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  • 301.
    Hudson, Elton P.
    et al.
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Nikoshkov, Andrej
    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.
    Rockberg, Johan
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Automated Solid-Phase Subcloning Based on Beads Brought into Proximity by Magnetic Force2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 5, p. e37429-Article in journal (Refereed)
    Abstract [en]

    In the fields of proteomics, metabolic engineering and synthetic biology there is a need for high-throughput and reliable cloning methods to facilitate construction of expression vectors and genetic pathways. Here, we describe a new approach for solid-phase cloning in which both the vector and the gene are immobilized to separate paramagnetic beads and brought into proximity by magnetic force. Ligation events were directly evaluated using fluorescent-based microscopy and flow cytometry. The highest ligation efficiencies were obtained when gene- and vector-coated beads were brought into close contact by application of a magnet during the ligation step. An automated procedure was developed using a laboratory workstation to transfer genes into various expression vectors and more than 95% correct clones were obtained in a number of various applications. The method presented here is suitable for efficient subcloning in an automated manner to rapidly generate a large number of gene constructs in various vectors intended for high throughput applications.

  • 302.
    Hultin, Emelie
    et al.
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Käller, Max
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Ahmadian, Afshin
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Competitive enzymatic reaction to control allele-specific extensions2005In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 33, no 5, p. e48:1-e48:10Article in journal (Refereed)
    Abstract [en]

    Here, we present a novel method for SNP genotyping based on protease-mediated allele-specific primer extension (PrASE), where the two allele-specific extension primers only differ in their 3'-positions. As reported previously [Ahmadian, A., Gharizadeh, B., O'Meara, D., Odeberg, J. and Lundeberg, J. (2001), Nucleic Acids Res., 29, e121], the kinetics of perfectly matched primer extension is faster than mismatched primer extension. In this study, we have utilized this difference in kinetics by adding protease, a protein-degrading enzyme, to discriminate between the extension reactions. The competition between the polymerase activity and the enzymatic degradation yields extension of the perfectly matched primer, while the slower extension of mismatched primer is eliminated. To allow multiplex and simultaneous detection of the investigated single nucleotide polymorphisms (SNPs), each extension primer was given a unique signature tag sequence on its 50 end, complementary to a tag on a generic array. A multiplex nested PCR with 13 SNPs was performed in a total of 36 individuals and their alleles were scored. To demonstrate the improvements in scoring SNPs by PrASE, we also genotyped the individuals without inclusion of protease in the extension. We conclude that the developed assay is highly allele-specific, with excellent multiplex SNP capabilities.

  • 303.
    Hultin, Emilie
    KTH, School of Biotechnology (BIO).
    Genetic Sequence Analysis by Microarray Technology2007Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Developments within the field of genetic analysis have during the last decade become enormous. Advances in DNA sequencing technology have increased throughput from a thousand bases to over a billion bases in a day and decreased the cost thousandfold per base. Nevertheless, to sequence complex genomes like the human is still very expensive and efforts to attain even higher throughputs for less money are undertaken by researchers and companies.

    Genotyping systems for single nucleotide polymorphism (SNP) analysis with whole genome coverage have also been developed, with low cost per SNP. There is, however, a need for genotyping assays that are more cost efficient per sample with considerably higher accuracy. This thesis is focusing on a technology, based on competitive allele-specific extension and microarray detection, for genetic analysis. To increase specificity in allele-specific extension (ASE), a nucleotide degrading enzyme, apyrase, was introduced to compete with the polymerase, only allowing the fast, perfect matched primer extension to occur. The aim was to develop a method for analysis of around twenty loci in hundreds of samples in a high-throughput microarray format.

    A genotyping method for human papillomavirus has been developed, based on a combination of multiplex competitive hybridization (MUCH) and apyrase-mediated allele-specific extension (AMASE). Human papillomavirus (HPV), which is the causative agent in cervical cancer, exists in over a hundred different types. These types need to be determined in clinical samples. The developed assay can detect the twenty-three most common high risk types, as well as semi-quantifying multiple infections, which was demonstrated by analysis of ninety-two HPV-positive clinical samples.

    More stringent conditions can be obtained by increased reaction temperature. To further improve the genotyping assay, a thermostable enzyme, protease, was introduced into the allele-specific extension reaction, denoted PrASE. Increased sensitivity was achieved with an automated magnetic system that facilitates washing. The PrASE genotyping of thirteen SNPs yielded higher conversion rates, as well as more robust genotype scoring, compared to ASE. Furthermore, a comparison with pyrosequencing, where 99.8 % of the 4,420 analyzed genotypes were in concordance, indicates high accuracy and robustness of the PrASE technology.

    Single cells have also been analyzed by the PrASE assay to investigate loss of alleles during skin differentiation. Single cell analysis is very demanding due to the limited amounts of DNA. The multiplex PCR and the PrASE assay were optimized for single cell analysis. Twenty-four SNPs were genotyped and an increased loss of genetic material was seen in cells from the more differentiated suprabasal layers compared to the basal layer.

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  • 304.
    Hultin, Emilie
    et al.
    KTH, School of Biotechnology (BIO).
    Asplund, Anna
    KTH, School of Biotechnology (BIO).
    Berggren, Lovisa
    KTH, School of Biotechnology (BIO).
    Edlund, Karolina
    KTH, School of Biotechnology (BIO).
    Ahmadian, Afshin
    KTH, School of Biotechnology (BIO).
    Sundberg, Rolf
    Pontén, Fredrik
    KTH, School of Biotechnology (BIO).
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO).
    Random loss of genetic segments during skin differentiation indicated by analysis of single cellsArticle in journal (Other academic)
  • 305.
    Hultström, Jessica
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Manneberg, Otto
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Dopf, Katja
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Hertz, Hans M.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Wiklund, Martin
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Proliferation and viability of adherent cells manipulated by standing-wave ultrasound in a microfluidic chip2007In: Ultrasound in Medicine and Biology, ISSN 0301-5629, E-ISSN 1879-291X, Vol. 33, p. 145-151Article in journal (Refereed)
    Abstract [en]

    Ultrasonic-standing-wave (USW) technology has potential to become a standard method for gentle and contactless cell handling in microfluidic chips. We investigate the viability of adherent cells exposed to USWs by studying the proliferation rate of recultured cells following ultrasonic trapping and aggregation of low cell numbers in a microfluidic chip. The cells form 2-D aggregates inside the chip and the aggregates are held against a continuous flow of cell culture medium perpendicular to the propagation direction of the standing wave. No deviations in the doubling time from expected values (24 to 48 h) were observed for COS-7 cells held in the trap at acoustic pressure amplitudes up to 0.85 MPa and for times ranging between 30 and 75 min. Thus, the results demonstrate the potential of ultrasonic standing waves as a tool for gentle manipulation of low cell numbers in microfluidic systems.

  • 306. Idris, Shaza Bushra
    et al.
    Arvidson, Kristina
    Plikk, Peter
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Ibrahim, Lah
    Finne-Wistrand, Anna
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Albertsson, Ann-Christine
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Bolstad, Anne Isine
    Mustafa, Kama
    Polyester copolymer scaffolds enhance expression of bone markers in osteoblast-like cells2010In: J BIOMED MATER RES PART A, ISSN 1549-3296, Vol. 94A, no 2, p. 631-639Article in journal (Refereed)
    Abstract [en]

    In tissue engineering, the resorbable aliphatic polyester poly(L-lactide) (PLLA) is used as scaffolds in bone regeneration. Copolymers of poly(L-lactide)-co-(epsilon-caprolactone) [poly(LLA-co-CL)] and poly(L-lactide)-co-(1,5-dioxepan-2-one) [poly(LLA-co-DXO)], with superior mechanical properties to PLLA, have been developed to be used as scaffolds, but the influence on the osteogenic potential is unclear. This in vitro study of test scaffolds of poly(LLA-co-CL) and poly(LLA-co-DXO) using PLLA scaffolds as a control demonstrates the attachment and proliferation of human osteoblast-like cells (HOB) as measured by SEM and a methylthiazol tetrazolium (MTT) colorimetric assay, and the progression of HOB osteogenesis for up to 3 weeks; expressed as synthesis of the osteoblast differentiation markers: collagen type 1 (Col 1), alkaline phosphatase, bone sialoprotein, osteocalcin (OC), osteopontin and runt related gene 2 (Runx2). Surface analysis disclosed excellent surface attachment, spread and penetration of the cells into the pores of the test scaffolds compared to the PLLA. MTT results indicated that test scaffolds enhanced the proliferation of HOBs. Cells grown on the test scaffolds demonstrated higher synthesis of Col 1 and OC and also increased bone markers mRNA expression. Compared to scaffolds of PLLA, the poly(LLA-co-CL) and poly(LLA-co-DXO) scaffolds enhanced attachment, proliferation, and expression of osteogenic markers by HOBs in vitro. Therefore, these scaffolds might be appropriate carriers for bone engineering. (C) 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 94A: 631-639, 2010

  • 307. Jacobsson, Josefin A.
    et al.
    Almen, Markus Sallman
    Benedict, Christian
    Hedberg, Lilia A.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Michaelsson, Karl
    Brooks, Samantha
    Kullberg, Joel
    Axelsson, Tomas
    Johansson, Lars
    Ahlstrom, Hakan
    Fredriksson, Robert
    Lind, Lars
    Schioth, Helgi B.
    Detailed Analysis of Variants in FTO in Association with Body Composition in a Cohort of 70-Year-Olds Suggests a Weakened Effect among Elderly2011In: PLOS ONE, ISSN 1932-6203, Vol. 6, no 5, p. e20158-Article in journal (Refereed)
    Abstract [en]

    Background: The rs9939609 single-nucleotide polymorphism (SNP) in the fat mass and obesity (FTO) gene has previously been associated with higher BMI levels in children and young adults. In contrast, this association was not found in elderly men. BMI is a measure of overweight in relation to the individuals' height, but offers no insight into the regional body fat composition or distribution.

