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  • 1.
    Abrahamsson, Thomas
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Center of Paediatrics and Gynaecology and Obstetrics, Department of Paediatrics in Linköping.
    Sherman, Philip M.
    University of Toronto, Canada .
    Editorial Material: Multifaceted Effects of Human Milk Oligosaccharides2014In: Journal of Infectious Diseases, ISSN 0022-1899, E-ISSN 1537-6613, Vol. 209, no 3, p. 323-324Article in journal (Other academic)
    Abstract [en]

    n/a

  • 2.
    Aili, Daniel
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Polypeptide-Based Nanoscale Materials2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Self-assembly has emerged as a promising technique for fabrication of novel hybrid materials and nanostructures. The work presented in this thesis has been focused on developing nanoscale materials based on synthetic de novo designed polypeptides. The polypeptides have been utilized for the assembly of gold nanoparticles, fibrous nanostructures, and for sensing applications.

    The 42-residue polypeptides are designed to fold into helix-loop-helix motifs and dimerize to form four-helix bundles. Folding is primarily driven by the formation of a hydrophobic core made up by the hydrophobic faces of the amphiphilic helices. The peptides have either a negative or positive net charge at neutral pH, depending on the relative abundance of Glu and Lys. Charge repulsion thus prevents homodimerization at pH 7 while promoting hetero-dimerization through the formation of stabilising salt bridges. A Cys incorporated in position 22, located in the loop region, allowed for directed, thiol-dependent, immobilization on planar gold surfaces and gold nanoparticles. The negatively charged (Glu-rich) peptide formed homodimers and folded in solution at pH < 6 or in the presence of certain metal ions, such as Zn2+. The folding properties of this peptide were retained when immobilized directly on gold, which enabled reversible assembly of gold nanoparticles resulting in aggregates with well-defined interparticle separations. Particle aggregation was found to induce folding of the immobilized peptides but folding could also be utilized to induce aggregation of the particles by exploiting the highly specific interactions involved in both homodimerization and hetero-association. The possibility to control the assembly of polypeptide-functionalized gold nanoparticles was utilized in a colorimetric protein assay. Analyte binding to immobilized ligands prevented the formation of dense particle aggregates when subjecting the particles to conditions normally causing extensive aggregation. Analyte binding could hence easily be distinguished by the naked eye. Moreover, the peptides were utilized to assemble gold nanoparticles on planar gold and silica substrates.

    Fibrous nanostructures were realized by linking monomers through a disulphide-bridge. The disulphide-linked peptides were found to spontaneously assemble into long and extremely thin peptide fibres as a result of a propagating association mediated by folding into four-helix bundles.

    List of papers
    1. Alpha-helix-inducing dimerization of synthetic polypeptide scaffolds on gold
    Open this publication in new window or tab >>Alpha-helix-inducing dimerization of synthetic polypeptide scaffolds on gold
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    2005 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 21, no 6, p. 2480-2487Article in journal (Refereed) Published
    Abstract [en]

    Designed, synthetic polypeptides that assemble into four-helix bundles upon dimerization in solution were studied with respect to folding on planar gold surfaces. A model system with controllable dimerization properties was employed, consisting of negatively and positively charged peptides. Circular dichroism spectroscopy and surface plasmon resonance based measurements showed that at neutral pH, the peptides were able to form heterodimers in solution, but unfavorable electrostatic interactions prevented the formation of homodimers. The dimerization propensity was found to be both pH- and buffer-dependent. A series of infrared absorption−reflection spectroscopy experiments of the polypeptides attached to planar gold surfaces revealed that if the negatively charged peptide was immobilized from a loading solution where it was folded, its structure was retained on the surface provided it had a cysteine residue available for anchoring to gold. If it was immobilized as random coil, it remained unstructured on the surface but was able to fold through heterodimerization if subsequently exposed to a positively charged polypeptide. When the positively charged peptide was immobilized as random coil, heterodimerization could not be induced, probably because of high-affinity interactions between the charged primary amine groups and the gold surface. These observations are intended to pave the way for future engineering of functional surfaces based on polypeptide scaffolds where folding is known to be crucial for function.

    Place, publisher, year, edition, pages
    ACS Publications, 2005
    National Category
    Other Basic Medicine
    Identifiers
    urn:nbn:se:liu:diva-15115 (URN)10.1021/la048029u (DOI)
    Available from: 2008-10-16 Created: 2008-10-16 Last updated: 2018-01-12Bibliographically approved
    2. Aggregation-Induced Folding of a de novo Designed Polypeptide Immobilized on Gold Nanoparticles
    Open this publication in new window or tab >>Aggregation-Induced Folding of a de novo Designed Polypeptide Immobilized on Gold Nanoparticles
    Show others...
    2006 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 128, no 7, p. 2194 -2195Article in journal (Refereed) Published
    Abstract [en]

    This communication reports the first steps in the construction of a novel, nanoparticle-based hybrid material for biomimetic and biosensor applications. Gold nanoparticles were modified with synthetic polypeptides to enable control of the particle aggregation state in a switchable manner, and particle aggregation was, in turn, found to induce folding of the immobilized peptides.

    Place, publisher, year, edition, pages
    ACS Publications, 2006
    Keywords
    Not aviable
    National Category
    Other Basic Medicine
    Identifiers
    urn:nbn:se:liu:diva-14041 (URN)10.1021/ja057056j (DOI)
    Available from: 2006-09-28 Created: 2006-09-28 Last updated: 2018-01-13Bibliographically approved
    3. Folding Induced Assembly of Polypeptide Decorated Gold Nanoparticles
    Open this publication in new window or tab >>Folding Induced Assembly of Polypeptide Decorated Gold Nanoparticles
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    2008 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, no 17, p. 5780-5788Article in journal (Refereed) Published
    Abstract [en]

    Reversible assembly of gold nanoparticles controlled by the homodimerization and folding of an immobilized de novo designed synthetic polypeptide is described. In solution at neutral pH, the polypeptide folds into a helix–loop–helix four-helix bundle in the presence of zinc ions. When immobilized on gold nanoparticles, the addition of zinc ions induces dimerization and folding between peptide monomers located on separate particles, resulting in rapid particle aggregation. The particles can be completely redispersed by removal of the zinc ions from the peptide upon addition of EDTA. Calcium ions, which do not induce folding in solution, have no effect on the stability of the peptide decorated particles. The contribution from folding on particle assembly was further determined utilizing a reference peptide with the same primary sequence but containing both D and L amino acids. Particles functionalized with the reference peptide do not aggregate, as the peptides are unable to fold. The two peptides, linked to the nanoparticle surface via a cysteine residue located in the loop region, form submonolayers on planar gold with comparable properties regarding surface density, orientation, and ability to interact with zinc ions. These results demonstrate that nanoparticle assembly can be induced, controlled, and to some extent tuned, by exploiting specific molecular interactions involved in polypeptide folding.

