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  • 751.
    Wang, Shule
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Catalytic fast pyrolysis of softwood under N2 and H2 atmosphere2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Bio-oil generated from biomass is becoming one of the most promising alternatives as potential energy sources to replace fossil fuels in the transportation sector. Fast pyrolysis of biomass is one of the most economically feasible ways to produce bio-oil according to recent research on thermochemical conversion of biomass. Upgrading of oils derived from to hydrocarbon fuels requires oxygen removal and molecular weight reduction.  Catalytic cracking and hydrotreating are two efficient processes to upgrade bio-oil. Hydrotreating requires that hydrogen is added in the process to increase the H/C ratio of the product. Normally, catalytic fast pyrolysis and hydrotreating are two separated processes.

    In order to increase the energy efficiency of the process, exploring the fast pyrolysis of biomass with in-situ catalyst under the hydrogen atmosphere, i.e. catalytic hydropyrolysis shall be very interesting, and this is the objective of this work.

    In this work, biomass pyrolysis experiments using softwood have been performed in hydrogen and nitrogen atmospheres with/without catalyst. It was found that in the case of the H2 atmosphere, a higher yield on oil phase and a reduced water production is found. More oxygen was removed as CO and CO2. The catalytic fast pyrolysis (CFP) under H2 atmosphere also produce relatively more PAH (polymer aromatic hydrocarbon) and less MAH (monomer aromatic hydrocarbon) than under N2 atmosphere.

     

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  • 752.
    Wang, Shule
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Persson, Henry
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Weihong, Yang
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Jönsson, Pär
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Effect of H2 as Pyrolytic Agent on the Product Distribution during Catalytic Fast Pyrolysis of Biomass Using Zeolites2018In: Energy & Fuels, ISSN 0887-0624, E-ISSN 1520-5029, Vol. 32, no 8, p. 8530-8536Article in journal (Refereed)
    Abstract [en]

    Bio-oil generated from catalytic fast pyrolysis or hydrotreating processes represents one of the most promising alternatives to liquid fossil fuels. The use of H2 as carrier gas in the pyrolysis of biomass requires further research to study the catalytic fast pyrolysis reactions in the case of using reactive atmosphere. In this work, pyrolysis experiments with lignocellulosic biomass have been performed in a fixed bed reactor in H2 and N2 atmospheres with/without HZSM-5 additions to investigate the influence of the pyrolytic agents during fast pyrolysis of biomass and upgrading of pyrolytic vapors over a zeolitic catalyst. It was found that in a H2 atmosphere, H2 was consumed in both noncatalytic and catalytic pyrolysis processes, respectively. Higher yields of nonaqueous liquids and permanent gases are obtained in a H2 atmosphere compared to a N2 atmosphere. A catalytic pyrolysis process using HZSM-5 in a H2 atmosphere increased the production of polymer aromatic hydrocarbons and suppressed the production of monomer aromatic hydrocarbons compared to similar tests performed in a N2 atmosphere. The results show an overall increased activity of HZSM-5 in the reactive H2 atmosphere compared to a N2 atmosphere.

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  • 753.
    Wang, Shule
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Persson, Henry
    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.
    Jönsson, Pär
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Pyrolysis study of hydrothermal carbonization-treated digested sewage sludge using a Py-GC/MS and a bench-scale pyrolyzer2019In: Fuel, ISSN 0016-2361, E-ISSN 1873-7153, FuelArticle in journal (Refereed)
    Abstract [en]

    The disposal of digested sewage sludge is becoming a global problem. Hydrothermal carbonization (HTC) combined with the pyrolysis of digested sewage sludge was investigated by using a new conversion route for the exploitation of sewage sludge in energy applications. The thermochemical properties of the material were investigated by using HTC pre-treatments, thermogravimetric analyses, pyrolysis tests in Py-GC/MS and a bench-scale fixed bed reactor at temperatures of 450, 550, and 650 °C. It was found that the thermal decomposition of the hydrothermally treated digested sewage sludge takes place in a two-stage reaction. After pyrolysis, the ash in the sample was oxidized in the O2 atmosphere at 900 °C. Therefore, a new characterization method for determination of the non-oxdized ash content and fixed carbon content was proposed. The result from Py-GC/MS shows that the abundance of aromatic hydrocarbons in pyrolytic vapors present a positive correlation with increased temperature. In the bench-scale experiments, the highest HHV of the organic fraction was obtained at 650 °C as 38.46 MJ/kg.

  • 754. Wang, X.
    et al.
    Nordlander, E.
    Thorin, E.
    Yan, Jinyue
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Energy Processes. School of Sustainable Development of Society and Technology, Mälardalen University, 72123 Västerås, Sweden.
    Microalgal biomethane production integrated with an existing biogas plant: A case study in Sweden2013In: Applied Energy, ISSN 0306-2619, E-ISSN 1872-9118, Vol. 112, no SI, p. 478-484Article in journal (Refereed)
    Abstract [en]

    Microalgae are considered as potential sources for biodiesel production due to the higher growth rate than terrestrial plants. However, the large-scale application of algal biodiesel would be limited by the downstream cost of lipid extraction and the availability of water, CO2 and nutrients. A possible solution is to integrate algae cultivation with existing biogas plant, where algae can be cultivated using the discharges of CO2 and digestate as nutrient input, and then the attained biomass can be converted directly to biomethane by existing infrastructures. This integrated system is investigated and evaluated in this study. Algae are cultivated in a photobioreactor in a greenhouse, and two cultivation options (greenhouse with and without heating) are included. Life cycle assessment of the system was conducted, showing that algal biomethane production without greenhouse heating would have a net energy ratio of 1.54, which is slightly lower than that (1.78) of biomethane from ley crop. However, land requirement of the latter is approximately 68 times that of the former, because the area productivity of algae could reach at about 400t/ha (dry basis) in half a year, while the annual productivity of ley crop is only about 5.8t/ha. For the case of Växtkraft biogas plant in Västerås, Sweden, the integrated system has the potential to increase the annual biomethane output by 9.4%. This new process is very simple, which might have potential for scale-up and commercial application of algal bioenergy.

  • 755.
    Wang, Yang
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Discovery and investigation of glycoside hydrolase family 5 enzymes with potential use in biomass conversion2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Glycoside hydrolases (GHs) cleave glycosidic bonds in glycoconjugates, oligosaccharides and polysaccharides such as cellulose and various hemicelluloses. Mannan is a major group of hemicelluloses. In higher plants, they usually serve as storage carbohydrates in seeds and tubers or as structural polysaccharides cross-linking with cellulose/lignin in cell walls. In industrial fields, this renewable biomass component can be used in various areas such as production of biofuels and health-benefit manno-oligosaccharides; and mannan degrading enzymes, especially mannanases, are important molecular tools for controlling mannan polysaccharides properties in biomass conversion. In this thesis, the evolution, substrate specificity and subfamily classification of the most important GH family, i.e., glycoside hydrolase family 5 (GH5), are presented providing a powerful tool for exploring GH5 enzymes in search for enzymes with interesting properties for sustainable biomass conversion. Additionally, three GH5_7 mannanases from Arabidopsis thaliana (AtMan5-1, AtMan5-2 and AtMan5-6) were investigated in the present study. Bioinformatics tools, heterologous expression, and enzymology were applied in order to reveal the catalytic properties of the target enzymes, increase understanding of plant mannanase evolution, and evaluate their potential use in biomass conversion. This approach revealed: (1) AtMan5-1 exhibits mannan hydrolase/transglycosylase activity (MHT), (2) AtMan5-2 preferably degrades mannans with a glucomannan backbone, and (3) AtMan5-6 is a relatively thermotolerant enzyme showing high catalytic efficiency for conversion of glucomannan and galactomannan making this plant mannanase an interesting candidate for biotechnological applications of digesting various mannans. Moreover, these studies suggest an evolutionary diversification of plant mannanase enzymatic function.