    Objective: To examine whether the FTO gene is associated with overweight and body composition-related phenotypes rather than BMI, we measured waist circumference, total fat mass, trunk fat mass, leg fat mass, visceral and subcutaneous adipose tissue, and daily energy intake in 985 humans (493 women) at the age of 70 years. In total, 733 SNPs located in the FTO gene were genotyped in order to examine whether rs9939609 alone or the other SNPs, or their combinations, are linked to obesity-related measures in elderly humans.

    Design: Cross-sectional analysis of the Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) cohort.

    Results: Neither a single SNP, such as rs9939609, nor a SNP combination was significantly linked to overweight, body composition-related measures, or daily energy intake in elderly humans. Of note, these observations hold both among men and women.

    Conclusions: Due to the diversity of measurements included in the study, our findings strengthen the view that the effect of FTO on body composition appears to be less profound in later life compared to younger ages and that this is seemingly independent of gender.

  • 308. Jansen, Mickel LA
    et al.
    Bracher, Jasmine M
    Papapetridis, Ioannis
    Verhoeven, Maarten D
    de Bruijn, Hans
    de Waal, Paul P
    van Maris, Antonius JA
    KTH, School of Biotechnology (BIO), Industrial Biotechnology. AlbaNova University Center, SE 106 91, Stockholm, Sweden.; Delft Univ Technol, Dept Biotechnol, Van der Maasweg 9, NL-2629 HZ Delft, Netherlands.
    Klaassen, Paul
    Pronk, Jack T
    Saccharomyces cerevisiae strains for second-generation ethanol production: from academic exploration to industrial implementation2017In: FEMS Yeast Research, Vol. 17, no 5Article in journal (Refereed)
    Abstract [en]

    The recent start-up of several full-scale 'second generation' ethanol plants marks a major milestone in the development of Saccharomyces cerevisiae strains for fermentation of lignocellulosic hydrolysates of agricultural residues and energy crops. After a discussion of the challenges that these novel industrial contexts impose on yeast strains, this minireview describes key metabolic engineering strategies that have been developed to address these challenges. Additionally, it outlines how proof-of-concept studies, often developed in academic settings, can be used for the development of robust strain platforms that meet the requirements for industrial application. Fermentation performance of current engineered industrial S. cerevisiae strains is no longer a bottleneck in efforts to achieve the projected outputs of the first large-scale second-generation ethanol plants. Academic and industrial yeast research will continue to strengthen the economic value position of second-generation ethanol production by further improving fermentation kinetics, product yield and cellular robustness under process conditions.

  • 309.
    Jansson, Magnus
    et al.
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Dixelius, J
    Uhlén, M
    Nilsson, B O
    Binding affinities of insulin-like growth factor-I (IGF-I) fusion proteins to IGF binding protein 1 and IGF-I receptor are not correlated with mitogenic activity.1997In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 416, no 3, p. 259-264Article in journal (Refereed)
    Abstract [en]

    In this report, comparisons between molecular affinities and cellular proliferation activities have been made for insulin-like growth factor-I (IGF-I) and two IGF-I fusion proteins in order to evaluate fusion proteins as tools for receptor binding studies. Binding affinities and growth promoting effects of the N-terminal fusion Z-IGF-I and the C-terminal fusion IGF-I-Z, and native recombinant human IGF-I, were analyzed. Binding kinetic properties of the three IGF-I variants were analyzed using BIAcore kinetic interaction analysis testing for binding to both human IGF binding protein 1 (IGFBP-1) and a soluble form of the human IGF type I receptor extracellular domains (sIGF-IR). The growth promoting effects on SaOS-2 human osteosarcoma cells of the different fusion proteins were analyzed. A comparison of receptor binding affinities and growth promoting effects shows that the fusion protein receptor affinity does not correlate with proliferative potential. The IGF-I-Z fusion, with the lowest receptor affinity, shows similar proliferative potential to native IGF-I. However, the Z-IGF-I fusion protein, with twice the receptor affinity of IGF-I-Z, displays only about 70% of the IGF-I-Z growth promoting activity. Both IGF-I fusion proteins possess similar affinity to IGFBP-1. These results indicate that determinants other than the receptor affinity could be involved in the regulation of IGF-I proliferative action. This study demonstrates that ligand fusion proteins may be useful to study mechanisms of ligand induced receptor activation.

  • 310.
    Jansson, Magnus
    et al.
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Hallén, D
    Koho, H
    Andersson, G
    Berghard, L
    Heidrich, J
    Nyberg, E
    Uhlén, M
    Kördel, J
    Nilsson, B
    Characterization of ligand binding of a soluble human insulin-like growth factor I receptor variant suggests a ligand-induced conformational change.1997In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 272, no 13, p. 8189-8197Article in journal (Refereed)
    Abstract [en]

    Details of the signal transduction mechanisms of the tyrosine kinase family of growth factor receptors remain elusive. In this work, we describe an extensive study of kinetic and thermodynamic aspects of growth factor binding to a soluble extracellular human insulin-like growth factor-I receptor (sIGF-IR) variant. The extracellular receptor domains were produced fused to an IgG-binding protein domain (Z) in transfected human 293 cells as a correctly processed secreted alpha-beta'-Z dimer. The receptor was purified using IgG affinity chromatography, rendering a pure and homogenous protein in yields from 1 to 5 mg/liter of conditioned cell media. Biosensor technology (BIAcore) was applied to measure the insulin-like growth factor-I (IGF-I), des(1-3)IGF-I, insulin-like growth factor-II, and insulin ligand binding rate constants to the immobilized IGF-IR-Z. The association equilibrium constant, Ka, for the IGF-I interaction is determined to 2.8 x 10(8) M-1 (25 degrees C). Microcalorimetric titrations on IGF-I/IGF-IR-Z were performed at three different temperatures (15, 25, and 37 degrees C) and in two different buffer systems at 25 degrees C. From these measurements, equilibrium constants for the 1:1 (IGF-I:(alpha-beta'-Z)2) receptor complex in solution are deduced to 0.96 x 10(8) M-1 (25 degrees C). The determined heat capacity change for the process is large and negative, -0.51 kcal (K mol)-1. Further, the entropy change (DeltaS) at 25 degrees C is large and negative. Far- and near-UV circular dichroism measurements display significant changes over the entire wavelength range upon binding of IGF-I to IGF-IR-Z. These data are all consistent with a significant change in structure of the system upon IGF-I binding.

  • 311. Jansson, R.
    et al.
    Lau, C. H.
    Ishida, T.
    Ramström, M.
    Sandgren, M.
    Hedhammar, My
    KTH, School of Biotechnology (BIO), Protein Technology. Swedish University of Agricultural Sciences, Sweden.
    Functionalized silk assembled from a recombinant spider silk fusion protein (Z-4RepCT) produced in the methylotrophic yeast Pichia pastoris2016In: Biotechnology Journal, ISSN 1860-6768, E-ISSN 1860-7314, Vol. 11, no 5, p. 687-699Article in journal (Refereed)
    Abstract [en]

    Functional biological materials are a growing research area with potential applicability in medicine and biotechnology. Using genetic engineering, the possibility to introduce additional functions into spider silk-based materials has been realized. Recently, a recombinant spider silk fusion protein, Z-4RepCT, was produced intracellularly in Escherichia coli and could after purification self-assemble into silk-like fibers with ability to bind antibodies via the IgG-binding Z domain. In this study, the use of the methylotrophic yeast Pichia pastoris for production of Z-4RepCT has been investigated. Temperature, pH and production time were influencing the amount of soluble Z-4RepCT retrieved from the extracellular fraction. Purification of secreted Z-4RepCT resulted in a mixture of full-length and degraded silk proteins that failed to self-assemble into fibers. A position in the C-terminal domain of 4RepCT was identified as being subjected to proteolytic cleavage by proteases in the Pichia culture supernatant. Moreover, the C-terminal domain was subjected to glycosylation during production in P. pastoris. These observed alterations of the CT domain are suggested to contribute to the failure in fiber assembly. As alternative approach, Z-4RepCT retrieved from the intracellular fraction, which was less degraded, was used and shown to retain ability to assemble into silk-like fibers after enzymatic deglycosylation.

  • 312.
    Jarmander, Johan
    KTH, School of Biotechnology (BIO), Bioprocess Technology (closed 20130101).
    Improved detection and performance of surface expression from the AIDA-I autotransporter2013Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Surface expression of recombinant proteins has attracted a lot of attention due to its potential in applications such as enzyme production, vaccine delivery and bioremediation. Autotransporters have been used for surface expression of a variety of proteins, but the expression systems reported in literature have typically been inflexible and incapable of detecting proteolysis, thereby limiting surface expression yield.

