and they are regarded as an effective treatment for congestive heart failure (CHF), cardiac arrhythmia and atrial fibrillation. Furthermore, increasing evidence has indicated the potential cytotoxic effects of CGs against various types of cancer. In this review, we highlight some of the structural features of this class of natural products that are crucial for their efficacy, some methods of isolating these compounds from natural resources, and the structural elucidation tools that have been used. We also describe their physicochemical properties and several modern biotechnological approaches for preparing CGs that do not require plant sources.

  • 159.
    Enefalk, Tommy
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Industrial Ecology.
    Ersöz, Timur
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Industrial Ecology.
    Optimal rening av biogas för småskalig produktion och användning: En studie om energioptimering av biogasanläggningar2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Biogas is a renewable fuel, and the demand for this particular fuel type is increasing around the world. In order to use biogas as a fuel for vehicles it must first be upgraded from its raw state. By separation of carbon dioxide and other impurities, the methane content in the raw biogas is increased so that the biogas can be used in engines. Several methods of purification exist, but this report mainly focuses on water scrubbing. This thesis aims to investigate the optimal methane content in biogas with respect to net energy and the lifespan of the engines that are being fueled with biogas. The focus of the report is on the purification process in biogas production for small to medium sized farms. The thesis is conducted by putting up an energy balance formula for the components in the biogas production system. This formula was used for creating a mathematical model of the system, and the calculations were made with the computer programme Matlab. The optimal methane content in the biogas was found to be around 80 % (78 – 83 %), which is less than the lower limit (85 %) that is recommended by other sources. The purification facility’s own energy demand corresponds to 2,5 – 8,6 % of the energy content in the biogas, depending on whether high pressure compression is used or not. These results are highly consistent with previous research. The methane content of the biogas does not reduce the lifespan of the engines notably, but there is a risk of ignition failures which could lead to damages in the catalyzer. Since the optimal methane content is lower than 85 %, it would be appropriate to test the biogas in order to analyze if it is suitable to be used as a fuel. The results are heavily influenced by the engine efficiency, which is also a relevant subject for future work. 

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    fulltext
  • 160.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Affinity Tag Purification Method and Immobilization of the Promiscuous Enzyme Alanine Racemase2006Conference paper (Refereed)
  • 161.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Affinity Tag Purification Method of the Promiscuous Enzyme Alanine Racemase2006In: Book of abstracts, 2006Conference paper (Other academic)
  • 162.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Immobilization Method for the Promiscuous Enzyme Alanine Racemase2007In: BIOTRANS Oviedo 2007 / [ed] Vicente Gotor, 2007Conference paper (Refereed)
  • 163.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Branneby, Cecilia
    Cambrex Karlskoga AB.
    Sjöstrand, Ulf
    Cambrex Karlskoga AB.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    High Yield Transamination with Isopropyl Amine as Donor, by Employment of YADH and in situ Cofactor Regeneration2009Conference paper (Refereed)
  • 164.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Branneby, Cecilia
    Cambrex Karlskoga AB.
    Sjöstrand, Ulf
    Cambrex Karlskoga AB.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    High Yield Transamination with Isopropyl Amine as Donor, by Employment of YADH and in situ Cofactor Regeneration2009In: Book of abstracts, 2009Conference paper (Refereed)
  • 165.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Kourist, Robert
    University of Greifswald, Germany.
    Lindberg, Diana
    Uppsala university, SE.
    Wittrup Larsen, Marianne
    KTH, School of Biotechnology (BIO), Biochemistry.
    Widersten, Mikael
    Uppsala university, SE.
    Bornscheuer, Uwe T
    University of Greifswald, DE.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    A One Step Enzyme Extraction and Immobilization Method for Organic and Aqueous Solvents2008In: Biocat2008 / [ed] Ralf Grote, Garabed Antranikian, Hamburg, Germany: TuTech Innovation GmbH , 2008Conference paper (Refereed)
  • 166.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Kourist, Robert
    University of Greifswald, Germany.
    Lindberg, Diana
    Uppsala university, SE.
    Wittrup Larsen, Marianne
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Widersten, Mikael
    Uppsala university, SE.
    Bornscheuer, Uwe T
    University of Greifswald, DE.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    A One Step General Enzyme Immobilization Method for Organic and Aqueous Solvents2008In: Book of Abstracts, 2008Conference paper (Refereed)
  • 167.
    Engelmark Cassimjee, Karim
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Svedendahl, Maria
    KTH, School of Biotechnology (BIO), Biochemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Rational Redesign of omega-Transaminase2010In: Biocat2010, Hamburg, Germany: TuTech Verlag , 2010Conference paper (Refereed)
  • 168.
    Engvall, Klas
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Chemical Technology.
    Liliedahl, Truls
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Chemical Technology.
    Dahlquist, E.
    Biomass and black liquor gasification2013In: Technologies for Converting Biomass to Useful Energy: Combustion, Gasification, Pyrolysis, Torrefaction and Fermentation, CRC Press , 2013, p. 175-216Chapter in book (Other academic)
    Abstract [en]

    Modern society is profoundly dependent on fossil feed stocks to produce multiple products, such as transportation fuels, fine chemicals, pharmaceuticals, detergents, synthetic fibers, plastics, fertilizers, lubricants, solvents, waxes, etc., as well as heat and power (Demirbas, 2006). The fossil resources are not endless. Their price is increasing continuously due to increasing scarcity, and not regarded as sustainable from an environmental point of view (Kamm, 2006). A versatile resource, especially in terms of producing carbon-based products, to replace fossil feedstocks is biomass (Vlachos, 2010) or other sources originating form biomass, such as black liquor (BL). Conversion of biomass to other products can be performed either by biochemical or thermochemical processes. In the case of large-scale production of, for example, carbon-based products, thermo-chemical conversion is considered more efficient compared to biochemical processes (Zhang, 2010). Techniques for thermo-chemical conversion can be divided into pyrolysis, gasification, combustion and liquefaction. Among these techniques, gasification is a versatile platform for production of multiple products, as illustrated in Figure 6.1. 