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  • 756.
    Wang, Yang
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Azhar, Shoaib
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Gandini, Rosaria
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Divne, Christina
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Ezcurra, Ines
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Biochemical characterization of the novel endo-β-mannanase AtMan5-2 from Arabidopsis thalianaManuscript (preprint) (Other academic)
  • 757.
    Wang, Yang
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Azhar, Shoaib
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Gandini, Rosaria
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Divne, Christina
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Ezcurra, Ines
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Investigating the function and biochemical properties of Arabidopsis mannanase 5-6Manuscript (preprint) (Other academic)
  • 758. Watton, P. N.
    et al.
    Selimovic, A.
    Raberger, N. B.
    Huang, P.
    Holzapfel, Gerhard
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.), Biomechanics.
    Ventikos, Y.
    Modelling evolution and the evolving mechanical environment of saccular cerebral aneurysms2011In: Biomechanics and Modeling in Mechanobiology, ISSN 1617-7959, E-ISSN 1617-7940, Vol. 10, no 1, p. 109-132Article in journal (Refereed)
    Abstract [en]

    A fluid-solid-growth (FSG) model of saccular cerebral aneurysm evolution is developed. It utilises a realistic two-layered structural model of the internal carotid artery and explicitly accounts for the degradation of the elastinous constituents and growth and remodelling (G&R) of the collagen fabric. Aneurysm inception is prescribed: a localised degradation of elastin results in a perturbation in the arterial geometry; the collagen fabric adapts, and the artery achieves a new homeostatic configuration. The perturbation to the geometry creates an altered haemodynamic environment. Subsequent degradation of elastin is explicitly linked to low wall shear stress (WSS) in a confined region of the arterial domain. A sidewall saccular aneurysm develops, the collagen fabric adapts and the aneurysm stabilises in size. A quasi-static analysis is performed to determine the geometry at diastolic pressure. This enables the cyclic stretching of the tissue to be quantified, and we propose a novel index to quantify the degree of biaxial stretching of the tissue. Whilst growth is linked to low WSS from a steady (systolic) flow analysis, a pulsatile flow analysis is performed to compare steady and pulsatile flow parameters during evolution. This model illustrates the evolving mechanical environment for an idealised saccular cerebral aneurysm developing on a cylindrical parent artery and provides the guidance to more sophisticated FSG models of aneurysm evolution which link G&R to the local mechanical stimuli of vascular cells.

  • 759. Wettergren, E E
    et al.
    Gussing, F
    Sest, Maike
    KTH, School of Biotechnology (BIO), Molecular Biotechnology (closed 20130101).
    Graslund, T
    Lundberg, Cecilia
    KTH, School of Biotechnology (BIO), Molecular Biotechnology (closed 20130101).
    Regulation of Endogenous GAD67 Expression Using Artificial Transcription Factors2011In: Molecular Therapy, ISSN 1525-0016, E-ISSN 1525-0024, Vol. 19, no 7Article in journal (Other academic)
  • 760.
    Widhe, Mona
    et al.
    KTH, School of Biotechnology (BIO), Protein Technology.
    Shalaly, Nancy Dekki
    KTH, School of Biotechnology (BIO), Protein Technology.
    Hedhammar, My
    KTH, School of Biotechnology (BIO), Protein Technology.
    A fibronectin mimetic motif improves integrin mediated cell biding to recombinant spider silk matrices2016In: Biomaterials, ISSN 0142-9612, E-ISSN 1878-5905, Vol. 74, p. 256-266Article in journal (Refereed)
    Abstract [en]

    The cell binding motif RGD is the most widely used peptide to improve cell binding properties of various biomaterials, including recombinant spider silk. In this paper we use genetic engineering to further enhance the cell supportive capacity of spider silk by presenting the RGD motif as a turn loop, similar to the one found in fibronectin (FN), but in the silk stabilized by cysteines, and therefore denoted FNCC. Human primary cells cultured on FNCC-silk showed increased attachment, spreading, stress fiber formation and focal adhesions, not only compared to RGD-silk, but also to silk fused with linear controls of the RGD containing motif from fibronectin. Cell binding to FNCC-silk was shown to involve the alpha 5 beta 1 integrin, and to support proliferation and migration of keratinocytes. The FNCC-silk protein allowed efficient assembly, and could even be transformed into free standing films, on which keratinocytes could readily form a monolayer culture. The results hold promise for future applications within tissue engineering.

  • 761.
    Wikman, Maria
    et al.
    KTH, School of Biotechnology (BIO).
    Friedman, Mikaela
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Pinitkiatisakul, S.
    Andersson, Christin
    KTH, School of Biotechnology (BIO).
    Hemphill, A.
    Lovgren-Bengtsson, K.
    Lunden, A.
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    General strategies for efficient adjuvant incorporation of recombinant subunit immunogens2005In: Vaccine, ISSN 0264-410X, E-ISSN 1873-2518, Vol. 23, no 17-18, p. 2331-2335Article in journal (Refereed)
    Abstract [en]

    We have previously reported strategies for Escherichia coli production of recombinant immunogens fused to hydrophobic peptides or lipid tags to improve their capacity to be incorporated into an adjuvant formulation, e.g., immunostimulating complexes (iscoms). Recently, we also explored the strong interaction between biotin and streptavidin to achieve iscom association of recombinant immunogens. Plasmodium falciparum, Toxoplasma gondii and Neospora caninum antigens have served as model immunogens in the different studies. Generated fusion proteins have been found to be successfully incorporated into iscoms and high-titer antigen-specific antibody responses have been obtained upon immunization of mice. We believe that the different concepts presented, utilizing either hydrophobic peptide or lipid tags, or the recently explored biotin-streptavidin principle, offer convenient methods to achieve efficient adjuvant incorporation of recombinant immunogens.

  • 762.
    Winzell, Anders
    et al.
    KTH, School of Biotechnology (BIO).
    Rajangam, Alex
    KTH, School of Biotechnology (BIO).
    Arvestad, Lars
    KTH, School of Computer Science and Communication (CSC).
    Filling, Charlotta
    KTH, School of Biotechnology (BIO).
    Divine, Christina
    KTH, School of Biotechnology (BIO).
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO).
    Master, Emma R.
    KTH, School of Biotechnology (BIO).
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO).
    Sequence Analysis and Recombinant Expression of Family 43 GlycosyltransferasesManuscript (preprint) (Other academic)
  • 763.
    Wirta, Valtteri
    KTH, School of Biotechnology (BIO).
    Mining the transcriptome - methods and applications2006Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Regulation of gene expression occupies a central role in the control of the flow of genetic information from genes to proteins. Regulatory events on multiple levels ensure that the majority of the genes are expressed under controlled circumstances to yield temporally controlled, cell and tissue-specific expression patterns. The combined set of expressed RNA transcripts constitutes the transcriptome of a cell, and can be analysed on a large-scale using both sequencing and microarray-based methods.

    The objective of this work has been to develop tools for analysis of the transcriptomes (methods), and to gain new insights into several aspects of the stem cell transcriptome (applications). During recent years expectations of stem cells as a resource for treatment of various disorders have emerged. The successful use of endogenously stimulated or ex vivo expanded stem cells in the clinic requires an understanding of mechanisms controlling their proliferation and self-renewal.

    This thesis describes the development of tools that facilitate analysis of minute amounts of stem cells, including RNA amplification methods and generation of a cDNA array enriched for genes expressed in neural stem cells. The results demonstrate that the proposed amplification method faithfully preserves the transcript expression pattern. An analysis of the feasibility of a neurosphere assay (in vitro model system for study of neural stem cells) clearly shows that the culturing induces changes that need to be taken into account in design of future comparative studies. An expressed sequence tag analysis of neural stem cells and their in vivo microenvironment is also presented, providing an unbiased large-scale screening of the neural stem cell transcriptome. In addition, molecular mechanisms underlying the control of stem cell self-renewal are investigated. One study identifies the proto-oncogene Trp53 (p53) as a negative regulator of neural stem cell self-renewal, while a second study identifies genes involved in the maintenance of the hematopoietic stem cell phenotype.

    To facilitate future analysis of neural stem cells, all microarray data generated is publicly available through the ArrayExpress microarray data repository, and the expressed sequence tag data is available through the GenBank.

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  • 764.
    Wittrup Larsen, Marianne
    et al.
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Bornscheuer, Uwe T.
    Expression of Candida antarctica lipase B in Pichia pastoris and various Escherichia coli systems2008In: Protein Expression and Purification, ISSN 1046-5928, E-ISSN 1096-0279, Vol. 62, p. 90-97Article in journal (Refereed)
    Abstract [en]

    Candida antarctica lipase B (CALB) carrying a point mutation, N74S, resulting in a non-glycosylated protein was actively expressed in Pichia pastoris yielding 44 mg/L which was similar to that of the glycosylated CALB wild type expressed in A pastoris. Hence, the major obstacle in the Escherichia coli expression of CALB is not the lack of glycosylation. To understand and improve the expression of CALB in E. coli, a comprehensive investigation of four different systems were tested: periplasmic expression in Rosetta (DE3), cytosolic expression in Rosetta-gami 2(DE3) and Origami 2(DE3) as well as co-expression with chaperones groES and groEL in Origami B(DE3), all using the pET-22b(+) vector and the T7lac promoter.