    In this thesis, a modular surface expression system, utilizing dual tag detection, was therefore created. It was based on the adhesin involved in diffuse adherence (AIDA-I) autotransporter, and was here used to express the model proteins SefA and H:gm on the cell surface of Escherichia coli. Due to the dual tag detection system, proteolysed H:gm could be successfully verified on the cell surface. By optimizing cultivation conditions, surface expression yield of SefA was increased by 300 %, and proteolysis reduced by 33 %. While proteolysis could not be eliminated completely, the work presented in this thesis is a major step towards a general system for surface expression of a wide range of proteins in varied applications.

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    JJ_licentiat_130502
  • 313.
    Jarmander, Johan
    et al.
    KTH, School of Biotechnology (BIO), Bioprocess Technology (closed 20130101).
    Gustavsson, Martin
    KTH, School of Biotechnology (BIO), Bioprocess Technology (closed 20130101).
    Do, Thi-Huyen
    Samuelson, Patrik
    KTH, School of Biotechnology (BIO), Bioprocess Technology (closed 20130101).
    Larsson, Gen
    KTH, School of Biotechnology (BIO), Bioprocess Technology (closed 20130101).
    A dual tag system for facilitated detection of surface expressed proteins in Escherichia coli2012In: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 11, article id 118Article in journal (Refereed)
    Abstract [en]

    Background: The discovery of the autotransporter family has provided a mechanism for surface expression of proteins in laboratory strains of Escherichia coli. We have previously reported the use of the AIDA-I autotransport system to express the Salmonella enterica serovar Enteritidis proteins SefA and H: gm. The SefA protein was successfully exposed to the medium, but the orientation of H:gm in the outer membrane could not be determined due to proteolytic cleavage of the N-terminal detection-tag. The goal of the present work was therefore to construct a vector containing elements that facilitates analysis of surface expression, especially for proteins that are sensitive to proteolysis or otherwise difficult to express. Results: The surface expression system pAIDA1 was created with two detection tags flanking the passenger protein. Successful expression of SefA and H:gm on the surface of E. coli was confirmed with fluorescently labeled antibodies specific for the N-terminal His(6)-tag and the C-terminal Myc-tag. While both tags were detected during SefA expression, only the Myc-tag could be detected for H: gm. The negative signal indicates a proteolytic cleavage of this protein that removes the His(6)-tag facing the medium. Conclusions: Expression levels from pAIDA1 were comparable to or higher than those achieved with the formerly used vector. The presence of the Myc- but not of the His(6)-tag on the cell surface during H:gm expression allowed us to confirm the hypothesis that this fusion protein was present on the surface and oriented towards the cell exterior. Western blot analysis revealed degradation products of the same molecular weight for SefA and H:gm. The size of these fragments suggests that both fusion proteins have been cleaved at a specific site close to the C-terminal end of the passenger. This proteolysis was concluded to take place either in the outer membrane or in the periplasm. Since H:gm was cleaved to a much greater extent then the three times smaller SefA, it is proposed that the longer translocation time for the larger H:gm makes it more susceptible to proteolysis.

  • 314.
    Jegerschöld, Caroline
    et al.
    KTH, School of Technology and Health (STH), Structural Biotechnology (Closed 20130701).
    Paweizik, Sven-Christian
    Purhonen, Pasi
    KTH, School of Technology and Health (STH), Structural Biotechnology (Closed 20130701).
    Bhakat, Priyaranian
    KTH, School of Technology and Health (STH), Structural Biotechnology (Closed 20130701).
    Gheorghe, Karina Roxana
    KTH, School of Technology and Health (STH), Structural Biotechnology (Closed 20130701).
    Gyobu, Nobuhiko
    Mitsuoka, Kaoru
    Morgenstern, Ralf
    Jakobsson, Per-Johan
    Hebert, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology (Closed 20130701).
    Structural basis for induced formation of the inflammatory mediator prostaglandin E-22008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 32, p. 11110-11115Article in journal (Refereed)
    Abstract [en]

    Prostaglandins (PG) are bioactive lipids produced from arachidonic acid via the action of cyclooxygenases and terminal PG synthases. Microsomal prostaglandin E synthase 1 (MPGES1) constitutes an inducible glutathione-dependent integral membrane protein that catalyzes the oxidoreduction of cyclooxygenase derived PGH(2) into PGE(2). MPGES1 has been implicated in a number of human diseases or pathological conditions, such as rheumatoid arthritis, fever, and pain, and is therefore regarded as a primary target for development of novel antiinflammatory drugs. To provide a structural basis for insight in the catalytic mechanism, we determined the structure of MPGES1 in complex with glutathione by electron crystallography from 2D crystals induced in the presence of phospholipids. Together with results from site-directed mutagenesis and activity measurements, we can thereby demonstrate the role of specific amino acid residues. Glutathione is found to bind in a U-shaped conformation at the interface between subunits in the protein trimer. It is exposed to a site facing the lipid bilayer, which forms the specific environment for the oxidoreduction of PGH(2) to PGE(2) after displacement of the cytoplasmic half of the IN-terminal transmembrane helix. Hence, insight into the dynamic behavior of MPGES1 and homologous membrane proteins in inflammation and detoxification is provided.

  • 315. Jeong, Yunjin
    et al.
    Svedberg, Gustav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Réu, Pedro
    Lee, Yongju
    Song, Seo Woo
    Na, Hunjong
    Lee, Amos Chungwon
    Choi, Yeongjae
    Gantelius, Jesper
    Andersson Svahn, Helene
    Kwon, Sunghoon
    Solid-phase PCR on graphically encoded microparticles for multiplexed colorimetric detection of bacterial DNAManuscript (preprint) (Other academic)
  • 316.
    Jiang, Jun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A generalized quantum chemical approach for nano- and bio-electronics2005Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    A generalized quantum chemical approach for electron transport in molecular devices is developed. It allows to treat the devices where the metal electrodes and the molecule are either chemically or physically bonded on equal footing. Effects of molecular length and hydrogen bonding on the current-voltage (I-V) characteristics of molecular devices are discussed. An extension to include the vibration motions of the molecule has been derived and implemented. It provides the inelastic electron tunneling spectroscopy (IETS) of molecular devices with unprecedented accuracy, and reveals important information about the molecular structures that are not accessible in the experiment. The IETS is shown to be a powerful characterization tool for molecular devices.

    An effective elongation method has been developed to study the electron transport in nanoand bio-electronic devices at hybrid density functional theory level. It enables to study electronic structures and transportation properties of a 40 nm long self-assembled conjugated polymer junction, a 21 nm long single-walled carbon nanotubes (SWCNT), and a 60 basepairs DNA molecule. It is the first time that systems consisting of more than 10,000 electrons have been described at such a sophisticated level. The calculations have shown that the electron transport in sub-22 nm long SWCNT and short DNA molecules is dominated by the coherent scattering through the delocalized unoccupied states. The derived length dependence of coherent electron transport in these nanostructured systems will be useful for the future experiments. Moreover, some unexpected behaviors of these devices have been discovered.

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  • 317.
    Jiang, Jun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Liu, Kai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Lu, Wei
    Luo, Yi
    Coherent Electron Transport in DNA MoleculesManuscript (preprint) (Other academic)
  • 318.
    Jiang, Jun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Lu, Wei
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    First-Principles Study of Electron Transport in Single-Walled Carbon Nanotubesthat are 2 to 22 nm in Length.Article in journal (Other academic)
  • 319.
    Jiang, Yun
    et al.
    Biovitrum/SOBI, Sweden.
    Svensson, Erik
    Biovitrum/SOBI, Sweden.
    Chotteau, Veronique
    Improvement of a CHO Fed-Batch Process by Fortifying with Plant Peptones2010In: Cells and Culture: ESACT Proceedings, 2010, Volume 4, Part 3 / [ed] Noll T, Springer, 2010, p. 281-284Conference paper (Other academic)
    Abstract [en]

    A serum-free fed-batch process was developed for production of a human monoclonal antibody in Chinese hamster ovary (CHO) cells based on Biovitrum’s proprietary low protein serum-free medium without animal derived components (BVT4). The cells were fed with glucose, glutamine and Biovitrum’s proprietary low protein serum-free feed medium without animal derived components enriched with amino acids, vitamins, metal traces, peptones, and biosynthesis precursors. To improve the performance of the fed-batch process, we developed the use of plant peptones by studying the dose and timing of the peptone feeding. Different doses of peptone cocktail and amino acid cocktail, as well as different combinations of pep- tone and amino acid cocktails were first screened in 50 ml filter tubes on an AgCell shaker table. The best combinations were then assessed in spinner and 3 L bioreactor cultures. To reinforce our findings, the antibody-producing CHO cells were adapted to a disclosed serum-free medium DMEM/F12 and the beneficial effects of pep- tones were confirmed in a fed-batch process based on the DMEM/F12 serum-free medium.