  • 169.
    Eriksson, Cecilia
    et al.
    KTH, School of Biotechnology (BIO), Proteomics.
    Agaton, Charlotta
    KTH, School of Biotechnology (BIO).
    Kånge, Rikard
    Sundberg, Marten
    KTH, School of Biotechnology (BIO).
    Nilsson, Peter
    KTH, School of Biotechnology (BIO).
    Ek, Bo
    Uhlen, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Gustafsson, Magnus
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics.
    Microfluidic analysis of antibody specificity in a compact disk format2006In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 5, no 7, p. 1568-1574Article in journal (Refereed)
    Abstract [en]

    A new and flexible technology for high throughput analysis of antibody specificity and affinity is presented. The method is based on microfluidics and takes advantage of compact disks (CDs) in which the centrifugal force moves fluids through microstructures containing immobilized metal affinity chromatography columns. Analyses are performed as a sandwich assay, where antigen is captured to the column via a genetically attached His(6)-tag. The antibodies to be analyzed are applied onto the columns. Thereafter, fluorescently labeled secondary antibodies recognize the bound primary antibodies, and detection is carried out by laser-induced fluorescence. The CDs contain 104 microstructures enabling analysis of antibodies against more than 100 different proteins using a single CD. Importantly, through the three- dimensional visualization of the binding patterns in a column it is possible to separate high affinity from low affinity binding. The method presented here is shown to be very sensitive, flexible and reproducible.

  • 170.
    Eriksson, Cecilia
    et al.
    KTH, School of Biotechnology (BIO), Proteomics.
    Pereira, R. A.
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics.
    Towards an immunobased tool for the qualification of bookmarker candidates-compact disk enclosed nanocolumns with orientation-immobilized monospecific antibodies.Article in journal (Other academic)
  • 171.
    Eriksson, Cecilia
    et al.
    KTH, School of Biotechnology (BIO), Proteomics.
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO), Proteomics.
    Sjöberg, A.
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics.
    Affibody molecule mediated depletion of HSA and IgG performed in singlet or in a rapid high throughput format2009Article in journal (Other academic)
  • 172.
    Eriksson, Cecilia
    et al.
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Sjöberg, Anna
    KTH, School of Biotechnology (BIO).
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Affibody molecule-mediated depletion of HSA and IgG using different buffer compositions: a 15 min protocol for parallel processing of 1-48 samples2010In: Biotechnology and applied biochemistry, ISSN 0885-4513, E-ISSN 1470-8744, Vol. 56, p. 49-57Article in journal (Refereed)
    Abstract [en]

    High-abundant plasma proteins pose a challenge in a large number of proteomics-based technologies. Depletion of these high-abundant proteins has proven to be a fruitful strategy to circumvent masking of lower-abundant proteins that could serve as valuable biomarker candidates. However, current strategies often do not meet the throughput requirements of large-scale proteomic studies. In the present paper, a flexible and parallelized method for the depletion of high-abundant proteins is described, allowing the removal of the two most abundant proteins from 48 blood-derived samples in less than 15 min using Affibody molecules as affinity ligands. A sample-processing platform like this should be suitable for a number of proteomics technologies; its flexibility in buffer composition allows for different types of downstream applications.

  • 173.
    Eriksson, Ulrika
    KTH, School of Biotechnology (BIO).
    Impact of autocrine factors on physiology and productivity in Trichoplusia ni serum-free cultures2005Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    The aim of this study was to increase the understanding of the mechanisms regulating cell proliferation and recombinant protein production in serum-free cultures of Trichoplusia ni (T. ni) insect cells.

    Conditioned medium (CM) was shown to contain both stimulatory and inhibitory factors (CM factors) influencing cell growth. Metalloproteinase (MP) activity was the major factor responsible for the growth stimulating effect of CM as shown by using the specific MP inhibitor DL-thiorphan. MPs may exist in several different molecular mass forms due to autoproteolysis. Although the main band of the MP was determined to be around 48 kDa, precursor forms above 48 kDa as well as autocatalytic degradation products below the main band could be observed. It is not clear whether all forms of the MP or just the main band is involved in the growth regulation. Further, a proteinase inhibitor could be identified in the inhibitory fraction. Thus, we speculate that the proteinase inhibitor may be part of an autocrine system regulating cell proliferation.

    Analysis of the cell cycle phase distribution revealed a high proportion of cells in the G1 (80-90 %) and a low proportion of cells in the S and G2/M phases (10-20 %) during the whole culture, indicating that S and G2/M are short relative to G1. After inoculation, a drastic decrease in the S phase population together with a simultaneous increase of cells in G1 and G2/M could be observed as a lagphase on the growth curve and this may be interpreted as a temporary replication stop. When the cells were released from the initial arrest, the S phase population gradually increased again. This was initiated earlier in CM-supplemented cultures, and agrees with the earlier increase in cell concentration. Thus, these data suggests a correlation between CM factors and the cell cycle dynamics.

    In cultures supplied with CM, a clear positive effect on specific productivity was observed, with a 30 % increase in per cell productivity. The specific productivity was also maintained at a high level much longer time than in fresh-medium cultures. The positive effect observed after 20 h coincided with the time a stimulatory effect on cell growth first was seen. Thus, the productivity may be determined by the proliferation potential of the culture. A consequence of this would be that the secreted MP indirectly affects productivity.

    Finally, the yeast extract from Express Five SFM contains factors up to 35 kDa which are essential for T. ni cell growth. The optimal concentration was determined to be 2.5-fold that in normal medium, while higher concentrations were inhibitory. However although vital, they were not solely responsible for the growth-enhancing effect, as some other, more general, component present in yeast extract was needed for proliferation as well.

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    FULLTEXT01
  • 174.
    Eriksson, Ulrika
    et al.
    KTH, School of Biotechnology (BIO), Bioprocess Technology (closed 20130101).
    Hassel, Jenny
    Lüllau, Elke
    Häggström, Lena
    KTH, School of Biotechnology (BIO), Bioprocess Technology (closed 20130101).
    Metalloproteinase activity is the sole factor responsible for the growth-promoting effect of conditioned medium in Trichoplusia ni insect cell cultures2005In: Journal of Biotechnology, ISSN 0168-1656, E-ISSN 1873-4863, Vol. 119, no 1, p. 76-86Article in journal (Refereed)
    Abstract [en]

    Conditioned medium (CM) taken from a serum-free culture of Trichoplusia ni (BTI-Tn-5B 1-4, High Five) cells on days 2 and 3, shortened the lagphase and increased the maximum cell density when added to T ni cultures with low-inoculum cell density. Gel filtration fractions of CM, eluting at around 45 kDa, stimulated cell proliferation even better than CM. A protein in the gel filtration fraction was identified by N-terminal amino acid sequencing as a proteinase, related to a snake venom metalloproteinase. Casein zymography showed, multiple metalloproteinase bands between 48 and 25 kDa, as well as precursor forms above 48 kDa. Metalloproteinase bands below the main band at 48 kDa were autocatalytic degradation products. Metalloproteinase activity was the sole factor responsible for the growth stimulating effect of CM as shown by using the specific metalloproteinase inhibitor DL-thiorphan. Metalloproteinases have recently been shown to release growth factors from sequestering extracellular proteins. We propose that the metalloproteinase is involved in autocrine regulation of T ni proliferation in serum-free media. In addition, a gel filtration fraction of CM, eluting at about 10 kDa, inhibited cell growth. Apart from a lysozyme precursor protein and a cyclophilin-like protein, a kazal-type proteinase inhibitor could be identified in this fraction.