    Place, publisher, year, edition, pages
    ACS Publications, 2008
    National Category
    Other Basic Medicine
    Identifiers
    urn:nbn:se:liu:diva-15116 (URN)10.1021/ja711330f (DOI)
    Available from: 2008-10-16 Created: 2008-10-16 Last updated: 2018-01-12Bibliographically approved
    4. Controlled Assembly of Gold Nanoparticles using De Novo Designed Polypeptide Scaffolds
    Open this publication in new window or tab >>Controlled Assembly of Gold Nanoparticles using De Novo Designed Polypeptide Scaffolds
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    2008 (English)In: Proceedings SPIE, Vol. 6885, Photonic Biosensing and Microoptics, 2008, p. 688506-1-688506-8Conference paper, Published paper (Refereed)
    Abstract [en]

    Heterodimerization between designed helix-loop-helix polypeptides was utilized in order to assemble gold nanoparticles on planar substrates. The peptides were designed to fold into four-helix bundles upon dimerization. A Cys-residue in the loop region was used to immobilize one of the complementary peptides on a maleimide containing SAM on planar gold substrates whereas the second peptide was immobilized directly on gold nanoparticles. Introducing the peptide decorated particles over a peptide functionalized surface resulted in particle assembly. Further, citrate stabilized particles were assembled on amino-silane modified glass and silicon substrates. By subsequently introducing peptides and gold nanoparticles, particle-peptide hybrid multi layers could be formed.

    Keywords
    Heterodimerization, polypeptides, gold nanoparticles, four-helix bundle, helix-loop-helix, self-assembly
    National Category
    Other Basic Medicine
    Identifiers
    urn:nbn:se:liu:diva-15118 (URN)10.1117/12.775806 (DOI)
    Available from: 2008-10-16 Created: 2008-10-16 Last updated: 2018-01-12Bibliographically approved
    5. Self-Assembly of Fibers and Nanorings from Disulfide-Linked Helix–Loop–Helix Polypeptides
    Open this publication in new window or tab >>Self-Assembly of Fibers and Nanorings from Disulfide-Linked Helix–Loop–Helix Polypeptides
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    2008 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 47, no 30, p. 5554-5556Article in journal (Refereed) Published
    Place, publisher, year, edition, pages
    Wiley InterScience, 2008
    Keywords
    fibers, helical structures, nanostructures, polypeptides, self-assembly
    National Category
    Other Basic Medicine
    Identifiers
    urn:nbn:se:liu:diva-15120 (URN)10.1002/anie.200801155 (DOI)
    Available from: 2008-10-16 Created: 2008-10-16 Last updated: 2018-01-12Bibliographically approved
    6. Assembly of Polypeptide-Functionalized Gold Nanoparticles through a Heteroassociation- and Folding-Dependent Bridging
    Open this publication in new window or tab >>Assembly of Polypeptide-Functionalized Gold Nanoparticles through a Heteroassociation- and Folding-Dependent Bridging
    2008 (English)In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 8, no 8, p. 2473-2478Article in journal (Refereed) Published
    Abstract [en]

    Gold nanoparticles were functionalized with a synthetic polypeptide, de novo-designed to associate with a charge complementary linker polypeptide in a folding-dependent manner. A heterotrimeric complex that folds into two disulphide-linked four-helix bundles is formed when the linker polypeptide associates with two of the immobilized peptides. The heterotrimer forms in between separate particles and induces a rapid and extensive aggregation with a well-defined interparticle spacing. The aggregated particles are redispersed when the disulphide bridge in the linker polypeptide is reduced.

    Place, publisher, year, edition, pages
    ACS Publications, 2008
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:liu:diva-15121 (URN)10.1021/nl8014796 (DOI)
    Note
    The original title of this article was "Assembly of Decorated Gold Nanoparticles through a Hetero-Association and Folding-Dependent Bridging".Available from: 2008-10-16 Created: 2008-10-16 Last updated: 2017-12-07
    7. Colorimetric Protein Sensing by Controlled Assembly of Gold Nanoparticles Functionalized with Synthetic Receptors
    Open this publication in new window or tab >>Colorimetric Protein Sensing by Controlled Assembly of Gold Nanoparticles Functionalized with Synthetic Receptors
    Show others...
    2009 (English)In: Small, ISSN 1613-6810, Vol. 5, no 21, p. 2445-2452Article in journal (Refereed) Published
    Abstract [en]

    A strategy for colorimetric sensing of proteins, based on the induced assembly of polypeptide-functionalized gold nanoparticles, is described. Recognition was accomplished using a polypeptide sensor scaffold designed to specifically bind the model analyte, human carbonic anhydrase II (HCAII). The extent of particle aggregation, induced by the Zn2+-triggered dimerization and folding of a second polypeptide also present on the surface of the gold nanoparticle, gave a readily detectable colorimetric shift that was dependent on the concentration of the target protein. In the absence of HCAII, particle aggregation resulted in a major redshift of the plasmon peak whereas analyte binding prevented formation of dense aggregates, significantly reducing the magnitude of the redshift. The limit of detection of HCAII was estimated to be around 15 nM. The versatility of the technique was demonstrated using a second model system based on the recognition of a peptide sequence from the tobacco mosaic virus coat protein (TMVP by a recombinant antibody fragment. This strategy is proposed as a generic platform for robust and specific protein analysis that can be further developed for monitoring a wide range of target proteins.