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    Jiang 2010 Improvement of a CHO Fed-Batch Process by Fortifying with Plant Peptones
  • 320. Johansson, H
    et al.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Mohammad Amini, Amini Bahram
    KTH, Superseded Departments, Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Kleczkowski, L A
    Molecular cloning of UPD-glucose dehydrogenase from cambium of poplar (Populus tremula x tremuloides)Article in journal (Other academic)
  • 321. Johansson, P.
    et al.
    Brumer, Harry
    KTH, Superseded Departments, Biotechnology.
    Baumann, Martin J.
    KTH, Superseded Departments, Biotechnology.
    Kallas, Åsa
    KTH, Superseded Departments, Biotechnology.
    Henriksson, Hongbin
    KTH, Superseded Departments, Biotechnology.
    Denman, Stuart
    KTH, Superseded Departments, Biotechnology.
    Teeri, Tuula
    KTH, Superseded Departments, Biotechnology.
    Jones, A.
    Crystal structures of a poplar xyloglucan endotransglycosylase reveal details of the transglycosylation acceptor binding2004In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 16, no 4, p. 874-886Article in journal (Refereed)
    Abstract [en]

    Xyloglucan endotransglycosylases (XETs) cleave and religate xyloglucan polymers in plant cell walls via a transglycosylation mechanism. Thus, XET is a key enzyme in all plant processes that require cell wall remodeling. To provide a basis for detailed structure-function studies, the crystal structure of Populus tremula x tremuloides XET16A (PttXET16A), heterologously expressed in Pichia pastoris, has been determined at 1.8-Angstrom resolution. Even though the overall structure of PttXET16A is a curved beta-sandwich similar to other enzymes in the glycoside hydrolase family GH16, parts of its substrate binding cleft are more reminiscent of the distantly related family GH7. In addition, XET has a C-terminal extension that packs against the conserved core, providing an additional beta-strand and a short alpha-helix. The structure of XET in complex with a xyloglucan nonasaccharide, XLLG, reveals a very favorable acceptor binding site, which is a necessary but not sufficient prerequisite for transgilycosylation. Biochemical data imply that the enzyme requires sugar residues in both acceptor and donor sites to properly orient the glycosidic bond relative to the catalytic residues.

  • 322.
    Johansson, Staffan
    et al.
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Eklund, Anders
    Umeå University.
    Malm, Jan
    Umeå University.
    Stemme, Göran
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Roxhed, Niclas
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    A MEMS-based passive hydrocephalus shunt with adaptive flow characteristics2013Conference paper (Refereed)
    Abstract [en]

    This paper reports a novel MEMS valve with adaptive flow characteristics for improved treatment of hydrocephalus, a disease that is characterized by elevated pressure in the cerebrospinal fluid (CSF) that surrounds the brain and spinal cord. In contrast to conventional valves with two ports, the valve presented here features a third port, called compensation port, which utilizes hydrostatic pressure to adapt CSF drainage based on body position. A prototype has been fabricated using standard MEMS manufacturing processes and the experimental evaluation successfully showed that the flow rate was adjustable with a varying hydrostatic pressure on the compensation port. Extracted data shows that flow rate was at near ideal values at both standing and laying body position showing an effective adaptation to body position. This is the first passive hydrocephalus valve intended for body position dependent CSF pressure regulation.

  • 323.
    Johansson, Staffan
    et al.
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Stemme, Göran
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Roxhed, Niclas
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    A MEMS-based passive air flow regulator for handheld breath diagnostics2014In: Sensors and Actuators A-Physical, ISSN 0924-4247, E-ISSN 1873-3069, Vol. 215, p. 65-70Article in journal (Refereed)
    Abstract [en]

    This paper reports on a passive MEMS-based flow regulator designed to maintain a steady flow during asthma diagnostics. A prototype consisting of six in-plane moving pistons that restrict the flow through six flow orifices has been fabricated from three wafers using standard silicon micromachining. The in-plane design enables relatively large flows and tuning of the flow and pressure range to specific application requirements by changing a wafer thickness. In particular, for FENO asthma monitoring, regulatory guidelines specifies that measurements should be made at steady flow of approximately 50 ml/s and within a pressure range of 1–2 kPa. Experimental evaluation of the prototype shows that the flow rate is controlled within a dynamic pressure range of 770 Pa compared to only 430 Pa for a dummy structure and that it can be achieved on a chip measuring only 2 mm × 2 mm × 4 mm. The evaluation also showed that condensation of exhaled air that expectedly occurs in the flow regulator at room temperature can be eliminated by local heating of the device to 40◦C.

  • 324.
    Johnson, Francis X
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology, Energy and Climate Studies, ECS.
    Bioenergy and the Sustainability Transition: from local resource to global commodity2007Conference paper (Refereed)
  • 325.
    Johnson, Francis X.
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology, Energy and Climate Studies, ECS.
    Seebaluck, Vikram
    Bioenergy for Sustainable Development and International Competitiveness: The Role of Sugar Cane in Africa2012Collection (editor) (Other academic)
    Abstract [en]

    Growing concerns about the impacts of climate change and dependence on fossil fuels have intensified interest in bioenergy from sugar cane and other crops, highlighting important links between energy, environment and development goals. Southern and Eastern Africa are characterized by severe poverty; the possibility to exploit a renewable energy resource offers valuable avenues for sustainable development and could support a more dynamic and competitive economy. This book describes how the bioenergy expansion will improve rural livelihoods, reduce costly energy imports, reduce GHG emissions, and offer new development paths.

    Drawing on international experience, particularly from Brazil and India, it is shown that harnessing this potential will require significant increases in investment, technology transfer, and international cooperation. Because of its high efficiency, the authors argue that sugar cane should be viewed as a global resource for sustainable development and should command much greater focus and concerted policy action. Through an analysis of the agronomy, land suitability and industrial processing of sugar cane and its co-products, along with an assessment of the energy, economic and environmental implications, this volume demonstrates that sugar cane offers a competitive and environmentally beneficial resource for Africa's economic development and energy security.

    With fourty-four authors representing thirty organisations in sixteen countries, the book offers a truly international and interdisciplinary perspective by combining technical and economic principles with social, political and environmental assessment and policy analysis.

  • 326.
    Jonsson Rudsander, Ulla
    KTH, School of Biotechnology (BIO), Wood Biotechnology.
    Functional studies of a membrane-anchored cellulase from poplar2007Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Cellulose in particular and wood in general are valuable biomaterials for humanity, and cellulose is now also in the spotlight as a starting material for the production of biofuel. Understanding the processes of wood formation and cellulose biosynthesis could therefore be rewarding, and genomics and proteomics approaches have been initiated to learn more about wood biology. For example, the genome of the tree Populus trichocarpa has been completed during 2006. A single-gene approach then has to follow, to elucidate specific patterns and enzymatic details.

    This thesis depicts how a gene encoding a membrane-anchored cellulase was isolated from Populus tremula x tremuloides Mich, how the corresponding protein was expressed in heterologous hosts, purified and characterized by substrate analysis using different techniques. The in vivo function and modularity of the membrane-anchored cellulase was also addressed using overexpression and complementation analysis in Arabidopsis thaliana.

    Among 9 genes found in the Populus EST database, encoding enzymes from glycosyl hydrolase family 9, two were expressed in the cambial tissue, and the membrane-anchored cellulase, PttCel9A1, was the most abundant transcript. PttCel9A1 was expressed in Pichia pastoris, and purified by affinity chromatography and ion exchange chromatography. The low yield of recombinant protein from shake flask experiments was improved by scaling up in the fermentor. PttCel9A1 was however highly heterogenous, both mannosylated and phosphorylated, which made the protein unsuitable for crystallization experiments and 3D X-ray structure determination. Instead, a homology model using a well-characterized, homologous bacterial enzyme was built. From the homology model, interesting point mutations in the active site cleft that would highlight the functional differences of the two proteins could be identified. The real-time cleavage patterns of cello-oligosaccharides by mutant bacterial enzymes, the wildtype bacterial enzyme and PttCel9A1 were studied by 1H NMR spectroscopy, and compared with results from HPAEC-PAD analysis. The inverting stereochemistry for the hydrolysis reaction of the membrane-anchored poplar cellulase was also determined by 1H NMR spectroscopy, and it was concluded that transglycosylation in vivo is not a possible scenario.

    The preferred in vitro polymeric substrates for PttCel9A1 were shown to be long, low-substituted cellulose derivatives, and the endo-1,4--glucanase activity was not extended to branched or mixed linkage substrates to detectable levels. This result indicates an in vivo function in the hydrolysis of “amorphous” regions of cellulose, either during polymerization or crystallization of cellulose. In addition, overexpressing PttCel9A1 in A. thaliana, demonstrated a correlation with decreased crystallinity of cellulose. The significance of the different putative modules of PttCel9A1 was investigated by the construction of hybrid proteins, that were introduced into a knock-out mutant of A. thaliana, and the potential complementation of the phenotype was examined. A type B plant cellulase catalytic domain could not substitute for a type A plant cellulase catalytic domain, although localization and interaction motifs were added to the N- and C-terminus.