  • 175.
    Eriksson, Ulrika
    et al.
    KTH, School of Biotechnology (BIO), Bioprocess Technology (closed 20130101).
    Häggström, Lena
    KTH, School of Biotechnology (BIO), Bioprocess Technology (closed 20130101).
    Yeast extract from express five serum-free medium contains factors at about 35 kDa, essential for growth of Trichoplusia ni insect cells2005In: Biotechnology letters, ISSN 0141-5492, E-ISSN 1573-6776, Vol. 27, no 20, p. 1623-1627Article in journal (Refereed)
    Abstract [en]

    The yeast extract (of unknown origin) present in the commercially available serum-free medium 'Express Five' contains factors ('yeast extract factors') up to 35 kDa which are essential for growth of Trichoplusia ni insect cells. A yeast extract brand lacking these components could not support growth of T. ni cells. However, cell proliferation was restored by adding chromatographic fractions containing the yeast extract factors. The yeast extract factors were not solely responsible for the growth enhancing effect of yeast extract but some other components, which seem to be generally present in yeast extracts, are also required for T. ni proliferation.

  • 176.
    Evangelopoulos, Panagiotis
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Kantarelis, Efthymios
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology.
    Yang, Weihong
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Experimental Investigation of Pyrolysis of Printed Circuit Boards for Energy and Materials Recovery under Nitrogen and Steam Atmosphere2017In: 8th International Conference on Applied Energy, ICAE 2016; Beijing; China; 8 October 2016 through 11 October 2016, Elsevier, 2017, Vol. 105, p. 986-991Conference paper (Refereed)
    Abstract [en]

    Printed circuit boards (PCB) are one of the most challenging fractions of e-waste in terms of material recycling and energy recovery. In this study, pyrolysis of PCBs in inert and steam atmosphere has been investigated as a valuable alternative for energy recovery of the organic fraction with simultaneous recycling of metals. The decomposition of two different PCB fractions has been investigated by means of thermogravimetric analysis (TGA) and lab scale pyrolysis experiments in steam and nitrogen atmospheres. The composition of the gas obtained from the pyrolysis experiments was strongly influenced by the reactive atmosphere. The characterization of the solid residue by X-ray Powder Diffraction (XRD) and scanning electron microscopy (SEM) showed high influence of steam to the migration of the antimony in the produced vapors.

  • 177.
    Fagerberg, Linn
    et al.
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Sandler, Charlotte
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Skogs, Marie
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hjelmare, Martin
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Jonasson, Kalle
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Wiking, Mikaela
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Åbergh, Annica
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mapping the subcellular protein distribution in three human cell lines2011In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 10, no 8, p. 3766-3777Article in journal (Refereed)
    Abstract [en]

    The subcellular locations of proteins are closely related to their function and constitute an essential aspect for understanding the complex machinery of living cells. A systematic effort has been initiated to map the protein distribution in three functionally different cell lines with the aim to provide a subcellular localization index for at least one representative protein from all human protein-encoding genes. Here, we present the results of over 4,000 proteins mapped to 16 subcellular compartments. The results indicate a ubiquitous protein expression with a majority of the proteins found in all three cell lines and a large portion localized to two or more compartments. The inter-relationships between the subcellular compartments are visualized in a protein-compartment network based on all detected proteins. Hierarchical clustering was performed to determine how closely related the organelles are in terms of protein constituents and compare the proteins detected in each cell type. Our results show distinct organelle proteomes, well conserved across the cell types, and demonstrate that biochemically similar organelles are grouped together.

  • 178.
    Fagerberg, Linn
    et al.
    KTH, School of Biotechnology (BIO), Proteomics.
    Strömberg, Sara
    El-Obeid, Adila
    Gry, Marcus
    KTH, School of Biotechnology (BIO), Proteomics.
    Nilsson, Kenneth
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Ponten, Fredrik
    Adplund, Anna
    The Global Protein Expression Pattern in Human Cell LinesManuscript (preprint) (Other academic)
    Abstract [en]

    Human cancer cell lines grown in vitro are frequently used to decipher basic cell biological phenomena but also to specifically study different forms of cancer. Here we present the first large-scale study of protein expression patterns in cell lines using an antibody-based proteomics approach. We analyzed the expression pattern of 5436 proteins in 45 different cell lines using hierarchical clustering, principal component analysis and two-group comparisons for the identification of differentially expressed proteins. The results show that protein profiles of cell lines, as determined using immunohistochemistry, allow for a hierarchical clustering that overall reflects tumor tissues of origin. Hematological cell lines appear to retain their protein profiles to a higher degree than cell lines established from solid tumors, resulting in a clustering that well reflects progenitor cell types. The discrepancy may reflect different levels of in vitro induced alterations in adherent and suspension grown cell lines, respectively. In addition, multiple myeloma cells and cells of myeloid origin were found to share a protein profile, relative the protein profile of lymphoid leukemia and lymphoma cells, possibly reflecting their common dependency of bone marrow microenvironment.