    Keywords
    Not available.
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:liu:diva-15122 (URN)10.1002/smll.200900530 (DOI)
    Available from: 2008-10-16 Created: 2008-10-16 Last updated: 2019-01-22Bibliographically approved
  • 3.
    Aili, Daniel
    et al.
    Linköping University, The Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Enander, Karin
    Linköping University, The Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Rydberg, Johan
    Linköping University, The Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Nesterenko, Irina
    Linköping University, The Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Björefors, Fredrik
    Linköping University, The Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Baltzer, Lars
    Division of Organic Chemistry, Department of Biochemistry and Organic Chemistry, BMC, Box 599, Uppsala University, SE-751 24 Uppsala, Sweden..
    Liedberg, Bo
    Linköping University, The Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Controlled Assembly of Gold Nanoparticles using De Novo Designed Polypeptide Scaffolds2008In: Proceedings SPIE, Vol. 6885, Photonic Biosensing and Microoptics, 2008, p. 688506-1-688506-8Conference paper (Refereed)
    Abstract [en]

    Heterodimerization between designed helix-loop-helix polypeptides was utilized in order to assemble gold nanoparticles on planar substrates. The peptides were designed to fold into four-helix bundles upon dimerization. A Cys-residue in the loop region was used to immobilize one of the complementary peptides on a maleimide containing SAM on planar gold substrates whereas the second peptide was immobilized directly on gold nanoparticles. Introducing the peptide decorated particles over a peptide functionalized surface resulted in particle assembly. Further, citrate stabilized particles were assembled on amino-silane modified glass and silicon substrates. By subsequently introducing peptides and gold nanoparticles, particle-peptide hybrid multi layers could be formed.

  • 4.
    Aili, Daniel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Enander, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Rydberg, Johan
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Nesterenko, Irina
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Björefors, Fredrik
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Baltzer, Lars
    Department of Biochemistry and Organic Chemistry, BMC, Box 599, Uppsala UniVersity, SE-751 24 Uppsala, Sweden.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Folding Induced Assembly of Polypeptide Decorated Gold Nanoparticles2008In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, no 17, p. 5780-5788Article in journal (Refereed)
    Abstract [en]

    Reversible assembly of gold nanoparticles controlled by the homodimerization and folding of an immobilized de novo designed synthetic polypeptide is described. In solution at neutral pH, the polypeptide folds into a helix–loop–helix four-helix bundle in the presence of zinc ions. When immobilized on gold nanoparticles, the addition of zinc ions induces dimerization and folding between peptide monomers located on separate particles, resulting in rapid particle aggregation. The particles can be completely redispersed by removal of the zinc ions from the peptide upon addition of EDTA. Calcium ions, which do not induce folding in solution, have no effect on the stability of the peptide decorated particles. The contribution from folding on particle assembly was further determined utilizing a reference peptide with the same primary sequence but containing both D and L amino acids. Particles functionalized with the reference peptide do not aggregate, as the peptides are unable to fold. The two peptides, linked to the nanoparticle surface via a cysteine residue located in the loop region, form submonolayers on planar gold with comparable properties regarding surface density, orientation, and ability to interact with zinc ions. These results demonstrate that nanoparticle assembly can be induced, controlled, and to some extent tuned, by exploiting specific molecular interactions involved in polypeptide folding.

  • 5.
    Aili, Daniel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Tai, Feng-I
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Enander, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Baltzer, Lars
    Department of Biochemistry andOrganic Chemistry Uppsala University, BMC, Box 576, 75123 Uppsala, Sweden.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Self-Assembly of Fibers and Nanorings from Disulfide-Linked Helix–Loop–Helix Polypeptides2008In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 47, no 30, p. 5554-5556Article in journal (Refereed)
  • 6.
    Aili, Daniel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Enander, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Rydberg, Johan
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Lundström, Ingemar
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics . Linköping University, The Institute of Technology.
    Baltzer, Lars
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Aggregation-Induced Folding of a de novo Designed Polypeptide Immobilized on Gold Nanoparticles2006In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 128, no 7, p. 2194 -2195Article in journal (Refereed)
    Abstract [en]

    This communication reports the first steps in the construction of a novel, nanoparticle-based hybrid material for biomimetic and biosensor applications. Gold nanoparticles were modified with synthetic polypeptides to enable control of the particle aggregation state in a switchable manner, and particle aggregation was, in turn, found to induce folding of the immobilized peptides.

  • 7.
    Buznyk, Oleksiy
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. National Academic Medical Science Ukraine, Ukraine.
    Pasyechnikova, Nataliya
    National Academic Medical Science Ukraine, Ukraine.
    Islam, Mohammad Mirazul
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Karolinska Institute, Sweden.
    Iakymenko, Stanislav
    National Academic Medical Science Ukraine, Ukraine.
    Fagerholm, Per
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Ophthalmology in Linköping.
    Griffith, May
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Karolinska Institute, Sweden.
    Bioengineered Corneas Grafted as Alternatives to Human Donor Corneas in Three High-Risk Patients2015In: Clinical and Translational Science, ISSN 1752-8054, E-ISSN 1752-8062, Vol. 8, no 5, p. 558-562Article in journal (Refereed)
    Abstract [en]

    Corneas with severe pathologies have a high risk of rejection when conventionally grafted with human donor tissues. In this early observational study, we grafted bioengineered corneal implants made from recombinant human collagen and synthetic phosphorylcholine polymer into three patients for whom donor cornea transplantation carried a high risk of transplant failure. These patients suffered from corneal ulcers and recurrent erosions preoperatively. The implants provided relief from pain and discomfort, restored corneal integrity by promoting endogenous regeneration of corneal tissues, and improved vision in two of three patients. Such implants could in the future be alternatives to donor corneas for high-risk patients, and therefore, merits further testing in a clinical trial.