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    FULLTEXT01
  • 327.
    Jonsson Rudsander, Ulla
    et al.
    KTH, School of Biotechnology (BIO), Centres, Swedish Center for Biomimetic Fiber Engineering, BioMime.
    Sandstrom, Corine
    Piens, Kathleen
    KTH, School of Biotechnology (BIO), Centres, Swedish Center for Biomimetic Fiber Engineering, BioMime.
    Master, Emma
    KTH, School of Biotechnology (BIO), Centres, Swedish Center for Biomimetic Fiber Engineering, BioMime.
    Wilson, David B.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Centres, Swedish Center for Biomimetic Fiber Engineering, BioMime. KTH, School of Biotechnology (BIO), Glycoscience.
    Kenne, Lennart
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO), Centres, Swedish Center for Biomimetic Fiber Engineering, BioMime. KTH, School of Biotechnology (BIO), Glycoscience.
    Comparative NMR analysis of cellooligosaccharide hydrolysis by GH9 bacterial and plant endo-1,4-ss-glucanases2008In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 47, no 18, p. 5235-5241Article in journal (Refereed)
    Abstract [en]

    H-1 NMR spectroscopy has been used to analyze the product profiles arising from the hydrolysis of cellooligosaccharides by family GH9 cellulases. The product profiles obtained with the wild type and several active site mutants of a bacterial processive endoglucanase, Tf Cel9A, were compared with those obtained by a randomly acting plant endoglucanase, PttCe19A. PttCe19A is an orthologue of the Arabidopsis endocellulase, Korrigan, which is required for efficient cellulose biosynthesis. As expected, poplar PttCe19A was shown to catalyze the degradation of cellooligosaccharides by inversion of the configuration of the anomeric carbon. The product analyses showed that the number of interactions between the glucose units of the substrate and the aromatic residues in the enzyme active sites determines the point of cleavage in both enzymes.

  • 328.
    Jönsson, Håkan
    KTH, School of Biotechnology (BIO), Nano Biotechnology.
    Droplet microfluidics for high throughput biological analysis2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many areas of biological research increasingly perform large-scale analyses.  In genomics the entire gene repertoire of an organism is analyzed.  Proteomics attempts to understand the function and expression patterns of all proteins in a cell or organism.  Cell biologists study large numbers of single cells to understand the heterogeneity of cell populations.  In biotechnology and synthetic biology researchers search for new functional biomolecules in large libraries of biomolecular diversity e.g. for uses in medicine or bioprocessing.  More and more all of these fields employ high throughput methods to achieve the scale of analysis necessary.

    Miniaturization and parallelization provide routes towards high throughput analysis, which have proven successful for microelectronics as well as for DNA sequencing.  For the analysis of cells and biomolecules, native to an aqueous environment, miniaturization and parallelization hinges on the handling and parallel processing of very small amounts of water.  Droplet microfluidics utilizes stable picoliter (water) droplets contained in inert fluorinated oils as compartments in which to isolate and analyze cells, molecules or reactions.  These droplets can be manipulated, detected and analyzed at rates of thousands per second in microfluidic modules combining top-down microscale fabrication with the self-assembly of droplets of exact size.

    The studies constituting this thesis involve new droplet based biomolecular and single cell assays, manipulation techniques and device fabrication methods to extend the capabilities of droplet microfluidics for high throughput biological analysis.

    The first paper in the thesis describes a novel analysis method for studying the low abundant biomarkers present on the surface individual cells at resolutions not available by flow cytometry, the current gold standard of single cell analysis.  The use of a fluorescent optical dye code enabled the analysis of several single cell samples concurrently, improving throughput.

    Further a deterministic lateral displacement module, providing passive separation of droplets by size in a microfluidic circuit at more than twice higher rates than previously achievable was demonstrated.  Using this module, droplets were separated for cell occupancy based on a cell induced droplet size transformation, which couples a biological property of the droplet contents to a physical property of the droplet.  This effect, which enables passive separation of at high throughput, indicates a potential novel assay format for clone selection.

    One important feature of droplets for encapsulated single cell analysis is retention of secreted molecules providing a genotype-phenotype link.  With the objective of detecting antibody molecules secreted by hybridoma for selection, Paper III demonstrates the adaption of a homogeneous fluorescence polarization based, “mix-incubate-read”, assay for antibody detection.  In the final paper of the thesis the development of inexpensive and robust optical filters monolithically integrated in the microfluidic chip is reported. These defined filters enable integration of multiple optical filters in a polymer microfluidic device.

    Overall, droplet microfluidics combines techniques for handling and manipulating millions of discrete biocompatible picoliter compartments per hour with dedicated assays for biomolecule and single cell analysis. The scale of analysis that this enables is certain to impact life science research.

     

  • 329.
    Jönsson, Håkan
    et al.
    KTH, School of Biotechnology (BIO), Nano Biotechnology (closed 20130101).
    Svahn Andersson, Helene
    KTH, School of Biotechnology (BIO), Nano Biotechnology (closed 20130101).
    Tröpfchen-Mikrofluidik für die Einzelzellanalyse2012In: Angewandte Chemie, ISSN 0044-8249, E-ISSN 1521-3757, Angewandte Chemie, Vol. 124, no 49, p. 12342-12359Article in journal (Refereed)
    Abstract [de]

    Die tröpfchenbasierte Mikrofluidik dient der Isolierung und Manipulation von einzelnen Zellen und Reagentien innerhalb von monodispersen, pikolitergroßen Flüssigkapseln bei einem Umsatz von tausenden Tröpfchen pro Sekunde. Diese Qualitäten machen die Tröpfchen‐Mikrofluidik geeignet für viele Anforderungen der Einzelzellanalyse. Durch die Monodispersität lässt sich die Konzentration in den Tröpfchen quantitativ einstellen. Die Tröpfchen bieten der Zelle und ihrer unmittelbaren Umgebung ein isoliertes Kompartiment, und bei einem Durchsatz von tausenden Tröpfchen pro Sekunde ist es möglich, zehntausende bis millionen verkapselte Zellen zu prozessieren. Heterogene Zellpopulationen lassen sich somit exakt beschreiben oder seltene Zellarten identifizieren. Das kleine Volumen der Tröpfchen macht auch sehr große Screenings ökonomisch machbar. Dieser Aufsatz gibt einen Überblick über den aktuellen Stand der Einzelzellanalyse durch die Tröpfchen‐Mikrofluidik und nennt Beispiele, bei denen sie biologische Vorgänge besser verstehen hilft.

  • 330.
    Jönsson, Håkan
    et al.
    KTH, School of Biotechnology (BIO), Nano Biotechnology (closed 20130101).
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Andersson-Svahn, Helene
    KTH, School of Biotechnology (BIO), Nano Biotechnology (closed 20130101).
    Deterministic lateral displacement device for droplet separation by size - Towards rapid clonal selection based on droplet shrinking2010In: 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2010, MicroTAS 2010: Volume 2, 2010, p. 1355-1357Conference paper (Refereed)
    Abstract [en]

    We present a novel method for robust passive separation of microfluidic droplets by size using deterministic lateral displacement(DLD). We also show that droplets containing Saccharomyces Cervisiae shrink significantly during incubation while droplets containing only yeast media retain their size. We demonstrate the DLD device by sorting out shrunken yeast-cell containing droplets from a 40-fold excess of ∼33% larger yeast-cell-free droplets generated at the same time, suggesting that DLD might be used for clonal selection. The same device also separates 11 μm from 30μm droplets at a rate of 12000droplets/second, more than twofold faster than previously demonstrated passive hydrodynamic separation devices [1].

  • 331.
    Jönsson, Håkan
    et al.
    KTH, School of Biotechnology (BIO), Nano Biotechnology.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Andersson-Svahn, Helene
    KTH, School of Biotechnology (BIO), Nano Biotechnology.
    Droplet size based separation by deterministic lateral displacement: separating droplets by cell-induced shrinking2011In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 11, no 7, p. 1305-1310Article in journal (Refereed)
    Abstract [en]

    We present a novel method for passive separation of microfluidic droplets by size at high throughput using deterministic lateral displacement (DLD). We also show that droplets containing Saccharomyces cerevisiae shrink significantly during incubation while droplets containing only yeast media retain or slightly increase their size. We demonstrate the DLD device by sorting out shrunken yeast-cell containing droplets from 31% larger diameter droplets which were generated at the same time containing only media, present at a >40-fold excess. This demonstrates the resolving power of droplet separation by DLD and establishes that droplets can be separated for a biological property of the droplet contents discriminated by a change of the physical properties of the droplet. Thus suggesting that this technique may be used for e.g. clonal selection. The same device also separates 11 µm from 30 µm droplets at a rate of 12000 droplets per second, more than twofold faster than previously demonstrated passive hydrodynamic separation devices.

  • 332.
    Kaczmarzyk, Danuta
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. Georg-August-University, Germany.
    Hudson, Elton P.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Fulda, Martin
    Arabidopsis acyl-acyl carrier protein synthetase AAE15 with medium chain fatty acid specificity is functional in cyanobacteria2016In: AMB Express, ISSN 2191-0855, E-ISSN 2191-0855, Vol. 6, no 1, p. 1-9, article id 7Article in journal (Refereed)
    Abstract [en]

    Cyanobacteria are potential hosts for the biosynthesis of oleochemical compounds. The metabolic precursors for such compounds are fatty acids and their derivatives, which require chemical activation to become substrates in further conversion steps. We characterized the acyl activating enzyme AAE15 of Arabidopsis encoded by At4g14070, which is a homologue of a cyanobacterial acyl-ACP synthetase (AAS). We expressed AAE15 in insect cells and demonstrated its AAS activity with medium chain fatty acid (C10-C14) substrates in vitro. Furthermore, we used AAE15 to complement a Synechocystis aas deletion mutant and showed that the new strain preferentially incorporates supplied medium chain fatty acids into internal lipid molecules. Based on this data we propose that AAE15 can be utilized in metabolic engineering strategies for cyanobacteria that aim to produce compounds based on medium chain fatty acids.