    Furthermore the E. coli expression was carried out at three different temperatures (16, 25 and 37 C) to optimise the expression. Periplasmic expression resulted in highest amount of active CALB of the four systems, yielding a maximum of 5.2 mg/L culture at 16 degrees C, which is an improvement to previous reports.

    The specific activity of CALB towards tributyrin in E. coli was found to be the same for periplasmic and cytosolic expression. Active site titration showed that the CALB mutant N74S had a lower specific activity in comparison to wild type CALB regardless of expression host. The expected protein identity was confirmed by LC-ESI-MS analysis in E. coli, whereas in P. pastoris produced CALB carried four additional amino acids from an incomplete protein processing.

  • 765.
    Woestenenk, Esmeeralda A.
    et al.
    KTH, Superseded Departments, Biotechnology.
    Hammarström, Martin
    KTH, Superseded Departments, Biotechnology.
    Härd, Torleif
    Screening methods to determine biophysical properties of proteins in structural genomics2003In: Analytical biochemistry, ISSN 0003-2697, Vol. 318, no 1, p. 71-79Article in journal (Refereed)
    Abstract [en]

    We have developed and tested a simple and efficient protein purification method for biophysical screening of proteins and protein fragments by nuclear magnetic resonance (NMR) and optical methods, such as circular dichroism spectroscopy. The method constitutes an extension of previously described protocols for gene expression and protein solubility screening [M. Hammarström et al., (2002), Protein Science 11, 313]. Using the present purification scheme it is possible to take several target proteins, produced as fusion proteins, from cell pellet to NMR spectrum and obtain a judgment on the suitability for further structural or biophysical studies in less than 1 day. The method is independent of individual protein properties as long as the target protein can be produced in soluble form with a fusion partner. Identical procedures for cell culturing, lysis, affinity chromatography, protease cleavage, and NMR sample preparation then initially require only optimization for different fusion partner and protease combinations. The purification method can be automated, scaled up or down, and extended to a traditional purification scheme. We have tested the method on several small human proteins produced in Escherichia coli and find that the method allows for detection of structured proteins and unfolded or molten globule-like proteins.

  • 766.
    Wright, Thomas
    KTH, School of Engineering Sciences (SCI), Mechanics.
    The linear and nonlinear biomechanics of the middle ear2005Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    This thesis addresses the biomechanics of the human middle ear, that part of the auditory system which converts sound pressure waves in air to fluid pressure waves in the cochlea. The middle ear's mechanism is analysed in four papers, three main and one supporting; in the main papers the middle ear is treated as a multi-particle, multi-rigid body ensemble possessing a variable number of degrees of freedom depending upon the case being investigated.

    It is confirmed, using the standard representation of a single fused incudo-malleal block, that the middle ear's motion is linear, but when this fused block restriction is lifted nonlinearity is present which significantly affects the mechanism's behaviour. In view of the linearity of the chain under the fused block conditions, the explanatory veracity of the conventionally accepted `fixed axis hypothesis' of ossicular motion is examined and found to be wanting as a realistic description of the chain's physical movement.

    The nonlinear behaviour of the ossicular chain centres around the action of the incudo-malleal joint. This joint is shown to have preferential planes of operation, principally the pitch or longitudinal plane and in general to act as an efficient energy dissipator at high driving pressures and low frequencies. Providing the pressure is high enough, it is shown this energy dissipator effect eventually becomes independent of frequency.

    The supporting paper discusses the dynamics of the imposition and removal of equation constraints justifying methods used to investigate the functioning of the incudo-malleal joint.

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  • 767.
    Wu, Yu-Tang
    et al.
    Univ Paris 11, Univ Paris Saclay, Inst Integrat Biol Cell, NanoBioPhoton Nanofret Com,CNRS,CEA, Orsay, France..
    Qiu, Xue
    Univ Paris 11, Univ Paris Saclay, Inst Integrat Biol Cell, NanoBioPhoton Nanofret Com,CNRS,CEA, Orsay, France..
    Lindbo, Sarah
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Technology.
    Susumu, Kimihiro
    US Naval Res Lab, Opt Sci Div, Code 5600, Washington, DC USA.;KeyW Corp, Hanover, MD 21076 USA..
    Medintz, Igor L.
    US Naval Res Lab, Ctr Bio Mol Sci & Engn, Code 6900, Washington, DC USA..
    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.
    Hildebrandt, Niko
    Univ Paris 11, Univ Paris Saclay, Inst Integrat Biol Cell, NanoBioPhoton Nanofret Com,CNRS,CEA, Orsay, France..
    Quantum Dot-Based FRET Immunoassay for HER2 Using Ultrasmall Affinity Proteins2018In: Small, ISSN 1613-6810, E-ISSN 1613-6829, Vol. 14, no 35, article id 1802266Article in journal (Refereed)
    Abstract [en]

    Engineered scaffold affinity proteins are used in many biological applications with the aim of replacing natural antibodies. Although their very small sizes are beneficial for multivalent nanoparticle conjugation and efficient Forster resonance energy transfer (FRET), the application of engineered affinity proteins in such nanobiosensing formats has been largely neglected. Here, it is shown that very small (approximate to 6.5 kDa) histidine-tagged albumin-binding domain-derived affinity proteins (ADAPTs) can efficiently self-assemble to zwitterionic ligand-coated quantum dots (QDs). These ADAPT-QD conjugates are significantly smaller than QD-conjugates based on IgG, Fab', or single-domain antibodies. Immediate applicability by the quantification of the human epidermal growth factor receptor 2 (HER2) in serum-containing samples using time-gated Tb-to-QD FRET detection on the clinical benchtop immunoassay analyzer KRYPTOR is demonstrated here. Limits of detection down to 40 x 10(-12)m (approximate to 8 ng mL(-1)) are in a relevant clinical concentration range and outperform previously tested assays with antibodies, antibody fragments, and nanobodies.

  • 768.
    Wållberg, Fredrik
    et al.
    KTH, School of Biotechnology (BIO).
    Sundström, Heléne
    KTH, School of Biotechnology (BIO).
    Ledung, E.
    Department of Biology and Chemical Engineering, Mälardalen University.
    Hewitt, C. J.
    Centre for Formulation Engineering, School of Engineering (Chemical Engineering), University of Birmingham.
    Enfors, Sven-Olof
    KTH, School of Biotechnology (BIO).
    Monitoring and quantification of inclusion body formation in Escherichia coli by multi-parameter flow cytometry2005In: Biotechnology letters, ISSN 0141-5492, E-ISSN 1573-6776, Vol. 27, no 13, p. 919-926Article in journal (Refereed)
    Abstract [en]

    Multi-parameter flow cytometry was used to monitor the formation of promegapoietin (PMP) inclusion bodies during a high cell density Escherichia coli fed-batch fermentation process. Inclusion bodies were labelled with a primary antibody and then with a secondary fluorescent antibody. Using this method it was possible to detect PMP inclusion body formation with a high specificity and it was possible to monitor the increased accumulation of the protein with process time (6-48 mg PMP/g CDW) whilst highlighting population heterogeneity.

  • 769.
    Xia, Q. L.
    et al.
    Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering college, Chongqing University, Chongqing, 400044, China.
    Wang, M. Q.
    Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering college, Chongqing University, Chongqing, 400044, China.
    Jiang, B.
    Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering college, Chongqing University, Chongqing, 400044, China.
    Hu, N.
    Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering college, Chongqing University, Chongqing, 400044, China.
    Wu, X. Y.
    Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering college, Chongqing University, Chongqing, 400044, China.
    Hou, W. S.
    Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering college, Chongqing University, Chongqing, 400044, China.
    Nyberg, Tobias
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Neuronic Engineering.
    Infrared Laser Pulses Excite Action Potentials in Primary Cortex Neurons in Vitro∗2019In: Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, 2019, p. 5184-5187Conference paper (Refereed)
    Abstract [en]

    Infrared neural modulation (INM) has been well studied in the peripheral nervous system (PNS) for potential clinical applications. However, limited research has been conducted on the central nervous systems (CNS). In this study, we aimed at investigating the feasibility of using pulsed infrared (IR) laser with a wavelength of 1940 nm to excite network activity of cultivated rat cortex neurons.We cultured rat cortex neurons, forming neural networks with spontaneous neural activity, on glass multi-electrode arrays (MEAs). Laser at a power of 600 mW and a pulse rate of 10 Hz were used to stimulate the neural networks using the optics of an inverted microscope. Pulse durations were varied from 200 μs to 1 ms. The spike rate was calculated to evaluate the change of the neural network activity during the IR stimuli and the corresponding frequency components of neural response were calculated to examine whether recorded spikes were evoked by the IR pulse or not. A temperature model was adapted from a previous study to estimate the temperature rise during laser pulsing.We observed that the IR irradiation with a pulse duration of 800 μs and 1 ms could excite neuronal action potentials. The temperature rose 18.5 and 23.9 °C, for pulse durations of 800 μs and 1 ms, respectively. Thus, in addition to previously shown inhibition of IR irradiation with a wavelength of 1550 nm, we demonstrate an optical method that can modulate neural network activity in vitro. The preliminary results from this paper also suggested that MEA recording technology coupled with a laser and microscope systems can be exploited as a new approach for future studies to understand mechanisms and characterize laser parameters of INM for CNS neurons.