  • 8.
    Carlsson, Jenny
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics . Linköping University, The Institute of Technology.
    Gullstrand, Camilla
    Linköping University, Department of Clinical and Experimental Medicine, Pediatrics . Linköping University, Faculty of Health Sciences.
    Westermark, Gunilla
    Linköping University, Department of Clinical and Experimental Medicine, Cell Biology. Linköping University, Faculty of Health Sciences.
    Ludvigsson, Johnny
    Linköping University, Department of Clinical and Experimental Medicine, Pediatrics . Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Centre of Paediatrics and Gynecology and Obstetrics, Department of Paediatrics in Linköping.
    Enander, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    An indirect competitive immunoassay for insulin autoantibodies based on surface plasmon resonance2008In: Biosensors and Bioelectronics, ISSN 0956-5663, Vol. 24, no 4, p. 876-881Article in journal (Refereed)
    Abstract [en]

    We have developed a sensitive and specific method based on surface plasmon resonance (SPR) for detection of insulin autoantibodies (IAA) in serum samples from individuals at high risk of developing type 1 diabetes (T1D). When measuring trace molecules in undiluted sera with label-free techniques like SPR, non-specific adsorption of matrix proteins to the sensor surface is often a problem, since it causes a signal that masks the analyte response. The developed method is an indirect competitive immunoassay designed to overcome these problems. Today, IAA is mainly measured in radio immunoassays (RIAs), which are time consuming and require radioactively labeled antigen. With our SPR-based immunoassay the overall assay time is reduced by a factor of >100 (4 days to 50 min), while sensitivity is maintained at a level comparable to that offered by RIA.

  • 9.
    Chaabane, Wiem
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Health Sciences. Tunis University, Tunisia.
    Cieślar-Pobuda, Artur
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Health Sciences. Silesian University of Technology, Gliwice, Poland.
    El-Gazzah, Mohamed
    Tunis University, Tunisia.
    Jain, Mayur V.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Health Sciences.
    Rzeszowska-Wolny, Joanna
    Silesian University of Technology, Gliwice, Poland.
    Rafat, Mehrdad
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, Faculty of Health Sciences.
    Stetefeld, Joerg
    University of Manitoba, Winnipeg, Canada.
    Ghavami, Saeid
    University of Manitoba, Winnipeg, Canada.
    Los, Marek
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Health Sciences. Pomeranian Medical University, Szczecin, Poland.
    Human-Gyrovirus-Apoptin Triggers Mitochondrial Death Pathway—Nur77 is Required for Apoptosis Triggering: 2014In: Neoplasia, ISSN 1522-8002, E-ISSN 1476-5586, Vol. 16, no 9, p. 679-693Article in journal (Refereed)
    Abstract [en]

    The human gyrovirus derived protein Apoptin (HGV-Apoptin) a homologue of the chicken anemia virus Apoptin (CAV-Apoptin), a protein with high cancer cells selective toxicity, trigger apoptosis selectively in cancer cells. In this paper, we show that HGV-Apoptin acts independently from the death receptor pathway as it induces apoptosis in similar rates in Jurkat cells deficient in either FADD-function or caspase-8 (key players of the extrinsic pathway) and their parental clones. HGV-Apoptin induces apoptosis via the activation of the mitochondrial intrinsic pathway. It induces both mitochondrial inner and outer membrane permebilization, characterized by the loss of the mitochondrial potential and the release into cytoplasm of the pro-apoptotic molecules including apoptosis inducing factor (AIF) and cytochrome c. HGV-Apoptin acts via the apoptosome, as lack of expression of APAF1 in murine embryonic fibroblast strongly protected the cells from HGV-Apoptin-induced apoptosis. Moreover, QVD-oph a broad-spectrum caspase inhibitor delayed HGV-Apoptin-induced death. On the other hand, overexpression of the anti-apoptotic BCL-XL confers resistance to HGV-Apoptin induced cell death. In contrast, cells that lack the expression of the pro-apoptotic BAX and BAK are protected from HGV-Apoptin induced apoptosis. Furthermore, HGV-Apoptin acts independently from p53 signal but triggers the cytoplasmic translocation of Nur77. Taking together this data indicate that HGV-Apoptin acts through the mitochondrial pathway, in a caspase-dependent manner but independently from the death receptor pathway.

  • 10.
    Colnerud Nilsson, Emma
    Linköping University, Department of Physics, Chemistry and Biology.
    Database for targeted drug screening with Liquid Chromatography - Time-Of-Flight Mass Spectrometry, (LC-TOFMS)2010Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Today there are no fully general analytical techniques available for detection and confirmation of known and unknown substances in toxicological screening, further tools are therefore needed. The development of mass spectrometry with time-of-flight (TOF) detection is promising but there are still areas to be further developed and evaluated, both instrumentation and applications.

    During 2009 The National Board of Forensic Medicine-Department of Forensic Genetics and Forensic Toxicology, (RMV) started cooperation with the instrumentation company Waters (Manchester, UK) and the Department of Clinical Pharmacology (KI, Solna) evaluating a new TOF-instrument for toxicological screening. My assignment as a part of this project has been to create a limited and relevant database of drugs and toxics in Excel, including monoisotopic mass, used when screening for pharmaceutical substances and their metabolites most probable to be found in Swedish autopsy material.

    A limited database has been developed based on information from several sources, it ended up in 875 analytes and metabolites. A limited but complete database is more reliable in practise than a big database, by means of a lower frequency of isobars and more information included (e.g. retention time from liquid chromatography) making analysis faster. Commercial databases are generally theoretical, lacking information about for example retention time that often is an important criterion for identification.