     

  • 179.
    Falk, Ronny
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Ramström, Margareta
    KTH, School of Biotechnology (BIO), Proteomics.
    Eriksson, Cecilia
    KTH, School of Biotechnology (BIO), Proteomics.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Wernérus, Henrik
    KTH, School of Biotechnology (BIO), Proteomics.
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics.
    Targeted protein pullout from human tissue samples using competitive elution2011In: Biotechnology Journal, ISSN 1860-6768, Vol. 6, no 1, p. 28-37Article in journal (Refereed)
    Abstract [en]

    One commonly used strategy to gain information on the proteins in a cell is to isolate the proteins of interest by specific binders, often antibodies. Not only the specificity of the capturing antibodies but also the washing and elution conditions are crucial to avoid false-positive protein identifications. Eluting the target protein from the matrix, while avoiding the release of unrelated background proteins, should both provide more correct information on the target protein and its interaction partners, and minimize the effort to perform downstream analyses through the reduced number of eluted proteins. In this study, a novel approach for selective protein pullout is presented. Monospecific antibodies were used to selectively pullout target proteins from a complex biosample. Subsequently, the target proteins were competitively eluted from the affinity media with the recombinant antigen. To deplete the antigen from the eluted sample, I MAC spin columns were utilized to bind the N-terminal His-tag of the antigens. The competitive elution method was applied both to a model system, and for the extraction of a native human target protein. In the model system the recombinant target protein BBC7 was spiked into a protein extract of human liver, whereas an endogenously expressed target protein, cTAGE5, was extracted from the liver extract directly. SDS-PAGE analysis and mass spectrometry confirmed affinity isolation of expected target proteins. More selective elution was obtained using the competitive procedure as compared to elution at low pH. Competitive elution has thus been shown to offer an effective approach for wide-scale pullout experiments where proteins and their interaction partners are to be studied.

  • 180.
    Fasterius, Erik
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Exploring genetic heterogeneity in cancer using high-throughput DNA and RNA sequencing2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    High-throughput sequencing (HTS) technology has revolutionised the biomedical sciences, where it is used to analyse the genetic makeup and gene expression patterns of both primary patient tissue samples and models cultivated in vitro. This makes it especially useful for research on cancer, a disease that is characterised by its deadliness and genetic heterogeneity. This inherent genetic variation is an important aspect that warrants exploration, and the depth and breadth that HTS possesses makes it well-suited to investigate this facet of cancer.

    The types of analyses that may be accomplished with HTS technologies are many, but they may be divided into two groups: those that analyse the DNA of the sample in question, and those that work on the RNA. While DNA-based methods give information regarding the genetic landscape of the sample, RNA-based analyses yield data regarding gene expression patterns; both of these methods have already been used to investigate the heterogeneity present in cancer. While RNA-based methods are traditionally used exclusively for expression analyses, the data they yield may also be utilised to investigate the genetic variation present in the samples. This type of RNA-based analysis is seldom performed, however, and valuable information is thus ignored.

    The aim of this thesis is the development and application of DNA- and RNA- based HTS methods for analysing genetic heterogeneity within the context of cancer. The present investigation demonstrates that not only may RNA-based sequencing be used to successfully differentiate different in vitro cancer models through their genetic makeup, but that this may also be done for primary patient data. A pipeline for these types of analyses is established and evaluated, showing it to be both robust to several technical parameters as well as possess a broad scope of analytical possibilities. Genetic variation within cancer models in public databases are evaluated and demonstrated to affect gene expression in several cases. Both inter- and intra-patient genetic heterogeneity is shown using the established pipeline, in addition to demonstrating that cancerous cells are more heterogeneous than their normal neighbours. Finally, two bioinformatic open source software packages are presented.

    The results presented herein demonstrate that genetic analyses using RNA-based methods represent excellent complements to already existing DNA-based techniques, and further increase the already large scope of how HTS technologies may be utilised.

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    PhD Thesis Erik Fasterius
  • 181. Fernández-Niño, Miguel
    et al.
    Pulido, Sergio
    Stefanoska, Despina
    Pérez, Camilo
    González-Ramos, Daniel
    van Maris, Antonius JA
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Marchal, Kathleen
    Nevoigt, Elke
    Swinnen, Steve
    Identification of novel genes involved in acetic acid tolerance of Saccharomyces cerevisiae using pooled-segregant RNA sequencing2018In: FEMS yeast research, Vol. 18, no 8Article in journal (Refereed)
    Abstract [en]

    Acetic acid tolerance of the yeast Saccharomyces cerevisiae is manifested in several quantifiable parameters, of which the duration of the latency phase is one of the most studied. It has been shown recently that the latter parameter is mostly determined by a fraction of cells within the population that resumes proliferation upon exposure to acetic acid. The aim of the current study was to identify genetic determinants of the difference in this parameter between the highly tolerant strain MUCL 11987-9 and the laboratory strain CEN. PK113-7D. To this end, a combination of genetic mapping and pooled-segregant RNA sequencing was applied as a new approach. The genetic mapping data revealed four loci with a strong linkage to strain MUCL 11987-9, each containing still a large number of genes making the identification of the causal ones by traditional methods a laborious task. The genes were therefore prioritized by pooled-segregant RNA sequencing, which resulted in the identification of six genes within the identified loci showing differential expression. The relevance of the prioritized genes for the phenotype was verified by reciprocal hemizygosity analysis. Our data revealed the genes ESP1 and MET22 as two, so far unknown, genetic determinants of the size of the fraction of cells resuming proliferation upon exposure to acetic acid.

  • 182. Filonova, Lada
    et al.
    Kallas, Åsa M.
    KTH, School of Biotechnology (BIO).
    Greffe, Lionel
    KTH, School of Biotechnology (BIO).
    Teeri, Tuula T.
    Daniel, Geoffrey
    Johansson, Gunnar
    Mapping of crystalline cellulose and mannan on the surfaces of wood tissues and pulp fibers using carbohydrate binding modules2007In: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 8, no 1, p. 91-97Article in journal (Refereed)
    Abstract [en]

    Carbohydrate binding modules (CBMs) are noncatalytic substrate binding domains of many enzymes involved in carbohydrate metabolism. Here we used fluorescent labeled recombinant CBMs specific for crystalline cellulose (CBM1(HjCel7A)) and mannans (CBM27(TmMan5) and CBM35(CjMan5C)) to analyze the complex surfaces of wood tissues and pulp fibers. The crystalline cellulose CBM1(HjCel7A) was found as a reliable marker of both bacterially produced and plant G-layer cellulose, and labeling of spruce pulp fibers with CBM1(HjCel7A) revealed a signal that increased with degree of fiber damage. The mannan-specific CBM27(TmMan5) and CBM35(CjMan5C) CBMs were found to be more specific reagents than a monoclonal antibody specific for (1 -> 4)-beta-mannan/galacto-(1 -> 4)-beta-mannan for mapping carbohydrates on native substrates. We have developed a quantitative fluorometric method for analysis of crystalline cellulose accumulation on fiber surfaces and shown a quantitative difference in crystalline cellulose binding sites in differently processed pulp fibers. Our results indicated that CBMs provide useful, novel tools for monitoring changes in carbohydrate content of nonuniform substrate surfaces, for example, during wood or pulping processes and possibly fiber biosynthesis.