  • 770.
    Yang, Xifeng
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Fu, Kai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Fu, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Strain effect in determining the geometric shape of self-assembled quantum dot2009In: Journal of Physics D: Applied Physics, ISSN 0022-3727, E-ISSN 1361-6463, Vol. 42, no 125414Article in journal (Refereed)
    Abstract [en]

    The geometric shape of a self-assembled quantum dot (QD) formed by the strain-induced Stranski-Krastanov mode has been studied as a function of strain energy by the short-range valence-force-field approach. It has been shown by dynamic bond relaxation through strain energy minimization that for the most commonly used InAs QD in GaAs and InP matrices and Ge QD in Si matrix, a pyramidal shape is energy favoured over an hemispherical shape when the QD is not capped due to the lattice relaxation at the QD surface. When the QD becomes totally embedded in the background material, the elastic strain energy of a hemispherical InAs QD is minimal. The results agree with experimental observations. We further studied the coupling of strain fields of QDs in adjacent QD layers which shows that QDs in multiply stacked QD layers can be aligned along the layer growth direction in order to minimize the strain energy.

  • 771.
    Ying, Zhang
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    A new generation density functional towards chemical accuracy2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Density functional theory (DFT) has become the leading method in calculating theelectronic structures and properties from first principles. In practical applicationsof DFT in the frame work of Kohn-Sham (KS) method, an approximate exchange-correlation functional has to be chosen. Hence, the success of a DFT calculationcritically depends on the quality of the exchange-correlation functional.This thesis focuses on the development and validation of the so-called dou-bly hybrid density functionals (DHDFs). DHDFs present a new generation offunctionals, which not only have a non-local orbital-dependent component in theexchange part, but also incorporate the information of unoccupied orbitals in thecorrelation part. I will first give an overview of modern DFT in the introductorychapters, emphasizing the theoretical bases of a newly developed DHDF, XYG3.I will then present further examination of XYG3 and new development on top ofXYG3, leading to XYG3o and XYG3s. Attempts have also been made to extractband structure information of a periodic system from cluster model calculations.

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    fulltext
  • 772. Yu, Meijuan
    et al.
    Yang, Feifei
    Chu, Wangsheng
    Wang, Yu
    Zhao, Haifeng
    Gao, Bin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhao, Wei
    Sun, Jianping
    Wu, Fangming
    Zhang, Xiaowei
    Shi, Yunyu
    Wu, Ziyu
    3D local structure around Zn in Kti11p as a representative Zn-(Cys)4 motif as obtained by MXAN2008In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 374, no 1, p. 28-32Article in journal (Refereed)
    Abstract [en]

    Zinc is an important component of many proteins that play key roles in transcription, translation, and catalysis. Kti11p, DESR1, both belonging to a protein family characterized by a CSL zinc finger domain, and the co-catalytic zinc-protein PML containing a Zn2+ binding domain called RING or C3HC4 finger are all structurally determined by NMR although the zinc sites are silent to this spectroscopical method. The comparison of X-ray absorption near-edge spectroscopy (XANES) data for the three proteins demonstrates that fingerprints effect is a reliable method for a primary characterization of ligand species. Ab initio full MS Calculations performed by MAN are applied to obtain chemical and stereo structural information around the Zn ion in Kti11p. For the first time this high-spatial resolution technique confirms the formation of a stable Zn tetrahedral configuration with four sulfur ligands, and returns extremely accurate bond angle information between ligands.

  • 773.
    Yu, Shengze
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Alkharusi, Amira
    Sultan Qaboos Univ, Coll Med & Hlth Sci, Muscat, Oman..
    Norstedt, Gunnar
    Sultan Qaboos Univ, Coll Med & Hlth Sci, Muscat, Oman.;Karolinska Inst, Ctr Mol Med, Stockholm, Sweden..
    Gräslund, Torbjörn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    An in vivo half-life extended prolactin receptor antagonist can prevent STAT5 phosphorylation2019In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, no 5, article id e0215831Article in journal (Refereed)
    Abstract [en]

    Increasing evidence suggests that signaling through the prolactin/prolactin receptor axis is important for stimulation the growth of many cancers including glioblastoma multiforme, breast and ovarian carcinoma. Efficient inhibitors of signaling have previously been developed but their applicability as cancer drugs is limited by the short in vivo half-life. In this study, we show that a fusion protein, consisting of the prolactin receptor antagonist PrlRA and an albumin binding domain for half-life extension can be expressed as inclusion bodies in Escherichia coli and efficiently refolded and purified to homogeneity. The fusion protein was found to have strong affinity for the two intended targets: the prolactin receptor (K-D = 2.3 +/- 0.2 nM) and mouse serum albumin (K-D = 0.38 +/- 0.01 nM). Further investigation showed that it could efficiently prevent prolactin mediated phosphorylation of STAT5 at 100 nM concentration and above, similar to the PrlRA itself, suggesting a potential as drug for cancer therapy in the future. Complexion with HSA weakened the affinity for the receptor to 21 +/- 3 nM, however the ability to prevent phosphorylation of STAT5 was still prominent. Injection into rats showed a 100-fold higher concentration in blood after 24 h compared to PrlRA itself.

  • 774. Yu, Tao
    et al.
    Zhou, Yongjin J.
    Wenning, Leonie
    Liu, Quanli
    Krivoruchko, Anastasia
    Siewers, Verena
    Nielsen, Jens
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Chalmers University of Technology, Sweden.
    David, Florian
    Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 15587Article in journal (Refereed)
    Abstract [en]

    Production of chemicals and biofuels through microbial fermentation is an economical and sustainable alternative for traditional chemical synthesis. Here we present the construction of a Saccharomyces cerevisiae platform strain for high-level production of very-long-chain fatty acid (VLCFA)-derived chemicals. Through rewiring the native fatty acid elongation system and implementing a heterologous Mycobacteria FAS I system, we establish an increased biosynthesis of VLCFAs in S. cerevisiae. VLCFAs can be selectively modified towards the fatty alcohol docosanol (C22H46O) by expressing a specific fatty acid reductase. Expression of this enzyme is shown to impair cell growth due to consumption of VLCFA-CoAs. We therefore implement a dynamic control strategy for separating cell growth from docosanol production. We successfully establish high-level and selective docosanol production of 83.5 mg l(-1) in yeast. This approach will provide a universal strategy towards the production of similar high value chemicals in a more scalable, stable and sustainable manner.