  • 333.
    Kallas, Åsa
    KTH, School of Biotechnology (BIO), Wood Biotechnology.
    Heterologous expression, characterization and applications of carbohydrate active enzymes and binding modules2006Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Wood and wood products are of great economical and environmental importance, both in Sweden and globally. Biotechnology can be used both for achieving raw material of improved quality and for industrial processes such as biobleaching. Despite the enormous amount of carbon that is fixed as wood, the knowledge about the enzymes involved in the biosynthesis, re-organization and degradation of plant cell walls is relatively limited. In order to exploit enzymes more efficiently or to develop new biotechnological processes, it is crucial to gain a better understanding of the function and mechanism of the enzymes. This work has aimed to increase the knowledge about some of the enzymes putatively involved in the wood forming processes in Populus. Xyloglucan endotransglycosylases and a putative xylanase represent transglycosylating and hydrolytic enzymes, respectively. Carbohydrate binding modules represent non-catalytic modules, which bind to the substrate.

    Among 24 genes encoding for putative xyloglucan endotransglycosylases or xyloglucan endohydrolases that were identified in the Populus EST database, two were chosen for further studies (PttXTH16-34 and PttXTH16-35). The corresponding proteins, PttXET16-34 and PttXET16-35, were expressed in P. pastoris, purified and biochemically characterized. The importance of the N-glycans was investigated by comparing the recombinant wild-type proteins with their deglycosylated counterparts. In order to obtain the large amounts of PttXET16-34 that were needed for crystallization and development of biotechnological applications, the conditions for the large-scale production of PttXET16-34 in a fermenter were optimized.

    In microorganisms, endo-(1,4)-β-xylanases are important members of the xylan degrading machinery. These enzymes are also present in plants where they might fulfill a similar, but probably more restrictive function. One putative endo-(1,4)-β-xylanase, denoted PttXYN10A, was identified in the hybrid aspen EST library. Sequence analysis shows that this protein contains three putative carbohydrate-binding modules (CBM) from family 22 in addition to the catalytic module from GH10. Heterologous expression and reverse genetics were applied in order to elucidate the function of the catalytic module as well as the binding modules of PttXYN10A.

    Just as in microorganisms, some of the carbohydrate active enzymes from plants have one or more CBM attached to the catalytic module. So far, a very limited number of plant CBMs has been biochemically characterized. A detailed bio-informatic analysis of the CBM family 43 revealed interesting modularity patterns. In addition, one CBM43 (CBM43PttGH17_84) from a putative Populus b-(1,3)-glucanase was expressed in E. coli and shown to bind to laminarin (β-(1,3)-glucan), mixed-linked β-(1,3)(1,4)-glucans and crystalline cellulose. Due to their high specificity for different carbohydrates, CBMs can be used as probes for the analysis of plant materials. Generally, they are more specific than both staining techniques and carbohydrate-binding antibodies. We have used cellulose- and mannan binding modules from microorganisms as tools for the analysis of intact fibers as well as processed pulps.

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    FULLTEXT01
  • 334.
    Kallas, Åsa M.
    et al.
    KTH, School of Biotechnology (BIO).
    Baumann, Martin J.
    KTH, School of Biotechnology (BIO).
    Fäldt, Jenny
    KTH.
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO).
    Denman, Stuart
    KTH.
    Mellerowicz, Ewa J.
    Nishikubo, Nobuyushi
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO).
    Enzymatic characterization of a recombinant xyloglucan endotransglycosylase PttXET16-35 from Populus tremula x tremuloidesManuscript (Other academic)
  • 335.
    Kallas, Åsa M.
    et al.
    KTH, School of Biotechnology (BIO).
    Coutinho, Pedro
    Bulone, Vincent
    KTH, School of Biotechnology (BIO).
    Mellerowicz, Ewa J.
    Gilbert, Harry J.
    Henrissat, Bernard
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO).
    Characterization of a CBM43 module from hybrid aspen (Populus tremula x tremuloides): specificity of polysaccharide interaction and bioinformatic analysisManuscript (Other academic)
  • 336.
    Kallas, Åsa M.
    et al.
    KTH, School of Biotechnology (BIO).
    Piens, Kathleen
    KTH, School of Biotechnology (BIO).
    Denman, Stuart E.
    KTH, School of Biotechnology (BIO).
    Henriksson, Hongbin
    KTH, School of Biotechnology (BIO).
    Fäldt, Jenny
    KTH, School of Chemical Science and Engineering (CHE).
    Johansson, Patrik
    Brumer, Harry
    KTH, School of Biotechnology (BIO).
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO).
    Enzymatic properties of native and deglycosylated hybrid aspen (Populus tremula x tremuloides) xyloglucan endotransglycosylase 16A expressed in Pichia pastoris2005In: Biochemical Journal, ISSN 0264-6021, Vol. 390, p. 105-113Article in journal (Refereed)
    Abstract [en]

    The cDNA encoding a xyloglucan endotransglycosylase, PttXET16A, from hybrid aspen (Populus tremula x tremuloides) has been isolated from an expressed sequence tag library and expressed in the methylotrophic yeast Pichia pastoris. Sequence analysis indicated a high degree of similarity with other proteins in the XTH (xyloglucan transglycosylase/hydrolase) gene subfamily of GH16 (glycoside hydrolase family 16). In addition to the conserved GH16 catalytic sequence motif, PttXET16A contains a conserved N-glycosylation site situated proximal to the predicted catalytic residues. MS analysis indicated that the recombinant PttXET16A expressed in P. pastoris is heterogeneous due to the presence of variable N-glycosylation and incomplete cleavage of the a-factor secretion signal peptide. Removal of the N-glycan by endoglycosidase H treatment did not influence the catalytic activity significantly. Similarly, site-directed mutagenesis of Asn(93) to serine to remove the N-glycosylation site resulted in an enzyme which was comparable with the wild-type enzyme in specific activity and thermal stability but had clearly reduced solubility. Hydrolytic activity was detected neither in wild-type PttXET16A before or after enzymatic deglycosylation nor in PttXET16A N93S (Asn(93) -> Ser) mutant.

  • 337. Kang, Min-Kyoung
    et al.
    Zhou, Yongjin J.
    Buijs, Nicolaas A.
    Nielsen, Jens
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Functional screening of aldehyde decarbonylases for long-chain alkane production by Saccharomyces cerevisiae2017In: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 16, article id 74Article in journal (Refereed)
    Abstract [en]

    Background: Low catalytic activities of pathway enzymes are often a limitation when using microbial based chemical production. Recent studies indicated that the enzyme activity of aldehyde decarbonylase (AD) is a critical bottleneck for alkane biosynthesis in Saccharomyces cerevisiae. We therefore performed functional screening to identify efficient ADs that can improve alkane production by S. cerevisiae. Results: A comparative study of ADs originated from a plant, insects, and cyanobacteria were conducted in S. cerevisiae. As a result, expression of aldehyde deformylating oxygenases (ADOs), which are cyanobacterial ADs, from Synechococcus elongatus and Crocosphaera watsonii converted fatty aldehydes to corresponding Cn-1 alkanes and alkenes. The CwADO showed the highest alkane titer (0.13 mg/L/OD600) and the lowest fatty alcohol production (0.55 mg/L/OD600). However, no measurable alkanes and alkenes were detected in other AD expressed yeast strains. Dynamic expression of SeADO and CwADO under GAL promoters increased alkane production to 0.20 mg/L/OD600 and no fatty alcohols, with even number chain lengths from C8 to C14, were detected in the cells. Conclusions: We demonstrated in vivo enzyme activities of ADs by displaying profiles of alkanes and fatty alcohols in S. cerevisiae. Among the AD enzymes evaluated, cyanobacteria ADOs were found to be suitable for alkane biosynthesis in S. cerevisiae. This work will be helpful to decide an AD candidate for alkane biosynthesis in S. cerevisiae and it will provide useful information for further investigation of AD enzymes with improved activities.