  • 183. Fink, Helen
    et al.
    Ahrenstedt, Lage
    KTH, School of Biotechnology (BIO), Glycoscience.
    Bodin, Aase
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Gatenholm, Paul
    Krettek, Alexandra
    Risberg, Bo
    Bacterial cellulose modified with xyloglucan bearing the adhesion peptide RGD promotes endothelial cell adhesion and metabolism - a promising modification for vascular grafts2011In: Journal of Tissue Engineering and Regenerative Medicine, ISSN 1932-6254, Vol. 5, no 6, p. 454-463Article in journal (Refereed)
    Abstract [en]

    Today, biomaterials such as polytetrafluorethylene (ePTFE) are used clinically as prosthetic grafts for vascular surgery of large vessels (>5 mm). In small diameter vessels, however, their performance is poor due to early thrombosis. Bacterial-derived cellulose (BC) is a new promising material as a replacement for blood vessels. This material is highly biocompatible in vivo but shows poor cell adhesion. In the native blood vessel, the endothelium creates a smooth non-thrombogenic surface. In order to sustain cell adhesion, BC has to be modified. With a novel xyloglucan (XG) glycoconjugate method, it is possible to introduce the cell adhesion peptide RGD (Arg-Gly-Asp) onto bacterial cellulose. The advantage of the XG-technique is that it is an easy one-step procedure carried out in water and it does not weaken or alter the fiber structure of the hydrogel. In this study, BC was modified with XG and XGRGD to asses primary human vascular endothelial cell adhesion, proliferation, and metabolism as compared with unmodified BC. This XG-RGD-modification significantly increased cell adhesion and the metabolism of seeded primary endothelial cells as compared with unmodified BC whereas the proliferation rate was affected only to some extent. The introduction of an RGD-peptide to the BC surface further resulted in enhanced cell spreading with more pronounced stress fiber formation and mature phenotype. This makes BC together with the XG-method a promising material for synthetic grafts in vascular surgery and cardiovascular research.

  • 184.
    Finnveden, Maja
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Enzyme catalysis towards bio-based UV-curable buildingblocks2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Polymeric materials are found in virtually all areas of daily life; they are found in everything from packages keeping our food safe to the buildings where we spend our days, and the production is a worldwide industry. Although polymeric materials play a big part in sustainable solution’s, a lot can be done to develop more environmental methods for producing them. Both the process conditions and the resources that go in are important to consider. As more people understand that we need to manage our planet’s resources and ecosystem differently the demand for sustainable materials is increasing.

    Catalysis is a key for designing chemistry for the environment and an interesting alternative is enzyme catalysis. Enzymes are proteins working as catalysts in biochemical reactions. One of the most prominent features of enzymes’ is their selectivity, which means that they have preferences towards forming one product over others. Using enzymes’ as catalysts in synthetic chemical reactions the selectivity can be used to produce a wide range of products without side reaction occurring. Further benefits of using enzyme catalysis include high rate acceleration and working under mild reaction conditions.

    In the work presented here the selectivity and efficiency of enzymes have been combined with photochemistry in new efficient methods for the synthesis ofpolymeric materials. The enzymes used were the well-known lipase B form Candida antarctica and an esterase/acyltransferase from Mycobacterium smegmatis.

    The thesis divides into three parts in which three kinds of components were synthesized by enzyme catalysis: (i) unsaturated polyesters; (ii) vinyl ether building-blocks; and (iii) bio-based polyamides. In the first two parts the efficiency and selectivity of enzyme catalysis at low temperatures were utilized to synthesize building-blocks that can be further used for photopolymerization. By using enzyme catalysis structures that can be difficult or even impossible to access with conventional chemistry have been made. In part (iii) photochemistry was used to synthesize a monomer that was polymerized by enzyme catalysis to produce polyamides.

    All three parts presented in this thesis show the potential of the combination of enzymes and photochemistry to give access to polymeric materials under benign conditions. The work thus advances the capacity to manufacture building-blocks to create new sustainable polymeric materials.

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    Enzyme catalysis towards bio-based UV-curable buildingblocks
  • 185.
    Finnveden, Maja
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology. KTH Royal Institute of Technology.
    Hendil-Forssell, Peter
    Claudino, Mauro
    Johansson, Mats
    KTH, Superseded Departments (pre-2005), Fibre and Polymer Technology.
    Martinelle, Mats
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Lipase Catalyzed Synthesis of renewable plant oil-based polyamidesManuscript (preprint) (Other academic)
    Abstract [en]

    Enzyme catalyzed synthesis towards renewable polyamides was investigated using Candida antarctica lipase B. A fatty acid-derived AB-type functional monomer, having one amine and one methyl ester functionality was homopolymerized at 80 and 140°C. Additionally, the organobase 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) was used as catalyst. The results from the two catalysts were comparable. However, the amount of lipase added was 1200 times lower showing that the lipase was a more efficient catalyst for this system as compared to TBD. Moreover, the AB type monomer was copolymerized with 1,12-diaminododecan to synthesize oligoamides of two different lengths.

  • 186.
    Finnveden, Maja
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Hendil-Forssell, Peter
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Claudino, Mauro
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Johansson, Mats
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Martinelle, Mats
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Lipase-Catalyzed Synthesis of Renewable Plant Oil-Based Polyamides.2019In: Polymers, ISSN 2073-4360, E-ISSN 2073-4360, Vol. 11, no 11, article id 1730Article in journal (Refereed)
    Abstract [en]

    Enzyme catalyzed synthesis of renewable polyamides was investigated using Candida antarctica lipase B. A fatty acid-derived AB-type functional monomer, having one amine and one methyl ester functionality, was homopolymerized at 80 and 140 °C. Additionally, the organobase 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) was used as a catalyst. The results from the two catalysts were comparable. However, the amount of lipase added was 1.2 × 103 times lower, showing that the lipase was a more efficient catalyst for this system as compared to TBD. Moreover, the AB-type monomer was copolymerized with 1,12-diaminododecane to synthesize oligoamides of two different lengths.