  • 11.
    El Serafi, Ibrahim
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences. Karolinska Inst, Sweden; Port Said Univ, Egypt.
    Remberger, Mats
    Uppsala Univ, Sweden; Uppsala Univ Hosp, Sweden.
    Ringden, Olle
    Karolinska Inst, Sweden.
    Torlen, Johan
    Karolinska Inst, Sweden; Karolinska Univ Hosp, Sweden.
    Sundin, Mikael
    Karolinska Inst, Sweden; Astrid Lindgren Childrens Hosp, Sweden.
    Bjorklund, Andreas
    Karolinska Univ Hosp, Sweden.
    Winiarski, Jacek
    Karolinska Inst, Sweden; Astrid Lindgren Childrens Hosp, Sweden.
    Mattsson, Jonas
    Karolinska Inst, Sweden; Univ Toronto, Canada; Univ Toronto, Canada.
    Reduced Risk of Sinusoidal Obstruction Syndrome of the Liver after Busulfan-Cyclophosphamide Conditioning Prior to Allogeneic Hematopoietic Stem Cell Transplantation2019In: Clinical and Translational Science, ISSN 1752-8054, E-ISSN 1752-8062Article in journal (Refereed)
    Abstract [en]

    The aim of this study is to evaluate the incidence of sinusoidal obstruction syndrome (SOS) of the liver and the clinical outcome after hematopoietic stem cell transplantation (HSCT) based on several modifications in our protocols. We retrospectively investigated 372 patients undergoing myeloablative conditioning with oral busulfan (Bu) and cyclophosphamide before allogeneic HSCT during 1990-2015. Patients supportive care was changed in order to reduce the regimen-related toxicities. Norethisterone use was terminated in 1998, therapeutic drug monitoring of Bu was initiated in 2000, and the use of liver supportive drugs, such as ursodeoxycholic acid and N-acetyl-L-cysteine, were started in 2002 and 2009, respectively. In total, 26 patients (7.0%) developed SOS at a median of 19 days after transplantation. Of these 26 patients, 20 died at a median of 119 days after HSCT and 102 days after the diagnosis of SOS. The incidence of SOS decreased over time in accordance with the improvements in supportive care. The highest incidence of SOS was during 1995-1999 (16.2%) compared with 2.3% during 2010-2015. Overall survival for patients with SOS was 62%, 46%, and 27% at 100 days, 1 year, and 5 years after HSCT, respectively, compared with 92%, 77%, and 66% for those who did not develop SOS (P amp;lt; 0.001). In conclusion, the incidence of SOS and related deaths were significantly decreased over the last years. Our institution pursues massive preventative and personalized measures for SOS. This strategy may also be applicable in other conditioning protocols in order to reduce the incidence of SOS and, hence, improve the clinical outcome.

  • 12.
    Enander, Karin
    et al.
    Division of Organic Chemistry, Uppsala University.
    Aili, Daniel
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Baltzer, Lars
    Division of Organic Chemistry, Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden.
    Lundström, Ingemar
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, The Institute of Technology.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Alpha-helix-inducing dimerization of synthetic polypeptide scaffolds on gold2005In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 21, no 6, p. 2480-2487Article in journal (Refereed)
    Abstract [en]

    Designed, synthetic polypeptides that assemble into four-helix bundles upon dimerization in solution were studied with respect to folding on planar gold surfaces. A model system with controllable dimerization properties was employed, consisting of negatively and positively charged peptides. Circular dichroism spectroscopy and surface plasmon resonance based measurements showed that at neutral pH, the peptides were able to form heterodimers in solution, but unfavorable electrostatic interactions prevented the formation of homodimers. The dimerization propensity was found to be both pH- and buffer-dependent. A series of infrared absorption−reflection spectroscopy experiments of the polypeptides attached to planar gold surfaces revealed that if the negatively charged peptide was immobilized from a loading solution where it was folded, its structure was retained on the surface provided it had a cysteine residue available for anchoring to gold. If it was immobilized as random coil, it remained unstructured on the surface but was able to fold through heterodimerization if subsequently exposed to a positively charged polypeptide. When the positively charged peptide was immobilized as random coil, heterodimerization could not be induced, probably because of high-affinity interactions between the charged primary amine groups and the gold surface. These observations are intended to pave the way for future engineering of functional surfaces based on polypeptide scaffolds where folding is known to be crucial for function.

  • 13.
    Guerrero-Bosagna, Carlos
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Optimized method for methylated DNA immuno-precipitation2015In: MethodsX, ISSN 1258-780X, E-ISSN 2215-0161, Vol. 2, p. e432-e439, article id eArticle in journal (Refereed)
    Abstract [en]

    Methylated DNA immunoprecipitation (MeDIP) is one of the most widely used methods to evaluate DNA methylation on a whole genome scale, and involves the capture of the methylated fraction of the DNA by an antibody specific to methyl-cytosine. MeDIP was initially coupled with microarray hybridization to detect local DNA methylation enrichments along the genome. More recently, MeDIP has been coupled with next generation sequencing, which highlights its current and future applicability. In previous studies in which MeDIP was applied, the protocol took around 3 days to be performed. Given the importance of MeDIP for studies involving DNA methylation, it was important to optimize the method in order to deliver faster turnouts. The present article describes optimization steps of the MeDIP method. The length of the procedure was reduced in half without compromising the quality of the results. This was achieved by:

    • Reduction of the number of washes in different stages of the protocol, after a careful evaluation of the number of indispensable washes.

    • Reduction of reaction times for detaching methylated DNA fragments from the complex agarose beads:antibody.

    • Modification of the methods to purify methylated DNA, which incorporates new devices and procedures, and eliminates a lengthy phenol and chloroform:isoamyl alcohol extraction.

  • 14.
    Gunnarsson, Stina
    et al.
    Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Rehabilitation Medicine. Linköping University, Department of Medical and Health Sciences, Division of Community Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Samuelsson, Kersti
    Östergötlands Läns Landsting, Anaesthetics, Operations and Specialty Surgery Center, Department of Rehabilitation Medicine. Linköping University, Department of Medical and Health Sciences, Division of Community Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Patient experiences with intrathecal baclofen as a treatment for spatsticity - a pilot study2015In: Disability and Rehabilitation, ISSN 0963-8288, E-ISSN 1464-5165, Vol. 37, no 10, p. 834-841Article in journal (Refereed)
    Abstract [en]

    Purpose: This study describes how patients experience intrathecal baclofen (ITB) treatment. Methods: Data were collected from interviews with 14 patients (19–76 years old) who were diagnosed with spinal cord injury (SCI), multiple sclerosis (MS), or cerebral palsy (CP). Data were analyzed using conventional content analysis. Result: The analysis resulted in 16 subcategories arranged into five main categories: procedures before treatment, the effect of ITB on daily life and activities, continuous follow-up, expected and unexpected consequences of ITB, and overall level of satisfaction with ITB. Together these categories described the patients' experiences with ITB treatment. When the patients were asked whether they would undergo ITB again, they all stated that they would. Conclusion: Patients stated that they were highly satisfied with the ITB treatment. However, the patients identified several areas that could be improved. Specifically, the patients wanted more information about the different steps in the treatment process and what to expect from ITB treatment.Implications for Rehabilitation

    • An overall satisfaction with the effect from ITB treatment was shown, but some areas still need to be improved.