  • 338.
    Kanje, Sara
    et al.
    KTH, School of Biotechnology (BIO), Protein Technology.
    Nilvebrant, Johan
    KTH, School of Biotechnology (BIO), Protein Technology.
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Protein Technology.
    An engineered Protein A derived domain for calcium dependent elution in antibody purificationManuscript (preprint) (Other academic)
  • 339.
    Kanje, Sara
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Technology.
    Venskutonytė, Raminta
    Lund University.
    Scheffel, Julia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Technology.
    Nilvebrant, Johan
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Engineering.
    Lindkvist-Petersson, Karin
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Centres, Centre for Bioprocess Technology, CBioPT. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Technology.
    Protein engineering allows for mild affinity-based elution of therapeutic antibodies2018In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 430, no 18, p. 3427-3438Article in journal (Refereed)
    Abstract [en]

    Presented here is an engineered protein domain, based on Protein A, that displays a calcium-dependent binding to antibodies. This protein, ZCa, is shown to efficiently function as an affinity ligand for mild purification of antibodies through elution with ethylenediaminetetraacetic acid. Antibodies are commonly used tools in the area of biological sciences and as therapeutics, and the most commonly used approach for antibody purification is based on Protein A using acidic elution. Although this affinity-based method is robust and efficient, the requirement for low pH elution can be detrimental to the protein being purified. By introducing a calcium-binding loop in the Protein A-derived Z domain, it has been re-engineered to provide efficient antibody purification under mild conditions. Through comprehensive analyses of the domain as well as the ZCa–Fc complex, the features of this domain are well understood. This novel protein domain provides a very valuable tool for effective and gentle antibody and Fc-fusion protein purification

  • 340.
    Kantarelis, Efthymios
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Yang, Weihong
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Blasiak, Włodzimierz
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Biomass pyrolysis for energy and fuel production2013In: Technologies for Converting Biomass to Useful Energy: Combustion, Gasification, Pyrolysis, Torrefaction and Fermentation, CRC Press , 2013, p. 245-278Chapter in book (Other academic)
    Abstract [en]

    Pyrolysis is the thermochemical decomposition of organic matter in the absence of oxygen and produces a wide range of useful products. The word is coined from the Greek-derived elements pyr "ρ-fire” and lysis "λUsσς-breakdown/separation” emphasizing the disintegration of matter due to heat. It is a standalone process or one of several reaction steps in gasification and combustion processes1 and is considered as the basic thermochemical process to produce valuable fuels and energy from biomass. Pyrolysis is also known as thermolysis, thermal cracking, dry distillation, destructive distillation, etc.; however, there are differences in those terms. During pyrolysis, complex macromolecules of biomass break down into relatively smaller molecules producing 3 major products which can be classified as follows: •a solid residue (which mainly consists of carbon and ash) known as char•gases (mainly CO, CO2, CH4, H2 and other light hydrocarbons)•Vapors/liquids known as bio-oil or bio-crude (mainly oxygenates, aromatics, water, products of low degree of polymerization, tars, etc.)

  • 341.
    Karlsson, Sara
    KTH, School of Industrial Engineering and Management (ITM), Industrial Ecology.
    Sustainable use of Baltic Sea natural resources based on ecological engineering and biogas production: System analysis and case study Trelleborg2009Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Eutrophication is one of the most serious environmental problems in the Baltic Sea due to factors such as nutrient discharges from different sources and long residence time. Eutrophication gives rise to increased primary production, often followed by oxygen depletion and disruption of important ecosystems. An action plan has been created by the Helsinki Commission (HELCOM) in order to achieve good ecological status of the Baltic Sea in the year of 2021. According to the action plan, 21 000 tonnes of nitrogen and 290 tonnes of phosphorus shall be decreased of the annual discharge from Sweden.

    The aim of methods within ecological engineering is to solve environmental problems, and the applications ranging from the harvesting of existing ecosystems to the construction of new ecosystems. This study evaluates if harvest of algae, reed, and mussels can help meeting the goals of the action plan considerably, in accordance with areas and biomass amounts that need to be harvested, and to assess the efficiency of the three biomasses with regards to nutrient reduction. The potential of harvested biomasses as substrates in biogas production and as fertilizers is investigated, and how much fossil CO2 that can be saved from being released to the atmosphere if net energy benefits, calculated from energy budgets in the biogas process, replaces fossil fuels.

    Life cycle inventories which extend from the harvest (i.e. from the Baltic coast of Sweden) to the production of biogas have been made in order to investigate the biogas potential of algal, reed, and mussel biomass. Suitability of the three biomasses as fertilizers has been assessed through comparison between nutrient sufficiency of crops and nutrient contents of the three biomasses (i.e. based on quotients of nitrogen).

    The quantity of biomass in the areas that can be harvested can help meeting the goals of the action plan drawn up by HELCOM, and mussels show to be most efficient with regards to nutrient reduction efficiency. Reed has the highest net energy benefit followed by algae, and both biomasses show potential of further investigation as substrates in the biogas production process. Mussels have low net energy benefit and thus are not a suitable substrate in biogas production. The three biomasses are suitable as fertilizers with respect to contents of nitrogen but the content of phosphorus occurs under the sufficiency levels for the crops (i.e. peas, grain, and sugar beets). For algae and reed, the potassium contents occur above the sufficiency level for peas and grain but under the level for sugar beets, mussels contain lower levels of potassium than the need of the investigated crops.

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  • 342. Karpinska, B.
    et al.
    Karlsson, M.
    Srivastava, M.
    Stenberg, A.
    Schrader, J.
    Sterky, Fredrik
    KTH, Superseded Departments, Biotechnology.
    Bhalerao, R.
    Wingsle, G.
    MYB transcription factors are differentially expressed and regulated during secondary vascular tissue development in hybrid aspen2004In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 56, no 2, p. 255-270Article in journal (Refereed)
    Abstract [en]

    More than 120,000 poplar ESTs have been sequenced from 20 different cDNA libraries by the Swedish Centre for Tree Functional Genomics. We screened this EST collection for MYB transcription factors involved in secondary vascular tissue formation, and genes assigned as PttMYB3Ra, PttMYB4a and PttMYB21a were selected for further characterisation. Three MYB genes showed different expression patterns in various organs, tissues and stem sub-sections representing different developmental stages of vascular tissue formation. Furthermore, the analysis showed that PttMYB21a expression was much higher in secondary cell wall formation zone of xylem and phloem fibers than in other developmental zones. Transgenic hybrid aspen plants, expressing the 3'-part of the PttMYB21a gene in antisense orientation were generated to assess the function of PttMYB21a gene in vascular tissue formation and lignification. All transgenic lines showed reduced growth and had fewer internodes compared to the wild-type. The analysis of selected lines showed that acid soluble lignin present in the bark was higher in transgenic lines as compared to wild-type plants. Moreover a higher transcript level of caffeoyl-CoA 3-O-methyltransferase [CCoAOMT];EC2.1.1.104) was found in the phloem of the transgenic plants, suggesting that PttMYB21a might function as a transcriptional repressor.

  • 343. Kaucka, Marketa
    et al.
    Zikmund, Tomas
    Tesarova, Marketa
    Gyllborg, Daniel
    Hellander, Andreas
    Jaros, Josef
    Kaiser, Jozef
    Petersen, Julian
    Szarowska, Bara
    Newton, Phillip T.
    Dyachuk, Vyacheslav
    li, Lei
    Qian, Hong
    Johansson, Anne-Sofie
    Mishina, Yuji
    Currie, Joshua D.
    Tanaka, Elly M.
    Erickson, Alek
    Dudley, Andrew
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cellular Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Southam, Paul
    Coen, Enrico
    Chen, Min
    Weinstein, Lee S.
    Hampl, Ales
    Arenas, Ernest
    Chagin, Andrei S.
    Fried, Kaj
    Adameyko, Igor
    Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage2017In: eLIFE, E-ISSN 2050-084X, Vol. 6, article id e25902Article in journal (Refereed)
    Abstract [en]

    Cartilaginous structures are at the core of embryo growth and shaping before the bone forms. Here we report a novel principle of vertebrate cartilage growth that is based on introducing transversally-oriented clones into pre-existing cartilage. This mechanism of growth uncouples the lateral expansion of curved cartilaginous sheets from the control of cartilage thickness, a process which might be the evolutionary mechanism underlying adaptations of facial shape. In rod-shaped cartilage structures (Meckel, ribs and skeletal elements in developing limbs), the transverse integration of clonal columns determines the well-defined diameter and resulting rod-like morphology. We were able to alter cartilage shape by experimentally manipulating clonal geometries. Using in silico modeling, we discovered that anisotropic proliferation might explain cartilage bending and groove formation at the macro-scale.

  • 344. Kennedy, S
    et al.
    Fasterius, Erik
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Al-Khalili Szigyarto, Cristina
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Kolch, W
    et al.,
    Adaptive rewiring of protein-protein interactions and signal flow in the EGFR signaling network by mutant RASManuscript (preprint) (Other academic)
  • 345.
    Khudur, Ivan
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology, Heat and Power Technology.
    Aluminium alloys ability to catalyse the oxidation of biodiesel: Development of a procedure to test alloys2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Biodiesel is a renewable and biodegradable fuel that has the possibility to replace conventional diesel fuel and reduce the environmental pollution. Despite its environmental benefits, it has been shown to cause damage to the vehicle engines, due to its oxidative properties. Different metals, such as copper, zinc and aluminium are present in the vehicle fuel system and have been shown to catalyse the oxidation of biodiesel. Several studies have been performed to investigate the interaction between these metals and fuel. However, some reports concluded contradicting results when it comes to the oxidation of biodiesel in contact with aluminium alloys. This project aimed therefore to investigate and create a simple method for comparing the catalytic effect on oxidation for metals, and use this method to evaluate the degradation rate of biodiesel in contact with aluminium alloys. Different heating methods and coating materials were tested using the biodiesel RME to develop the testing procedure. When a test procedure was established, three filter houses made from cast aluminium alloy and three aluminium ingots with different amount of copper were immersed in RME and the stability was evaluated. The results showed that using an oven at 80 °C to investigate the stability provided the most repeatable results, and the spray paint Auto K billack spray Universal appeared to be compatible to use with RME. The inner untreated surface of the fuel filter houses did not seem to increase the oxidation rate of biodiesel. Aluminium alloys with higher copper content degraded RME more than aluminium alloys with little/no copper, if the surface had been treated mechanically, but not to a large extent. This concludes that aluminium alloys may reduce the stability of biodiesel if it contains much copper and if the surface of the alloy has been treated. However, the detected reduction on oxidation stability could depend on other factors, and therefore it is recommended to conduct further experiments on test the aluminium alloys.