  • 775.
    Zajac, Pawel
    KTH, School of Biotechnology (BIO), Gene Technology.
    Parallel target selection by trinucleotide threading2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    DNA is the code for all life. Via intermediary RNA the information encoded by the genome is relayed to proteins executing the various functions in a cell. Together, this repertoire of inherently linked biological macromolecules determines all characteristics and features of a cell. Technological advancements during the last decades have enabled the pursuit of novel types of studies and the investigation of the cell and its constituents at a progressively higher level of detail. This has shed light on numerous cellular processes and on the underpinnings of several diseases. For the majority of studies focusing on nucleic acids, an amplification step has to be implemented before an analysis, scoring or interrogation method translates the amplified material into relevant biological information. This information can, for instance, be the genotype of particular SNPs or STRs, or the abundance level of a set of interesting transcripts. As such, amplification plays a significant role in nucleic acid assays. Over the years, a number of techniques – most notably PCR – has been devised to meet this amplification need, specifically or randomly multiplying desired regions. However, many of the approaches do not scale up easily rendering comprehensive studies cumbersome, time-consuming and necessitating large quantities of material.Trinucleotide threading (TnT) – forming the red thread throughout this thesis – is a multiplex amplification method, enabling simultaneous targeted amplification of several nucleic acid regions in a specific manner. TnT begins with a controlled linear DNA thread formation, each type of thread corresponding to a segment of interest, by a gap-fill reaction using a restricted trinucleotide set. The whole collection of created threads is subsequently subjected to an exponential PCR amplification employing a single primer pair. The generated material can thereafter be analyzed with a multitude of readout and detection platforms depending on the issue or characteristic under consideration.TnT offers a high level of specificity by harnessing the inherent specificities of a polymerase and a ligase acting on a nucleotide set encompassing three out of the four nucleotide types. Accordingly, several erroneous events have to occur in order to produce artifacts. This necessitates override of a number of control points.The studies constituting this thesis demonstrate integration of the TnT amplification strategy in assays for analysis of various aspects of DNA and RNA. TnT was adapted for expression profiling of intermediately-sized gene sets using both conventional DNA microarrays and massively parallel second generation 454 sequencing for readout. TnT, in conjunction with 454 sequencing, was also employed for allelotyping, defined as determination of allele frequencies in a cohort. In this study, 147 SNPs were simultaneously assayed in a pool comprising genomic DNA of 462 individuals. Finally, TnT was recruited for parallel amplification of STR loci with detection relying on capillary gel electrophoresis. In all investigations, the material generated with TnT was of sufficient quality and quantity to produce reliable and accurate biological information.Taken together, TnT represents a viable multiplex amplification technique permitting parallel amplification of genomic segments, for instance harboring polymorphisms, or of expressed genes. In addition to these, this versatile amplification module can be implemented in assays targeting a range of other features of genomes and transcriptomes.

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    ZajacP - Doctoral Thesis
  • 776.
    Zajac, Pawel
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Ahmadian, Afshin
    KTH, School of Biotechnology (BIO), Gene Technology.
    Targeted transcript profiling by sequencingManuscript (preprint) (Other academic)
    Abstract [en]

    In recent years, second generation sequencers have been employed to study various facets of the transcriptome in a comprehensive manner. However, intermediary gene sets featuring differentially expressed genes can reduce the dimensionality of experiments while providing researchers with the most significant data. Trinucleotide threading (TnT) is a multiplex amplification method previously implemented in an assay for expression profiling of moderate gene sets. Here, two additional detection systems were evaluated with a focus on lowering the input material requirements. 32 genes were simultaneously assayed with detection either by direct hybridization of TnT products or by sequencing these using the massively parallel 454 sequencer. Both approaches produced reliable transcript abundance data starting from total RNA from about 200 cells. The direct hybridization readout is beneficial for smaller-scale studies, while more ambitious efforts employing numerous individuals are, together with a sample barcoding and pooling scheme, well suited for the second generation sequencing approach. Moreover, with protocol optimizations the starting material requirements for the sequencing strategy may be further reduced. Accordingly, this study presents a targeted RNA-Seq method.

  • 777.
    Zajac, Pawel
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Pettersson, Erik
    KTH, School of Biotechnology (BIO), Gene Technology.
    Gry, Marcus
    KTH, School of Biotechnology (BIO), Gene Technology.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Ahmadian, Afshin
    KTH, School of Biotechnology (BIO), Gene Technology.
    Expression profiling of signature gene sets with trinucleotide threading2008In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 9, no 2, p. 209-217Article in journal (Refereed)
    Abstract [en]

    In recent years, studies have shown that expression profiling of carefully chosen intermediary gene sets, comprising approximately 10 to 100 genes, can convey the most relevant information compared to much more complex whole-genome studies. In this paper, we present a novel method suitable for expression profiling of moderate gene sets in a large number of samples. The assay implements the parallel amplification features of the trinucleotide threading technique (TnT), which encompasses linear transcript-based DNA thread formation in conjunction with exponential multiplexed thread amplification. The amplifications bestow the method with high sensitivity. The TnT procedure together with thread detection, relying on thread-specific primer extension followed by hybridization to universal tag arrays, allows for three distinction levels, thus offering high specificity. Additionally, the assay is easily automated and flexible. A gene set, comprising 18 protein epitope signature tags from the Swedish Human Protein Atlas program, was analyzed with the TnT-based approach and the data were compared with those generated by both real-time PCR and genome-wide cDNA arrays, with the highest correlation observed between TnT and real-time PCR. Taken together, expression profiling with trinucleotide threading represents a reliable approach for studies of intermediary gene sets.

  • 778.
    Zajac, Pawel
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Öberg, Christine
    KTH, School of Biotechnology (BIO), Gene Technology.
    Ahmadian, Afshin
    KTH, School of Biotechnology (BIO), Gene Technology.
    Analysis of Short Tandem Repeats by Parallel DNA Threading2009In: PLoS ONE, ISSN 1932-6203, Vol. 4, no 11, p. e7823-Article in journal (Refereed)
    Abstract [en]

    The majority of studies employing short tandem repeats (STRs) require investigation of several of these genetic markers. As such, we demonstrate the feasibility of the trinucleotide threading (TnT) approach for scalable analysis of STRs. The TnT method represents a parallel amplification alternative that addresses the obstacles associated with multiplex PCR. In this study, analysis of the STR fragments was performed with capillary gel electrophoresis; however, it should be possible to combine our approach with the massive 454 sequencing platform to considerably increase the number of targeted STRs.

  • 779.
    Zamani, Leila
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Zhang, Ye
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Aberg, Magnus
    Lindahl, Anna
    Mie, Axel
    Chotteau, Veronique
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Metabolic footprinting of CHO cell culture bioprocess data in fed-batch and perfusion mode using LC-MS data and multivariate analysisManuscript (preprint) (Other academic)
  • 780. Zamocky, M.
    et al.
    Hallberg, Martin
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Ludwig, R.
    Divne, Christina
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Haltrich, D.
    Ancestral gene fusion in cellobiose dehydrogenases reflects a specific evolution of GMC oxidoreductases in fungi2004In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 338, no 1, p. 1-14Article in journal (Refereed)
    Abstract [en]

    Cellobiose dehydrogenases (CDHs) are extracellular hemoflavoenzymes that are thought to be involved in the degradation of two of the most abundant biopolymers in the biosphere, cellulose and lignin. To date, these enzymes, consisting of a cytochrome domain and a flavin domain, have been detected and sequenced exclusively in the kingdom of fungi. Independent phylogenetic analyses of two distinct domains of CDH genes reveal that they evolved in parallel as fused genes. Whereas the cytochrome domains are unique sequence motifs, the flavin domains clearly belong to the glucose-methanol-choline (GMC) oxidoreductase family-an evolution line of widespread flavoproteins extending from the Archae to higher eukaryotes. The most probable unrooted phylogenetic tree obtained from our analysis of 52 selected GMC members reveals five principal evolutionary branches: cellobiose dehydrogenase, cholesterol oxidase (COX), hydroxynitrile lyase, alcohol oxidase (AOX)/glucose oxidase (GOX)/choline dehydrogetrase, and a branch of dehydrogenases with various specificities containing also an Archaeon open reading frame (ORF). Cellobiose dehydrogenases cluster with cholesterol oxidases and the clade of various specificities, whereas hydroxynitrile lyases are closely related to glucose oxidases, alcohol oxidases, and choline dehydrogenases. The results indicate that the evolutionary line from a primordial GMC flavoprotein to extant cellobiose dehydrogenases was augmented after an early acquisition of the cytochrome domain to form two distinct branches for basidiomycetes and ascomycetes. One ascomycetous evolutionary line of CDHs has acquired a carbohydrate-binding module (CBM) of type 1, the sequence of which is similar to that of corresponding domains in several glycosidases. This is the first attempt towards a comprehensive phylogenetic analysis of cellobiose dehydrogenases.

  • 781.
    Zandian, Arash
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Array-based Autoantibody Profiling and Epitope Mapping2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Antibodies are a class of proteins that are made by the immune system to recognize harmful organisms and molecules. Their exceptional capability of specifically recognizing molecules has been investigated for over a century and information thereof has been utilized for a variety of applications including vaccine and generation of therapeutic antibodies. Occasionally, instead of protecting the host against pathogens, antibodies can recognize constituents of the host and thereby cause an autoimmune reaction that eventually can lead to a disease. Therefore, it is of great interest to understand what the antibodies bind to and their specificities.

     

    The last decades of technical development and availability of protein and peptide microarrays have enabled large-scale profiling of antibodies and precise determination of their specificities through epitope mapping. In this thesis the aim was to use affinity proteomics tools to profile antibodies, determine their specificities, and discover potential associations of autoantigens to disease by analyzing blood-derived samples with microarray-based methods.