    • Complications following ITB treatment still remain a major concern for the patient group.

    • Future clinical practice, should address how to take into account patients' expectations and define relevant goals with respect to ITB treatment as well as how to supply professional information.

  • 15.
    Hallander, Hans O.
    et al.
    Swedish Institute for Infectious Disease Control (SMI), Solna, Sweden.
    Ljungman, Margretha
    Swedish Institute for Infectious Disease Control (SMI), Solna, Sweden.
    Jahnmatz, Maja
    Swedish Institute for Infectious Disease Control (SMI), Solna, Sweden.
    Storsaeter, Jann
    Norwegian institute of Public Health, Oslo, Norway.
    Nilsson, Lennart
    Linköping University, Department of Clinical and Experimental Medicine, Allergy Centre. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart and Medicine Center, Allergy Center.
    Gustafsson, Lennart
    Swedish Institute for Infectious Disease Control (SMI), Solna, Sweden.
    Should fimbriae be included in pertussis vaccines? Studies on ELISA IgG anti-Fim2/3 antibodies after vaccination and infection2009In: APMIS: Acta pathologica, microbiologica et immunologica Scandinavica. Supplementum, ISSN 0903-465X, E-ISSN 1600-5503, Vol. 117, no 9, p. 660-671Article in journal (Refereed)
    Abstract [en]

    The anti-Fim response and long-term persistence after vaccination and infection may be of importance in understanding population immunity. Longitudinal serum samples (n = 1330) from 542 non-infected children related to a Swedish vaccine trial showed that the post vaccination (DTPa5) antibody decay curve for pertussis ELISA IgG anti-fimbriae2/3 (anti-Fim2/3) was bi-phasic. A slower one followed an initial rapid decay approximately 5-6 months after the third dose at 12 months of age. After 71 months, however, 60% still had concentrations above > or =5 EU/ml, a level that had been shown to correlate with decreased risk of disease. Booster responses after re-vaccination with DTPa5 at 4, 5 and 6 years of age were strong and appeared within 1 week after vaccination, indicating immune memory. Ninety-six young children with verified pertussis infection, for whom we had serum samples both before, during and after the infection, showed a high response if they had been primed with fimbriae (either DTPa5 or DTPwc). In contrast, 76% of infected children not primed with fimbriae (a DTPa2 or DT group) only had concentrations below the minimum level of detection in all samples taken during and after the infection. In two Swedish seroepidemiological surveys, one from 1997 just after reintroduction of universal childhood vaccination against pertussis and one from 2007, the proportion of children 2-3 years with anti-Fim2/3 concentrations <5 EU/ml was similar and above 90%. This reflects that the two- or three-component pertussis vaccines (DTPa2 and DTPa3) that were introduced in Sweden in 1996 do not induce anti-Fim2/3 antibodies. In previous studies it was shown in multivariate analyses that levels of IgG anti-Fim2/3 > or =5 EU/ml reduced short-term risk of pertussis in small children. As the antibody response to Fim2/3 after infection is poor in children who have not been primed earlier in life, inclusion of immunogenic Fim2/3 in future pertussis vaccines should be considered.

  • 16.
    Hernandez, Frank J
    et al.
    Nucleic Acid Center, Biochemistry and Molecular Biology Department, University of of Southern Denmark, Campusvej 55, Odense M, 5230, Denmark.
    Kalra, Neerja
    Department of Physics and Chemistry, University of of Southern Denmark, Campusvej 55, Odense M, 5230, Denmark.
    Wengel, Jesper
    Department of Physics and Chemistry, University of of Southern Denmark, Campusvej 55, Odense M, 5230, Denmark.
    Vester, Birte
    Nucleic Acid Center, Biochemistry and Molecular Biology Department, University of of Southern Denmark, Campusvej 55, Odense M, 5230, Denmark.
    Aptamers as a model for functional evaluation of LNA and 2′-amino LNA2009In: Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, E-ISSN 1090-2120, Vol. 19, no 23, p. 6585-6587Article in journal (Refereed)
    Abstract [en]

    The affinity change upon incorporation of LNA and 2′-amino-LNA monomers into an avidin binding DNA aptamer is described. The kinetic profile of selected modified-aptamer was obtained by surface plasmon resonance experiments and compared with the profile of the parent unmodified DNA aptamer. We report significant improvement of avidin binding affinity by the incorporation of single LNA modifications into the aptamer, and successful incorporation of 2′-amino LNA as a novel monomer in aptamers with potential function as carrier unit for additional molecular entities. © 2009 Elsevier Ltd. All rights reserved.

  • 17.
    Jain, Mayur V.
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Health Sciences.
    Los, Marek Jan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Health Sciences. BioApplications Ent., Winnipeg, MB, Canada; Department of Pathomorphology, Pomeranian Medical University, Szczecin, Poland.
    Spatiotemporal cytometry—Simultaneous analysis of DNA replication and damage2013In: Cytometry Part A, ISSN 1552-4922, E-ISSN 1552-4930, Vol. 83, no 11, p. 975-976Article in journal (Refereed)
  • 18.
    Jansson, Emelie
    Linköping University, Department of Physics, Chemistry and Biology.
    Gaskromatografisk metod för analys av GHB i urin2009Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    A method for determination and quantification of gamma-hydroxyburyric acid (GHB) in urine samples is developed at Sahlgrenska universitetssjukhus. No time consuming procedures as derivatization and exctration is required, which makes the method fairly unique. Hydrochloric acid and internal standard, gamma-valerolakton, is added to the urine sample before the sample is injected to a gas chromatograph with a flame ionization detector and a column for glycols and alcohols. The hydrochloric acid makes the GHB convert into gamma-butyrolactone (GBL) which is easier to separate in the gas chromatograph. Limit of detection was found to be 100 μmol/L and test result is received after 6,5 minutes. There are still some question marks around the method, for example, there is a possibility that another substance elute at the same time as GHB. More tests are required to determine whether or not it is so. For now the method can be used as a screening analysis to hastily detect GHB presence. Verification can be done with GC-MS.