  • 187. Fiorati, Andrea
    et al.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Svedendahl Humble, Maria
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Tessaro, Davide
    Application of Transaminases in a Disperse System for the Bioamination of Hydrophobic Substrates2020In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 362, no 5, p. 1156-1166Article in journal (Refereed)
    Abstract [en]

    Abstract The challenging bioamination of hydrophobic substrates has been attained through the employment of a disperse system consisting of a combination of a low polarity solvent (e. g. isooctane or methyl-tert-butylether), a non-ionic surfactant and a minimal amount of water. In these conditions, amine transaminases (ATA) were shown to efficiently carry out the reductive amination of variously substituted cyclohexanones, providing good conversions often coupled with a superior stereoselectivity if compared with the corresponding chemical reductive amination. An array of synthetically useful 4-substituted aminocyclohexanes was consequentially synthesized through biocatalysis, analyzed and stereochemically characterized.

  • 188.
    Fleetwood, Filippa
    et al.
    KTH, School of Biotechnology (BIO), Protein Technology.
    Klint, Susanne
    Hanze, Martin
    KTH, School of Biotechnology (BIO), Protein Technology.
    Gunneriusson, Elin
    Frejd, Fredrik
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Protein Technology.
    Löfblom, John
    KTH, School of Biotechnology (BIO), Protein Technology.
    Simultaneous targeting of two ligand-binding sites on VEGFR2 using biparatopic Affibody molecules results in dramatically improved affinity2014In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, p. 7518-Article in journal (Refereed)
    Abstract [en]

    Angiogenesis plays an important role in cancer and ophthalmic disorders such as age-related macular degeneration and diabetic retinopathy. The vascular endothelial growth factor (VEGF) family and corresponding receptors are regulators of angiogenesis and have been much investigated as therapeutic targets. The aim of this work was to generate antagonistic VEGFR2-specific affinity proteins having adjustable pharmacokinetic properties allowing for either therapy or molecular imaging. Two antagonistic Affibody molecules that were cross-reactive for human and murine VEGFR2 were selected by phage and bacterial display. Surprisingly, although both binders independently blocked VEGF-A binding, competition assays revealed interaction with non-overlapping epitopes on the receptor. Biparatopic molecules, comprising the two Affibody domains, were hence engineered to potentially increase affinity even further through avidity. Moreover, an albumin-binding domain was included for half-life extension in future in vivo experiments. The best-performing of the biparatopic constructs demonstrated up to 180-fold slower dissociation than the monomers. The new Affibody constructs were also able to specifically target VEGFR2 on human cells, while simultaneously binding to albumin, as well as inhibit VEGF-induced signaling. In summary, we have generated small antagonistic biparatopic Affibody molecules with high affinity for VEGFR2, which have potential for both future therapeutic and diagnostic purposes in angiogenesis-related diseases.

  • 189. Flyborg, L.
    et al.
    Björlenius, Berndt
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Persson, K. M.
    Identification of important physiochemical properties for removal of pharmaceutical residuals in treated wastewater by nanofiltration2013In: AMTA/AWWA Membrane Technology Conference and Exposition 2013, 2013, p. 68-73Conference paper (Refereed)
  • 190. Flyborg, L.
    et al.
    Björlenius, Berndt
    Water Resource Engineering, Lund University.
    Persson, K.M.
    Can treated municipal wastewater be reused after ozonation and nanofiltration?: Results from a pilot study of pharmaceutical remval in Henriksdal WWTP, Sweden2010In: Water Science and Technology, ISSN 0273-1223, E-ISSN 1996-9732, Vol. 61, no 5, p. 1113-1120Article in journal (Refereed)
    Abstract [en]

    The objective of this study was to evaluate the potential of nanofiltration (NF) and ozonation for indirect potable reuse in terms of pharmaceutical residuals. To simultaneously obtain a reasonable retentate volume for further treatment, the tests were performed at a high volume reduction factor (VRF) of 60. The feed to the pilot plant was the effluent from a BNR plant with a final process step of chemical precipitation and rapid sand filtration. Two tests were performed 1) nanofiltration of treated wastewater followed by ozonation and 2) ozonated treated wastewater as feed to NF. Of the 95 pharmaceuticals analysed, three were not removed to the quantification limit, oxazepam in the first test and glibenclamide and ketoprofen in the second. The water quality after the two processes was similar, with an overall removal of pharmaceutical residuals of 99%. There are two advantages of ozonated water as feed to NF-a higher specific flux of 35% and a potential removal of ozonation by-products. The retention of some pharmaceuticals by NF was lower than anticipated, the major removal occurring in the ozonation. A tighter NF or RO is required in order to achieve higher pharmaceutical retention for further treatment of the retentate.

  • 191.
    Fransson, Linda
    KTH, School of Biotechnology (BIO), Biochemistry.
    Enzyme substrate solvent interactions: a case study on serine hydrolases2008Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Reaction rates and selectivities were measured for transacylation of fatty acid esters in solvents catalysed by Candida antarctica lipase B and by cutinase from Humicola insolens. With these enzymes classical water-based enzymology can be expanded to many different solvents allowing large variations in interaction energies between the enzymes, the substrates and the surrounding. Further ,hydrolysis reactions catalysed by Bacillus subtilis esterase 2 were investigated.

    Thermodynamics analyses revealed that the enzyme contribution to reaction rate acceleration compared to acid catalysis was purely entropic. On the other hand, studies of differences in activation entropy and enthalpy between enantiomers and between homologous esters showed that high substrate specificity was favoured by enthalpic stabilisation.

    Solvent was found to have a profound effect on enzyme catalysis, affecting both reaction rate and selectivity. Differences in substrate solubility will impact enzyme specificity since substrate binding is an equilibrium between enzyme-bound substrate and substrate in free solution. In addition, solven tmolecules were found to act as enzyme inhibitors, showing both competitive and non-competitive behaviour.

    In several homologous data series enthalpy-entropy compensation relationships were encountered. A possible extrathermodynamic relationship between enthalpy and entropy can easily be lost under co-varying errors propagated from the experiments. From the data in this thesis, one instance was found of a real enthalpy-entropy compensation that could be distinguished from statistical errors, while other examples could not be verified.

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  • 192.
    Fransson, Linda
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Bernhardt, Peter
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    On the benefit of an active siteManuscript (preprint) (Other academic)
  • 193.
    Friedman, Mikaela
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Affibody molecules targeting the epidermal growth factor receptor for tumor imaging applications2008Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Tumor targeting and molecular imaging of protein markers specific for or overexpressed in tumors can add useful information in deciding upon treatment and assessing the response to treatment for a cancer patient. The epidermal growth factor receptor (EGFR) is one such tumor-associated receptor, which expression is abnormal or upregulated in various cancers and associated with a poor patient prognosis. It is therefore considered a good target for imaging and therapy. Monoclonal antibodies and recently also antibody fragments have been investigated for in vivo medical applications, like therapy and imaging. In molecular imaging a small sized targeting agent is favorable to give high contrast and therefore, antibody fragments and lately also small affinity proteins based on a scaffold structure constitute promising alternatives to monoclonal antibodies. Affbody molecules are such affinity proteins that are developed by combinatorial protein engineering of the 58 amino acid residue Z-domain scaffold, derived from protein A.