     

    In Paper I, 57 serum samples from patients with the suggested autoimmune disease narcolepsy, were analyzed on planar antigen microarrays with 10,846 human protein fragments. Verification on an independent sample collection consisting of serum samples from 176 individuals, revealed METTL22 and NT5C1A as two potential autoantigens. In Paper II, antibodies from 53 plasma samples from patients with first-episode psychosis, a condition suggested to have a partial autoimmune component, were analyzed on planar antigen microarrays with 2,304 human protein fragments. After a follow-up study of the patients, antibodies toward an antigen representing the three proteins, PAGE2, PAGE2B, PAGE5, was found associated to an increased risk of developing schizophrenia. In Paper III, serum and plasma samples from patients with the autoimmune diseases multiple sclerosis and narcolepsy, were epitope mapped on high-density peptide microarrays with approximately 2.2 million peptides. Technical and biological verification, by using other microarray technology and analyzing  samples from 448 patients, revealed one peptide for multiple sclerosis and narcolepsy, representing the proteins MAP3K7 and NRXN1, with higher antibody reactivity towards in each group, respectively. In Paper IV, purified polyclonal antibodies raised against a surface antigen found on malaria-infected erythrocytes, were profiled on the peptide microarrays representing all proteins found on malaria-infected erythrocytes derived from Plasmodium falciparum. Then, different Plasmodium falciparum strains were analyzed by immunofluorescence microscopy and western blots, using the epitope mapped antibodies. The performance of the immunoassays were compared to the identified epitopes, and validated by RNA sequencing.

     

    In conclusion, these investigations describe multiplex methods to identify and characterize antibodies, their disease association and epitopes. Follow-up studies are needed to determine their potential use and clinical value.

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    DoctoralThesis_ArashZandian
  • 782.
    Zhan, Caijuan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Hydrodynamics considerations in cells systems from ocean flow to perfusion cultivation process2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Microorganisms and animal cells are grown surrounded by fluid, which is providing them with nutrients and removing their waste products. In nature and industry processes, cells/microbes can be subject to aggressive environments, such as turbulent flow or shear flow. Hydrodynamics force generated in these flows can affect the distribution of cells/microbes and even lead to cell damage. Understanding the mechanism and exploring the effect of hydrodynamic force in these environments could make the prediction of cells’ hydrodynamic response more systematic. In pharmaceutical industry, perfusion process is recognized as an attractive option for biologics production due to its high productivity. However, there are still some challenges and limitations for further process improvement due to lack of information of cell response to hydrodynamic force and nutrients. In both cases, hydrodynamics plays an important role and similar tool can be used to achieve a deeper understanding of these processes. This thesis is mainly aiming to elucidate the influence of hydrodynamic forces on microorganisms or cells in nature and during bioprocesses. In particular, shear stress in a natural environment and in a bioreactor operated in perfusion mode is studied.

    This work mainly investigates hydrodynamics in nature and bioprocess including three flow cases. The first study investigates the effect of turbulence on marine life by performing direct numerical simulations (DNS) of motile micro-organisms in isotropic homogeneous turbulence. The clustering level of micro-organisms with one preferential swimming direction (e.g. gyrotaxis) is examined. The second study uses Computation Fluid Dynamics (CFD) to simulate the fluid flow inside a Wave bioreactor bag. The phenomenon of mixing, oxygen transfer rate and shear stress in nine different operating conditions of rocking speeds and angles are discussed. In the third study, the cellular response to shear force including growth and metabolism in a cell retention device such as hollow fiber filters during a perfusion process is analyzed. Theoretical calculations and experiment validation is performed to compare two filtration modes, tangential flow filtration (TFF) or alternating tangential flow filtration (ATF). Further optimizations regarding mixing and feeding are performed in a screening scale of in a perfusion system of stirred tank bioreactor with cell separation device.

    The main findings can be summarized as that spherical gyrotaxis swimmers show significant clustering, whereas prolate swimmers remain more uniformly distributed due to their large sensitivity to the local shear. These results could explain how pure hydrodynamic effects can alter the ecology of micro-organisms for instance by varying shape and their preferential orientation (paper I). The simulations of Wave bioreactors show that the mixing and shear stress increase with the rocking angle but that increasing rocking speeds are not systematically associated with increasing mixing and shear stress. A resonance phenomenon is responsible for the fact that the lowest studied rocking speed generates the highest fluid velocity, mixing and shear stress (paper II). Theoretical velocity profile-based calculations suggested a lower shear stress for ATF by a factor 0.637 compared to TFF. This is experimentally validated by cultures of HEK (human embryonic kidney) 293 cells subjected to shear stress by a perfusion system that affects growth and metabolism using these cell separation devices (paper III). Thanks to optimization of mixing and oxygen transfer in a screening system for perfusion process, very high cell densities above 100 x 106 cells/mL of mammalian cells were achieved (paper IV).

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    CJ
  • 783.
    Zhan, Caijuan
    et al.
    KTH, School of Engineering Sciences (SCI). KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Hubert, Schwarz
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Malm, Magdalena
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Technology.
    Sellick, Christopher
    Rockberg, Johan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Technology.
    Chotteau, Véronique
    KTH, School of Engineering Sciences (SCI). KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Hydrodynamic shear stress in hollow filter for perfusion culture of human cellsManuscript (preprint) (Other academic)
    Abstract [en]

    High cell density perfusion process is an economical way to produce biopharmaceuticals at high yield. To achieve high density of healthy cells, the cell culture conditions should be free from mechanically detriment. Human embryonic kidney (HEK) K293 cells, interesting for the production of therapeutic glycoproteins, are known as shear sensitive. In order to obtain the optimal hydrodynamics conditions with reduced mechanical damage, we investigated the fact of the shear stress compatible with HEK293 cells. We reviewed hollow filter based tangential flow filtration strategies, tangential flow filtration (TFF) and alternating tangential flow filtration (ATF). We studied shear stress introduced by these two flow filtration methods. By theoretical study, we obtained that lower shear stress introduced by alternating tangential flow filtration result in lower average shear stress comparing to tangential flow filtration with same flow rate.  In our experimental runs, we achieved different shear stress levels by applying different flow rates. 5-Days batch cultivations were performed to examine the influence of shear stress on cell growing and metabolic behaviour. We identified that the shear stress potentially reduce the growth rate and productivity of HEK293 cells and found the cell metabolism associated with shear stress levels. By documenting these cell responses to shear stress, we confirmed our theoretical results and could further optimize the hydrodynamic conditions for perfusion process of HEK 293 cells. 

  • 784.
    Zhang, Liang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology. AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing.
    Development of mathematical modelling for the glycosylation of IgG in CHO cell cultures2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Chinese hamster ovary (CHO) cells are the most popular expression system for the production of biopharmaceuticals. More than 80% of the approved monoclonal antibodies (mAbs) or immunoglobulin G (IgG) are produced with these cells. Glycosylation is a usual post- translational modification important for therapeutic mAbs. It affects their stability, half-life and immunological activities. Substantial studies have shown that glycosylation can be affected by the culture conditions in manufacturing, e.g. pH, temperature and media components. To achieve a good control of the glycosylation, a number of mathematical models have been developed. However, most of them have been developed for the cell line engineering, while very few can be used to design the media components for matching a given glycoprofile.

    This thesis presents developments of mathematical modelling for glycosylation prediction and experimental design of feeding different combinations of carbon sources in CHO cell cultures. The first study investigates the impacts of mannose, galactose, fructose and fucose to the IgG glycoprofile. Specifically, we look at intracellular nucleotide sugars in fed-batch cultures, where glucose is absent and lactate is used as complementary carbon source. The second study is based on the concept of elementary flux mode (EFM) and the mass balance of the glycan residues. A mathematical model named Glycan Residue Balance Analysis (GReBA) is developed for the prediction of the glycosylation profiles of IgG in pseudo perfusion cultures by feeding combinations of glucose, mannose, galactose and lactate. The model is further optimized for a feeding strategy design of perfusion cell cultures to obtain a desired glycoprofile. In the last study, a probabilistic graphic model based on Bayesian network (BN) is developed for glycosylation prediction in cultures under different multiple variable factors affecting the glycosylation.

    The results show that the manipulation of different sugars in the media can be used to control the glycosylation. Both the GReBA and PGM models exhibit abilities for glycosylation prediction and experimental design.