  • 19.
    Johansson, Johannes D.
    et al.
    ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Sciences and Technology.
    Farzam, Parisa
    ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Sciences and Technology.
    Mireles, Miguel
    ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Sciences and Technology.
    Jiménez Valerio, Gabriela
    Bellvitge Biomedical Research Institute–IDIBELL.
    Martínez Lozano, Mar
    Bellvitge Biomedical Research Institute–IDIBELL.
    Casanovas, Oriol
    Bellvitge Biomedical Research Institute–IDIBELL.
    Durduran, Turgut
    ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Sciences and Technology.
    Optical investigation of antiangiogenic therapy in renal cell carcinoma2015Conference paper (Other academic)
    Abstract [en]

    Diffuse optical spectroscopy and diffuse correlation spectroscopy was used to monitor antiangiogenic therapy in renal cell carcinoma. The measurements allowed for hemodynamic characterization of the tumors and to monitor the initial antiangiogenic effect and relate it to final vessel density and tumor size.

  • 20.
    Lenz, Annika
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry . Linköping University, The Institute of Technology.
    Theoretical Investigations of Water Clusters, Ice Clathrates and Functionalized Nanoparticles2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Nanosized structures are of intermediate size between individual molecules and bulkmaterials which gives them several unique properties. At the same time their relative limitedsizes make them suitable for studies by the methods of computational chemistry. In this thesiswater clusters, ice clathrates and functionalized metal-oxide nanoparticles have been studiedby quantum-chemical calculations and statistical thermodynamics.

    The stabilities of water clusters composed of up to 100 molecules have been investigated. Themultitude of possible H-bonded topologies and their importance for determining theproperties of the clusters have been highlighted. Several structural characteristics of thehydrogen bonded network have been examined and the structural factors that determine thestability of an H-bonded network have been identified. The stability of two kinds of oxygenframeworks for water clusters have been analyzed, taking into account thermal energy andentropy corrections. Clusters with many 4-coordinated molecules have been found to be lowerin energy at low temperatures whereas the clusters with less-coordinated molecules dominateat higher temperatures. The equilibrium size distribution of water clusters as a function oftemperature and pressure has been computed using statistical thermodynamics. Themicroscopic local structure of liquid water has been probed by utilizing information from thestudied water clusters. The average number of H-bonds in liquid water has been predicted byfitting calculated average IR spectra for different coordination types in water clusters toexperimental IR spectra.

    Water can form an ice-like structure that encloses various molecules such as methane. Thesemethane hydrates are found naturally at the ocean floor and in permafrost regions and canconstitute a large unemployed energy resource as well as a source of an effective green-housegas. The pressure dependencies of the crystal structures, lattice energies and phase transitionsfor the three methane hydrates with the clathrate structures I, II and H have been mapped out.

    Zinc oxide is a semiconducting material with interesting luminescence properties that can beutilized in optical devices, such as photodetectors, light emitting devices and biomarkers. Theeffect of water molecules adsorbed on the ZnO surface when adsorbing organic acids havebeen investigated. Changes in optical properties by the adsorption of carboxylic acids havebeen studied and compared with experimental results. Aromatic alcohols at TiO2 metal-oxidenanoparticles have been studied as model systems for dye-sensitizied solar cells. Adsorptiongeometries are predicted and the influence from the adsorbed molecules on the electronicproperties has been studied.

    List of papers
    1. A theoretical study of water clusters: the relation between hydrogen-bond topology and interaction energy from quantum-chemical computations for clusters with up to 22 molecules
    Open this publication in new window or tab >>A theoretical study of water clusters: the relation between hydrogen-bond topology and interaction energy from quantum-chemical computations for clusters with up to 22 molecules
    2005 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 7, p. 1905-1911Article in journal (Refereed) Published
    Abstract [en]

    Quantum-chemical calculations of a variety of water clusters with eight, ten and twelve molecules were performed, as well as for selected clusters with up to 22 water molecules. Geometry optimizations were carried out at the B3LYP/cc-pVDZ level and single-point energies were calculated at the B3LYP/aug-cc-pVDZ level for selected clusters. The electronic energies were studied with respect to the geometry of the oxygen arrangement and six different characteristics of the hydrogen-bond arrangement in the cluster. Especially the effect of the placement of the non-hydrogen bonding hydrogens on the interaction energy was studied. Models for the interaction energy with respect to different characteristics of the hydrogen-bond arrangement were derived through least-square fits. The results from the study of the clusters with eight, ten and twelve molecules are used to predict possible low-energy structures for various shapes of clusters with up to 22 molecules.

    Place, publisher, year, edition, pages
    RCS Publishing, 2005
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-30387 (URN)10.1039/b502109j (DOI)15935 (Local ID)15935 (Archive number)15935 (OAI)
    Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2017-12-13
    2. On the stability of dense versus cage-shaped water clusters: quantum-chemical investigations of zero-point energies, free energies, basis-set effects and IR spectra of (H2O)12 and (H2O)20
    Open this publication in new window or tab >>On the stability of dense versus cage-shaped water clusters: quantum-chemical investigations of zero-point energies, free energies, basis-set effects and IR spectra of (H2O)12 and (H2O)20
    2006 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 418, p. 361-367Article in journal (Refereed) Published
    Abstract [en]

    The energetics of water clusters with 12 and 20 molecules are studied by quantum-chemical computations using the B3LYP, MP2, MP4 and CCSD methods. The effect of electron-correlation method, basis set, zero-point energy, thermal energy and Gibbs free energy on the relative stability of fused clusters (structures consisting of cubic- or prismatic-shaped subparts) versus cage-shaped clusters (more open structures with only three-coordinated molecules) are investigated. The O–H stretching IR vibrational spectra are studied. The contribution of zero-point and Gibbs free energy will diminish the energy difference between fused- and cage-shaped clusters, but the fused structures are still slightly more favorable.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-36194 (URN)10.1016/j.cplett.2005.11.013 (DOI)30469 (Local ID)30469 (Archive number)30469 (OAI)
    Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2017-12-13
    3. Theoretical IR spectra for water clusters (H2O)n (n = 6-22, 28, 30) and identification of spectral contributions from different H-Bond conformations in gaseous and liquid water
    Open this publication in new window or tab >>Theoretical IR spectra for water clusters (H2O)n (n = 6-22, 28, 30) and identification of spectral contributions from different H-Bond conformations in gaseous and liquid water
    2006 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 110, no 50, p. 13388-13393Article in journal (Refereed) Published
    Abstract [en]