    In this thesis, novel Affibody molecules specific for the EGFR have been selected from a combinatorial library using phage display technology. Affibody molecules with moderate high affinity demonstrated specific binding to native EGFR on the EGFR-expressing epithelial carcinoma A431 cell line. Further cellular assays showed that the EGFR-binding Affibody molecules could be labeled with radiohalogens or radiometals with preserved specific binding to EGFR-expressing cells. In vitro, the Affibody molecule demonstrated a high uptake and good retention to EGFR-expressing cells and was found to internalize. Furthermore, successful imaging of tumors in tumor-bearing mice was demonstrated. Low nanomolar or subnanomolar affinities are considered to be desired for successful molecular imaging and a directed evolution to increase the affinity was thus performed. This resulted in an approximately 30-fold improvement in affinity, yielding EGFR-binding Affibody molecules with KD´s in the 5-10 nM range, and successful targeting of A431 tumors in tumor-bearing mice. To find a suitable format and labeling, monomeric and dimeric forms of one affinity matured binder were labeled with 125I and 111In. The radiometal-labeled monomeric construct, 111In-labeled-ZEGFR:1907, was found to provide the best tumor-to-organ ratio due to good tumor localization and tumor retention. The tumor-to-blood ratio, which is often used as a measure of contrast, was 31±8 at 24 h post injection and the tumor was clearly visualized by gamma-camera imaging.

    Altogether, the EGFR-binding Affibody molecule is considered a promising candidate for further development of tumor imaging tracers for EGFR-expressing tumors and metastases. This could simplify the stratification of patients for treatment and the assessment of the response of treatment in patients.

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  • 194.
    Friedman, Mikaela
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Lindström, Sara
    KTH, School of Biotechnology (BIO), Nano Biotechnology.
    Andersson-Svahn, Helene
    KTH, School of Biotechnology (BIO), Nano Biotechnology.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Engineering and characterization of a bispecific HER2 × EGFR-binding affibody molecule2009In: Biotechnology and applied biochemistry, ISSN 0885-4513, E-ISSN 1470-8744, Vol. 54, p. 121-131Article in journal (Refereed)
    Abstract [en]

    HER2 (human epidermal-growth-factor receptor-2; ErbB2) and EGFR (epidermal-growth-factor receptor) are overexpressed in various forms of cancer, and the co-expression of both HER2 and EGFR has been reported in a number of studies. The simultaneous targeting of HER2 and EGFR has been discussed as a strategy with which to potentially increase efficiency and selectivity in molecular imaging and therapy of certain cancers. In an effort to generate a molecule capable of bispecifically targeting HER2 and EGFR, a gene fragment encoding a bivalent HER2-binding affibody molecule was genetically fused in-frame with a bivalent EGFR-binding affibody molecule via a (G(4)S)(3) [(Gly(4)-Ser)(3)]-encoding gene fragment. The encoded 30 kDa affibody construct (Z(HER2))(2)-(G(4)S)(3)-(Z(EGFR))(2), with potential for bs (bispecific) binding to HER2 and EGFR, was expressed in Escherichia coli and characterized in terms of its binding capabilities. The retained ability to bind HER2 and EGFR separately was demonstrated using both biosensor technology and flow-cytometric analysis, the latter using HER2- and EGFR-overexpressing cells. Furthermore, simultaneous binding to HER2 and EGFR was demonstrated in: (i) a sandwich format employing real-time biospecific interaction analysis where the bs affibody molecule bound immobilized EGFR and soluble HER2; (ii) immunofluorescence microscopy, where the bs affibody molecule bound EGFR-overexpressing cells and soluble HER2; and (iii) a cell-cell interaction analysis where the bs affibody molecule bound HER2-overexpressing SKBR-3 cells and EGFR-overexpressing A-431 cells. This is, to our knowledge, the first reported bs affinity protein with potential ability for the simultaneous targeting of HER2 and EGFR. The potential future use of this and similar constructs, capable of bs targeting of receptors to increase the efficacy and selectivity in imaging and therapy, is discussed.

  • 195.
    Friedman, Mikaela
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Nordberg, Erika
    Uppsala Univ, Dept Oncol Radiol & Clin Immunol, Rudbeck Lab.
    Höidén-Guthenberg, Ingmarie
    Affibody AB, Bromma.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Adams, Gregory P.
    Fox Chase Canc Ctr, Dept Med Oncol, Philadelphia.
    Nilsson, Fredrik Y.
    Uppsala Univ, Dept Oncol Radiol & Clin Immunol, Rudbeck Lab.
    Carlsson, Jörgen
    Uppsala Univ, Dept Oncol Radiol & Clin Immunol, Rudbeck Lab.
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Phage display selection of Affibody molecules with specific binding to the extracellular domain of the epidermal growth factor receptor2007In: Protein Engineering Design & Selection, ISSN 1741-0126, E-ISSN 1741-0134, Vol. 20, no 4, p. 189-199Article in journal (Refereed)
    Abstract [en]

    Affibody molecules specific for the epidermal growth factor receptor (EGFR) have been selected by Phage display technology from a combinatorial protein library based on the 58-residue, protein A-derived Z domain. EGFR is overexpressed in various malignancies and is frequently associated with poor patient prognosis, and the information provided by targeting this receptor could facilitate both patient diagnostics and treatment. Three selected Affibody variants were shown to selectively bind to the extracellular domain of EGFR (EGFR-ECD). Kinetic biosensor analysis revealed that the three monomeric Affibody molecules bound with similar affinity, ranging from 130 to 185 nM. Head-to-tail dimers of the Affibody molecules were compared for their binding to recombinant EGFR-ECD in biosensor analysis and in human epithelial cancer A431 cells. Although the dimeric Affibody variants were found to bind in a range of 2550 nM affinities in biosensor analysis, they were found to be low nanomolar binders in the cellular assays. Competition assays using radiolabeled Affibody dimers confirmed specific EGFR-binding and demonstrated that the three Affibody molecules competed for the same epitope. Immunofluorescence microscopy demonstrated that the selected Affibody dimers were initially binding to EGFR at the cell surface of A431, and confocal microscopy analysis showed that the Affibody dimers could thereafter be internalized. The potential use of the described Affibody molecules as targeting agents; for radionuclide based imaging applications in various carcinomas ils discussed.