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    fulltext
  • 785.
    Zhang, Liang
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology. AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing.
    Schwarz, Hubert
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology. ence Centre for Advanced Bioproduction by Continuous Processing.
    Wang, mingliang
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Decision and Control Systems (Automatic Control). AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing.
    Castan, Andreas
    Cytiva.
    Hjalmarsson, Håkan
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Decision and Control Systems (Automatic Control). AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing.
    Chotteau, Veronique
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology. AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing.
    Prediction of IgG glycosylation in CHO cell perfusion cultures by GReBA mathematical model supported by a novel targeted feed, TAFEManuscript (preprint) (Other academic)
    Abstract [en]

    The N-linked glycosylation pattern is an important quality attribute of therapeutic glycoproteins. It has been reported by our group and by others that different carbon sources, such as glucose, mannose and galactose, can differently impact the glycosylation profile of glycoproteins in mammalian cell culture. Acting on the sugar feeding is thus an attractive strategy to tune the glycan pattern. However, in case of feeding of more than one carbon source simultaneously, the cells give priority to the one with the highest uptake rate, which limits the usage of this tuning, e.g. the cells favor consuming glucose in comparison to galactose.

    We present here a new feeding strategy (named 'TAFE' for targeted feeding) for perfusion culture to adjust the concentrations of fed sugars influencing the glycosylation. The strategy consists in setting the sugar feeding such that the cells are forced to consume these substrates at a target cell specific consumption rate decided by the operator and taking into account the cell specific perfusion rate (CSPR). This strategy is applied in perfusion cultures of Chinese hamster ovary (CHO) cells, illustrated by ten different regimes of sugar feeding, including glucose, galactose and mannose. Applying the TAFE strategy, different glycan profiles were obtained using the different feeding regimes. Furthermore, we successfully forced the cells to consume higher proportions of non-glucose sugars, which have lower transport rates than glucose in presence of this latter, in a controlled way.

    In previous work, a mathematical model named Glycan Residues Balance Analysis (GReBA) was developed to model the glycosylation profile based on the fed carbon sources. The present data were applied to the GReBA to design a feeding regime targeting a given glycosylation profile. The ability of the model to achieve this objective was confirmed by a multi-round of leave-one- out cross-validation (LOOCV), leading to the conclusion, that the GReBA model can be used to design the feeding regime of a perfusion cell culture to obtain a desired glycosylation profile.

  • 786.
    Zhang, Liang
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology. AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing.
    Wang, mingliang
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Decision and Control Systems (Automatic Control). AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing.
    Castan, Andreas
    Cytiva.
    Hjalmarsson, Håkan
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Decision and Control Systems (Automatic Control). AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing.
    Chotteau, Veronique
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology. AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing.
    Probabilistic Graphic Model by Bayesian Network for the Prediction of Antibody Glycosylation in CHO Cell CulturesManuscript (preprint) (Other academic)
    Abstract [en]

    Glycosylation is a critical quality attribute of therapeutic monoclonal antibodies (mAbs). The glycan pattern can have a large impact on the immunological functions, serum half-life and stability. The medium components and cultivation parameters are known to potentially influence the glycosylation profile. Mathematical modelling provides a strategy for rational design and control of the upstream bioprocess. However, the kinetic models usually contain a very large number of unknown parameters, which limit their practical applications. In this article, we consider the metabolic network of N-linked glycosylation as a Bayesian network and calculate the fluxes of the glycosylation process as joint probability using the culture parameters as inputs. The modelling approach is validated with data of different CHO cell cultures in pseudo perfusion, perfusion and fed batch cultures, all showing very good predictive capacities. In cases where a large number of cultivation parameters is available, it is shown here that principal components analysis (PCA) can efficiently be employed for a dimension reduction of the inputs compared to Pearson correlation analysis and feature importance by decision tree. The present study demonstrates that Bayesian network model can be a powerful tool in upstream process and medium development for glycoprotein productions.

  • 787.
    Zhang, Qinglin
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Dor, L.
    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.
    CFD modeling of municipal solid waste gasification in a fixed-bed plasma gasification melting reactor2011In: Air Waste Manage. Assoc. - Int. Conf. Therm. Treat. Technol. Hazard. Waste Combustors, 2011, p. 252-278Conference paper (Refereed)
    Abstract [en]

    A steady CFD model is developed to simulate the gasification of municipal solid waste (MSW) in a moving-bed Plasma Gasification Melting (PGM) reactor. In this model, the Eulerian-Eulerian multiphase model is conducted, and the solid phase is treated as a plastic fluid. The conservation equations of both gas and solid phases are solved respectively. The momentum conservation equations of the solid phase are simplified by disregarding the interphase forces between gas and solid. Both heterogeneous reactions and homogeneous reactions are defined in this model to express the detailed gasification chemistry inside the reactor. A two-step pyrolysis model was used in this work, and the pyrolysis mechanisms of cellulosic and plastic fractions are considered separately. The predicted results of a base case are compared with the measured data of the trial reactor. The temperature distribution inside the PGM reactor is introduced. Based on the variation of temperature, the whole reaction shaft was divided into five layers. The 2D effect of the reactor is also discussed. The influence of two dimensionless parameters: the equivalence ratio (ER) and dimensionless plasma energy ratio (DPER) are introduced and discussed. With the variation of ER, two typical temperature distributions can be found for PGM reactor. The turning point of these two distributions stands in the ER range 0.120-0.133. This turning point is the optimal operation condition of PGM air gasification. It is also found that when the energy request for gasification is satisfied, further increment of DPER value does not significantly influence the characters of PGM process.

  • 788.
    Zhang, Xiaolei
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Energy and Furnace Technology.
    Micro-reaction Mechanism Study of the Biomass Thermal Conversion Process using Density Functional Theory2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biomass, or bio-energy, is one of the most important alternative energies because of environmental concerns and the future shortage of fossil fuels. Multi-scaled bioenergy studies have been performed in the division of Energy and Furnace Technology, which included studies of macroscopic systems such as systems and reactors, modeling of computational fluid dynamics (CFD), and atomic/molecular level studies. The present thesis focus on the atomic/molecular level that based on quantum chemistry methods.

    The microscopic structure study of biomass is the first and an important step for the investigation of the biomass thermal conversion mechanism. Cellulose, hemicellulose, and lignin are the three most important components for biomass. The atomic interactions among these three main components were studied, including the hydrogen bond linkages between cellulose and hemicellulose, and the covalent bond linkages between hemicellulose and lignin.

    The decomposition of biomass is complicated and includes cellulose decomposition, hemicellulose decomposition, and lignin decomposition. As the main component of biomass, the mechanism of cellulose pyrolysis mechanism was focused on in this thesis. The study of this mechanism included an investigation of the pathways from cellulose to levoglucosan then to lower-molecular-weight species. Three different pathways were studied for the formation of levoglucosan from cellulose, and three different pathways were studied for the levoglucosan decomposition. The thermal properties for every reactant, intermediate, and product were obtained. The kinetics parameters (rate constant, pre-exponential factor, and activation energy) for every elementary step and pathway were calculated. For the formation of levoglucosan, the levoglucosan chain-end mechanism is the favored pathway due to the lower energy barrier; for the subsequent levoglucosan decomposition process, dehydration is a preferred first step and C-C bond scission is the most difficult pathway due to the strength of the C-C bonds.

    The biomass gasification process includes pyrolysis, char gasification, and a gas-phase reaction; Char gasification is considered to be the rate-controlling step because of its slower reaction rate. Char steam gasification can be described as the adsorption of steam on the char surface to form a surface complex, which may transfer to another surface complex, which then desorbs to give the gaseous products (CO and H2) and the solid product of the remaining char. The influences of several radicals (O, H, and OH) and molecules (H2 and O2) on steam adsorption were investigated. It was concluded that the reactivity order for these particles adsorbed onto both zigzag and armchair surfaces is O > H2 > H > OH > O2. For water adsorbs on both zigzag and armchair carbon surfaces, O and OH radicals accelerate water adsorption, but H, O2, and H2 have no significant influence on water adsorption.

    It was also shown that quantum chemistry (also known as molecular modeling) can be used to investigate the reaction mechanism of a macroscopic system. Detailed atomic/molecular descriptions can provide further understanding of the reaction process and possible products.

  • 789.
    Zhang, Ye
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    High cell density perfusion process development for antibody producing Chinese Hamster Ovary cells2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Perfusion operation mode is currently under fast expansion in mammalian cell based manufacturing of biopharmaceuticals, not only for labile drug protein but also for stable proteins such as monoclonal antibodies (mAbs). Perfusion mode can advantageously offer a stable cell environment, long-term production with high productivity and consistent product quality. Intensified high cell density culture (HCDC) is certainly one of the most attractive features of a perfusion process due to the high volumetric productivity in a small footprint that it can provide. Advancements in single-use technology have alleviated the intrinsic complexity of perfusion processes while the maturing in cell retention devices has improved process robustness. The knowledge for perfusion process has been gradually built and the “continuous” concept is getting more and more acceptance in the field.