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    fulltext
  • 346.
    Khudur, Ivan
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology, Heat and Power Technology.
    Aluminium alloys ability to catalyse the oxidation of biodiesel: Development of a procedure to test alloys2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Biodiesel is a renewable and biodegradable fuel that has the possibility to replace conventional diesel fuel and reduce the environmental pollution. Despite its environmental benefits, it has been shown to cause damage to the vehicle engines, due to its oxidative properties. Different metals, such as copper, zinc and aluminium are present in the vehicle fuel system and have been shown to catalyse the oxidation of biodiesel. Several studies have been performed to investigate the interaction between these metals and fuel. However, some reports concluded contradicting results when it comes to the oxidation of biodiesel in contact with aluminium alloys. This project aimed therefore to investigate and create a simple method for comparing the catalytic effect on oxidation for metals, and use this method to evaluate the degradation rate of biodiesel in contact with aluminium alloys. Different heating methods and coating materials were tested using the biodiesel RME to develop the testing procedure. When a test procedure was established, three filter houses made from cast aluminium alloy and three aluminium ingots with different amount of copper were immersed in RME and the stability was evaluated. The results showed that using an oven at 80 °C to investigate the stability provided the most repeatable results, and the spray paint Auto K billack spray Universal appeared to be compatible to use with RME. The inner untreated surface of the fuel filter houses did not seem to increase the oxidation rate of biodiesel. Aluminium alloys with higher copper content degraded RME more than aluminium alloys with little/no copper, if the surface had been treated mechanically, but not to a large extent. This concludes that aluminium alloys may reduce the stability of biodiesel if it contains much copper and if the surface of the alloy has been treated. However, the detected reduction on oxidation stability could depend on other factors, and therefore it is recommended to conduct further experiments on test the aluminium alloys.

    Download full text (pdf)
    Aluminium alloys ability to catalyse the oxidation of biodiesel: Development of a procedure to test alloys
  • 347.
    Kiousis, Dimitrios
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.).
    Computer Aided Angioplasty: Patient-specific arterial modeling and smooth 3D contact analysis of the stent-balloon-artery interaction2006Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Paper A: In this paper, the development and implementation of a contact algorithm based on C2-continuous surface representations is discussed. In 3D contact simulations involving models with arbitrarily curved surfaces (as in the case of vessel walls), the discretization of the contact surfaces by means of facet-based techniques could lead to numerical instabilities and finally loss of quadratic convergence. These instabilities arise mainly due to the sliding of contractor (slave) nodes over the boundaries of target (master) contact facets, where jumps of the normal vector are experienced. The paper addresses successfully this problem, by discretization of the target surfaces by means of C2-continuous parameterization schemes. Initially, the uniform cubic B-spline surfaces are introduced. Next, in an attempt for more accurate representations of the geometric models of the contact surfaces, a new parameterization based on the expression of cubic B-splines is developed. The two approaches are implemented into a finite element framework and more specifically, into the multipurpose finite element analysis program FEAP. The special merits of the developed algorithms and the advantages of the smooth surfaces over facet-based approaches are exhibited through a classical contact mechanics problem, considering incompressibility, finite deformations and large slidings. Next, a simulation of balloon angioplasty with stenting is presented, where the contact between both medical devices (balloon and stent) with the arterial wall is modeled. The arterial wall is modeled in this first approach, as hyperelastic, homogeneous, isotropic, while a cylindrically orthotropic model is developed to capture the nonlinear, anisotropic behavior of the balloon catheter under pressure. Two stents with the same geometry but different strut thickness, are studied. Both are considered elasto-plastic. The performed simulations point out the outcome of the balloon angioplasty and stenting in terms of luminal gain and mechanical strains. Finally, a comparison between the two stent configurations is presented.

    Paper B: The second paper makes use of the contact tool developed in Paper A and focuses on the changes of the mechanical environment of the arterial wall due to stenting, as a function of a set of stent design parameters. In particular, Paper B presents a detailed geometric and material model of a postmortem human iliac artery, composed by distinct tissue components, each associated with specific mechanical properties. The constitutive formulation for the artery considers anisotropic, highly nonlinear mechanical characteristics under supraphysiological loadings. The material and structural parameters of the arterial model are obtained through uniaxial tensile tests on stripes extracted from the several arterial tissues that form the stenosis, axially and circumferentially oriented. Through cooperation with a well-established stent manufacturing company, an iliac stent was acquired. The dimensions of the stent are measured under a reflected-light microscope, while it is parameterized in such a way as to enable new designs to be simply generated through variations of its geometric parameters. The 3D balloon-stent-artery interaction is simulated by making use of the smooth contact surfaces with C2-continuity, as previously mentioned. Next, scalar quantities attempt to characterize the arterial wall changes after stenting, in form of contact forces induced by the stent struts, stresses within the individual components and luminal change. These numerically derived quantities allow the determination of the most appropriate stent configuration for an individual stenosis. Therefore, the proposed methodology has the potential to provide a scientific basis for optimizing treatment procedures, stent material and geometries on a patient-specific level.

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    FULLTEXT01
  • 348.
    Kiousis, Dimitrios
    et al.
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.).
    Gasser, T. Christian
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.).
    Holzapfel, Gerhard
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.), Biomechanics.
    A numerical model to study the interaction of vascular stents with human atherosclerotic lesions2007In: Annals of Biomedical Engineering, ISSN 0090-6964, E-ISSN 1573-9686, Vol. 35, no 11, p. 1857-1869Article in journal (Refereed)
    Abstract [en]

    A methodology is proposed that identifies optimal stent devices for specific clinical criteria. It enables to predict the effect of stent designs on the mechanical environment of stenotic arteries. In particular, we present a numerical study which is based on the interaction of a vascular stent with a patient-specific, atherosclerotic human iliac lesion of type V. The stress evolution in four different tissue components during and after stenting is investigated. The geometric model of the artery is obtained through MRI, while anisotropic material models are applied to describe the behavior of tissues at finite strains. In order to model the observed fissuring and dissection of the plaque under dilation, the undeformed configuration of the arterial wall incorporates two initial tears. The 3D balloon-stent-artery interaction problem is modeled by means of a contact algorithm, which is based on a C-2-continuous surface parametrization, hence avoiding numerical instabilities of standard facet-based techniques. In the simulations three different stent designs are studied. The performance of each stent is characterized by scalar quantities relating to stress changes in the artery, contact forces, and changes in lumen area after stenting. The study concludes by suggesting two optimal stent designs for two different clinically relevant parameters.

  • 349.
    Kiousis, Dimitrios
    et al.
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.).
    Gasser, Thomas
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.).
    Holzapfel, Gerhard
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.).
    Smooth contact strategies with emphasis on the modeling of balloon angioplasty with stenting2008In: International Journal for Numerical Methods in Engineering, ISSN 0029-5981, E-ISSN 1097-0207, Vol. 75, no 7, p. 826-855Article in journal (Refereed)
    Abstract [en]

    Critical to the simulation of balloon angioplasty is the modeling of the contact between the artery wall and the medical devices. In standard approaches, the 3D contact surfaces are described by means of C0-continuous facet-based techniques, which may lead to numerical problems. This work introduces a novel contact algorithm where the target surfaces are described by polynomial expressions with C2-continuity. On the basis of uniform cubic B-splines, two different parametrization techniques are presented and compared, while the related implementation of the algorithm into a finite element analysis program is described. Two numerical examples are selected to demonstrate the special merits of the proposed contact formulation. The first example is a benchmark contact problem selected to point out the special features of the proposed strategies. The second example is concerned with the simulation of balloon angioplasty and stenting, where the contact between the balloon, the stent and the artery wall is numerically modeled. A patient-specific 3D model of a stenotic femoral artery serves as a basis. The study concludes by identifying the changes in the mechanical environment of the artery in terms of contact forces and strains by considering two different stent designs.

  • 350. Kling, A.
    et al.
    Dincer, C.
    Armbrecht, L.
    Horak, Josef
    KTH, School of Biotechnology (BIO), Protein Technology.
    Kieninger, J.
    Urban, G.
    Electrochemical microfluidic platform for simultaneous multi-analyte detection2015In: Eurosensors 2015, Elsevier, 2015, Vol. 120, p. 916-919Conference paper (Refereed)
    Abstract [en]

    We present an electrochemical lab-on-a-chip (LOC) platform for the simultaneous detection of up to four different analytes. The possibility to separately immobilize different assays in a channel network, without active valves, was successfully demonstrated using a model assay linked to glucose oxidase. This enables the detection of various analytes even with different assay formats. For the assay immobilization, the channel surface, made out of dry film photoresist (DFR), could be activated by means of EDC/NHS-linker chemistry and used for the covalent binding of primary amines. Cross-sensitivity due to diffusion within the channel network could be experimentally excluded.

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