  • 196.
    Friedman, Mikaela
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Orlova, Anna
    Unit of Biomedical Radiation Sciences, Rudbeck Laboratory, Uppsala University.
    Johansson, Eva
    Affibody AB, Bromma.
    Eriksson, Tove L. J.
    Affibody AB, Bromma.
    Höidén-Guthenberg, Ingmarie
    Affibody AB, Bromma.
    Tolmachev, Vladimir
    Unit of Biomedical Radiation Sciences, Rudbeck Laboratory, Uppsala University.
    Nilsson, Fredrik Y.
    Unit of Biomedical Radiation Sciences, Rudbeck Laboratory, Uppsala University.
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Directed evolution to low nanomolar affinity of a tumor-targeting epidermal growth factor receptor-binding Affibody molecule2008In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 376, no 5, p. 1388-1402Article in journal (Refereed)
    Abstract [en]

    The epidermal growth factor receptor 1 (EGFR) is overexpressed in various malignancies and is associated with a poor patient prognosis. A small, receptor-specific, high-affinity imaging agent would be a useful tool in diagnosing malignant tumors and in deciding upon treatment and assessing the response to treatment. We describe here the affinity maturation procedure for the generation of Affibody molecules binding with high affinity and specificity to EGFR. A library for affinity maturation was constructed by rerandomization of selected positions after the alignment of first-generation binding variants. New binders were selected with phage display technology, using a single oligonucleotide in a single-library effort, and the best second-generation binders had an approximately 30-fold improvement in affinity (K-d = 5-10 nM) for the soluble extracellular domain of EGFR in biospecific interaction analysis using Biacore. The dissociation equilibrium constant, Kd, was also determined for the Affibody with highest affinity using EGFR-expressing A431 cells in flow cytometric analysis (K-d = 2.8 nM). A retained high specificity for EGFR was verified by a dot blot assay showing staining only of EGFR proteins among a panel of serum proteins and other EGFR family member proteins (HER2, HER3, and HER4). The EGFR-binding Affibody molecules were radiolabeled with indium-111, showing specific binding to EGFR-expressing A431 cells and successful targeting of the A431 tumor xenografts with 4-6% injected activity per gram accumulated in the tumor 4 h postinjection.

  • 197.
    Frisk, Thomas
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Khorshidi, Mohammad Ali
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Guldevall, Karolin
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Vanherberghen, Bruno
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Önfelt, Björn
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    A silicon-glass microwell platform for high-resolution imaging and high-content screening with single cell resolution2011In: Biomedical microdevices (Print), ISSN 1387-2176, E-ISSN 1572-8781, Vol. 13, no 4, p. 683-693Article in journal (Refereed)
    Abstract [en]

    We present a novel microwell array platform suited for various cell-imaging assays where single cell resolution is important. The platform consists of an exchangeable silicon-glass microchip for cell biological applications and a custom made holder that fits in conventional microscopes. The microchips presented here contain arrays of miniature wells, where the well sizes and layout have been designed for different applications, including single cell imaging, studies of cell-cell interactions or ultrasonic manipulation of cells. The device has been designed to be easy to use, to allow long-term assays (spanning several days) with read-outs based on high-resolution imaging or high-content screening. This study is focused on screening applications and an automatic cell counting protocol is described and evaluated. Finally, we have tested the device and automatic counting by studying the selective survival and clonal expansion of 721.221 B cells transfected to express HLA Cw6-GFP compared to untransfected 721.221 B cells when grown under antibiotic selection for 3 days. The device and automated analysis protocol make up the foundation for development of several novel cellular imaging assays.

  • 198.
    Frisk, Thomas
    et al.
    KTH, School of Electrical Engineering (EES), Microsystem Technology.
    Rydholm, Susanna
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Liebmann, Thomas
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Andersson-Svahn, Helene
    KTH, School of Biotechnology (BIO), Nano Biotechnology.
    Stemme, Göran
    KTH, School of Electrical Engineering (EES), Microsystem Technology.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    A microfluidic device for parallel 3-D cell cultures in asymmetric environments2007In: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 28, no 24, p. 4705-4712Article in journal (Refereed)
    Abstract [en]

    We demonstrate a concept for how a miniaturized 3-D cell culture in biological extracellular matrix (ECM) or synthetic gels bridges the gap between organ-tissue culture and traditional 2-D cultures. A microfluidic device for 3-D cell culture including microgradient environments has been designed, fabricated, and successfully evaluated. In the presented system stable diffusion gradients can be generated by application of two parallel fluid flows with different composition against opposite sides of a gel plug with embedded cello. Culture for up to two weeks was performed showing cells still viable and proliferating. The cell tracer dye calcein was used to verify gradient formation as the fluorescence intensity in exposed cells was proportional to the position in the chamber. Cellular response to an applied stimulus was demonstrated by use of an adenosine triphosphate gradient where the onset of a stimulated intracellular calcium release also depended on cell position.

  • 199.
    Fu, Kai
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fu, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Kinetic Monte Carlo study of metal organic chemical vapor deposition growth mechanism of GaSb quantum dots2008In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 93, no 101906Article in journal (Refereed)
    Abstract [en]

    The growth dynamics of self-assembled GaSb quantum dots (QDs) on GaAs substrate in the strain-induced Stranski-Krastanov mode was investigated using kinetic Monte Carlo method. The strain induced by the lattice mismatch between the epitaxial material and the substrate was shown to be directly responsible for the QD formation and the transition of growth mode from two dimensional to three dimensional.

  • 200.
    Fu, Kai
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fu, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Strain-induced Stranski-Krastanov three dimensional growth mode of GaSb quantum dot on GaAs substrate2009In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 94, no 181913Article in journal (Refereed)
    Abstract [en]

    The growth dynamics of self-assembled GaSb quantum dots (QDs) on GaAs substrate was investigated using kinetic Monte Carlo method. The strain induced by the lattice mismatch between the epitaxial material and the substrate was shown to be directly responsible for the three-dimensional QD formation. Different geometries of the initial seeds on the surface which are equally favorable from an energy point of view can result in different GaSb nanostructures (nanostrips and nanoring).

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