    This thesis presents the development of robust perfusion process at very high cell densities in various culture systems. Four HCDC perfusion systems were developed with industrial collaborators with three different mAb producing Chinese Hamster Ovary (CHO) cell lines: 1-2) WAVE Bioreactor™ Cellbag prototype equipped with cell separation by hollow fiber filter utilizing Alternating Tangential Flow (ATF) and Tangential Flow Filtration (TFF) techniques; 3) Fiber matrix based CellTank™ prototype; 4) Glass stirred tank bioreactor equipped with ATF. In all the systems, extremely high viable cell densities above 130 million viable cells per milliliter (MVC/mL) up to 214 MVC/mL were achieved. Steady states were maintained and studied at 20-30 MVC/mL and 100-130 MVC/mL for process development. Perfusion rate selection based on cell specific perfusion rate (CSPR) was systematically investigated and exometabolome study was performed to explore the metabolic footprint of HCDC perfusion process.

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  • 790.
    Zhang, Ye
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Zhan, Caijuan
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Girod, Pierre-Alain
    Martiné, Alexandra
    Chotteau, Veronique
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Optimization of the cell specific perfusion rate in high cell density perfusion processManuscript (preprint) (Other academic)
  • 791.
    Zhao, Ke
    KTH, School of Biotechnology (BIO).
    Theoretical study of light-molecule nonlinear interactions2007Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    The work presented in the thesis concerned theoretical study of light-matter nonlinear interactions. Two important aspects of such interactions have been examined, namely the nonlinear optical properties of a series of organic charge transfer molecules in solutions induced by the laser light and the propagation of the ultrafast high power laser through the nonlinear molecular medium.

    Special attention has been paid to understand the solvent effects on the two-photon absorption of a symmetrical diamino substituted distyrylbenzene chromophore, for which time-dependent density functional theory in combination with polarizable continuum model (PCM) have been employed. The dielectric medium alone has a rather small effect both on the bond length alternation and on the one-photon absorption spectrum, but noticeable effects on the two-photon absorption cross section. Both one- and two-photon absorptions are found to be extremely sensitive to the planarity of the molecule. Our calculations indicate that the experimentally observed anomalous solvent effect on the two-photon absorption of dialkylamino substituted distyrylbenzene chromophores can not be attributed to the intrinsic properties of a single molecule and its interaction with solvents. With the same theoretical approaches, two-photon absorption properties of interacting polar chromophores have been investigated to examine the validity of the widely used exciton model. Our first principles calculations have shown that the exciton model offers a conceptually simple interpretation for experimental observations, but is lack of predictability.

    The second part of the thesis is to investigate the propagation of ultrashort laser pulse through a one-dimensional asymmetric organic molecular medium by solving full Maxwell-Bloch equations using predictor-corrector finite-difference time-domain method. It focuses on the supercontinuum generation of spectra and the formation of attosecond pulses. It is shown that the supercontinuum generation is strongly modulated by both area and width of the pulse, which results from the interference between the splitting pulses in time-domain and is the implication of the time-energy uncertainty relation. The presence of permanent dipole moment in molecular medium has noticeable effects on the supercontinuum generation. Our calculations show that a well-shaped 132 attosecond pulse can be generated from a two femtosecond incoming pulse under certain conditions. Influences of carrier-envelope phase and time-dependent ionization on the spectral and temporal evolutions of the ultrashort pulses have also been discussed.

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  • 792.
    Zhao, Ke
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ferrighi, Lara
    Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø.
    Frediani, Luca
    Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø.
    Wang, Chuan-Kui
    College of Physics and Electronics, Shandong Normal University, Jinan .
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Solvent effects on two-photon absorption of dialkylamino substituted distyrylbenzene chromophore2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 126, no 20Article in journal (Refereed)
    Abstract [en]

    Solvent effects on the two-photon absorption of a symmetrical diamino substituted distyrylbenzene chromophore have been studied using the density functional response theory in combination with the polarizable continuum model. It is shown that the dielectric medium has a rather small effect both on the bond length alternation and on the one-photon absorption spectrum, but it affects significantly the two-photon absorption cross section. It is found that both one- and two-photon absorptions are extremely sensitive to the planarity of the molecule, and the absorption intensity can be dramatically reduced by the conformation distortion. It has led to the conclusion that the experimentally observed anomalous solvent effect on the two-photon absorption of dialkylamino substituted distyrylbenzene chromophores cannot be attributed to the intrinsic properties of a single molecule and its interaction with solvents.

  • 793.
    Zhao, Ke
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Liu, Ji-Cai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Wang, Chuan-Kui
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Modulation of supercontinuum generation and formation of an attosecond pulse from a generalized two-level medium2007In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 40, p. 1523-1534Article in journal (Refereed)
    Abstract [en]

    The propagation of ultrashort pulses in a generalized two- level system, consisting of permanent dipole moments, is simulated by solving the full Maxwell - Bloch equations. Special attention has been paid to the supercontinuum generation of spectra and the formation of attosecond ( as) pulses. It is found that the supercontinuum generation is strongly modulated by both area and width of the pulse, resulting from the interference between the splitting pulses in the time domain and the implication of the time - energy uncertainty relation. The effect of the permanent dipole moment on the supercontinuum generation is discussed in detail. Calculations show that a well- shaped 132 as pulse can be generated from a 2 fs incoming pulse under the condition where the permanent dipole moment difference between two levels is equal to the transition dipole moment between them. Influences of carrier- envelope phase and time- dependent ionization on the spectral and temporal evolution of the ultrashort pulses are also discussed at length.

  • 794.
    Zhao, Ke
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Wang, Chuan-Kui
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    Shandong Normal Univ, Coll Phys & Elect, Jinan.
    Two-photon absorbation activities of interating dipolar chromophores: a DFT study.Manuscript (preprint) (Other academic)
  • 795.
    Zhao, Ning-Wei
    KTH, School of Biotechnology (BIO).
    Recent Progress in the Methods of Genome Sequencing2010In: Brazilian archives of biology and technology, ISSN 1516-8913, E-ISSN 1678-4324, Vol. 53, no 2, p. 319-325Article in journal (Refereed)
    Abstract [en]

    Genome sequencing is a very important tool for the development of genetic diagnosis, drugs of gene engineering, pharmacogenetics, etc. As the HGP comes into people's ears, there is an emerging need for the genome sequencing. During the recent years, there are two different traditional strategies available for this target: shotgun sequencing and hierarchical sequencing. Besides these, many efforts are pursuing new ideas to facilitate fast and cost-effective genome sequencing, including 454 GS system, polony sequencing, single molecular array, nanopore sequencing, with each having different unique characteristics, but remains to be fully developed.

  • 796.
    Zhao, Ning-Wei
    et al.
    KTH, School of Biotechnology (BIO).
    Yao, Jin-Ting
    Characterization and sequence identification of angiotensin II by a novel method involving ultra-fast liquid chromatography assay coupled with matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight five tandem mass spectrometry analysis2010In: European journal of mass spectrometry, ISSN 1469-0667, E-ISSN 1751-6838, Vol. 16, no 6, p. 663-671Article in journal (Refereed)
    Abstract [en]

    High-throughput proteomics aims to investigate dynamically changing proteins expressed by a full organism, specific tissue or cellular compartment under certain conditions. High-sensitivity mass spectrometry has gradually become a significant tool for characterizing peptides. Here, we analyzed angiotensin II using ultra-fast liquid chromatography (UFLC) coupled with matrix-assisted laser desoprtion/ionization time-of-flight mass spectrometry (MALDI-ToF MS5). First, we applied UFLC in isolating and collecting the angiotensin II, and then Axima-Resonance (MALDI-QIT-ToF MS5) was adopted, which enables collision-induced dissociation-MS5 analysis for fine structural characterization of angiotensin II. Resultant MS, MS2, MS3 and MS4 spectra of interested [M+H](+) ions selected as precursor ions yielded detailed information about the sites of fragmentation as well as the amino acid sequence for angiotensin II; meanwhile, the average deviation between theoretical mass and actually measured mass from MS to MS5 spectra was only 0.32 Da. It indicated that Axima-Resonance was capable of analysing the peptide sequence accurately and providing the corresponding fragmentation information thoroughly, thus suggesting a potential strategy involving UFLC assay coupled with MALDI-QIT-ToF MS5 analysis for high-throughput proteomics studies in the future.

13141516 751 - 796 of 796
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