    The vibrational IR spectra in the O-H stretching region are computed for water clusters containing 6-22, 28, and 30 molecules using quantum-chemical calculations (B3LYP and an augmented basis set). For the cluster with 20 molecules, several different structures were studied. The vibrational spectrum was partitioned into contributions from different molecules according to their coordination properties. The frequency shifts depend on the number of donated/accepted H-bonds primarily of the two molecules participating in the H-bond, but also of the surrounding molecules H-bonding to these molecules. The frequencies of H-bonds between two molecules of the same coordination type are spread over a broad interval. The most downshifted hydrogen-bond vibrations are those donated by a single-donor 3-coordinated molecule where the H-bond is accepted by a single-acceptor molecule. The H-bonded neighbors influence the downshift, and their contribution can be rationalized in the same way as for the central dimer. Single donors/acceptors cause larger downshifts than 4-coordinated molecules, and the least downshift is obtained for double donors/acceptors. This result is at variance with the conception that experimental liquid water spectra may be divided into components for which larger downshifts imply higher H-bond coordination. A mean spectral contribution for each coordination type for the donor molecule was derived and fitted to the experimental liquid water IR spectrum, which enabled an estimation of the distribution of H-bond types and average number of H-bonds (3.0 ± 0.2) in the liquid. © 2006 American Chemical Society.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-36614 (URN)10.1021/jp066372x (DOI)31825 (Local ID)31825 (Archive number)31825 (OAI)
    Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2017-12-13
    4. A theoretical study of water equilibria: The cluster distribution versus temperature and pressure for (H2O)n, n=1–60, and ice
    Open this publication in new window or tab >>A theoretical study of water equilibria: The cluster distribution versus temperature and pressure for (H2O)n, n=1–60, and ice
    2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, no 13, p. 134302-134302-13Article in journal (Refereed) Published
    Abstract [en]

    The size distribution of water clusters at equilibrium is studied using quantum-chemical calculations in combination with statistical thermodynamics. The necessary energetic data is obtained by quantum-chemical B3LYP computations and through extrapolations from the B3LYP results for the larger clusters. Clusters with up to 60 molecules are included in the equilibrium computations. Populations of different cluster sizes are calculated using both an ideal gas model with noninteracting clusters and a model where a correction for the interaction energy is included analogous to the van der Waals law. In standard vapor the majority of the water molecules are monomers. For the ideal gas model at 1 atm large clusters [56-mer (0–120 K) and 28-mer (100–260 K)] dominate at low temperatures and separate to smaller clusters [21–22-mer (170–280 K) and 4–6-mer (270–320 K) and to monomers (300–350 K)] when the temperature is increased. At lower pressure the transition from clusters to monomers lies at lower temperatures and fewer cluster sizes are formed. The computed size distribution exhibits enhanced peaks for the clusters consisting of 21 and 28 water molecules; these sizes are for protonated water clusters often referred to as magic numbers. If cluster-cluster interactions are included in the model the transition from clusters to monomers is sharper (i.e., occurs over a smaller temperature interval) than when the ideal-gas model is used. Clusters with 20–22 molecules dominate in the liquid region. When a large icelike cluster is included it will dominate for temperatures up to 325 K for the noninteracting clusters model. Thermodynamic properties (Cp, H) were calculated with in general good agreement with experimental values for the solid and gas phase. A formula for the number of H-bond topologies in a given cluster structure is derived. For the 20-mer it is shown that the number of topologies contributes to making the population of dodecahedron-shaped cluster larger than that of a lower-energy fused prism cluster at high temperatures.

    Keywords
    water, vapour, ice, quantum chemistry, statistical thermodynamics, hydrogen bonding
    National Category
    Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-50778 (URN)10.1063/1.3239474 (DOI)
    Available from: 2009-10-14 Created: 2009-10-14 Last updated: 2017-12-12
    5. Computational studies of the stability of the (H2O)100 nanodrop
    Open this publication in new window or tab >>Computational studies of the stability of the (H2O)100 nanodrop
    2010 (English)In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 944, no 1-3, p. 163-167Article in journal (Refereed) Published
    Abstract [en]

    The stability of the (H2O)100 nanodrop, experimentally known from a polyoxomolybdatecrystal structure (Müller et al. Inorg. Chem. Commun., 2003, 6, 52) and other structuresinferred from clathrate structures, are studied by quantum-chemical B3LYP computations.The free energies are compared to the trends for smaller clusters with 15-30 molecules. Forthe small clusters both cage-based structures and denser structures with a larger number of Hbondsobtained by an evolutionary algorithm (Bandow and Hartke, J. Phys. Chem. A, 2006,110, 5809) are used. The dense structures are most often found to be lower in electronicenergy. The cage-based structures, to which the structure of the experimentally found(H2O)100 cluster can be categorized, become more stable when Gibbs free energy is calculatedat 298 K. Additional cage-based clusters in the 35-81 molecular range were constructed forcomparison. The experimental cluster with 100 molecules (C2h/Ci-symmetry for oxygens/allatoms) and the constructed cluster with 42 molecules are found to be lower in energy than aplausible overall trend. The (H2O)42 cluster has an extraordinary high symmetry (S6), evenwhen the hydrogens are considered. The (H2O)100 cluster is the only of the studied clusters forwhich ΔG is negative at 298 K.

    Keywords
    Water clusters, Quantum-chemical computations, Hydrogen bonding, B3LYP calculations, Gibbs free energy
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-53176 (URN)10.1016/j.theochem.2009.12.033 (DOI)000275688200022 ()
    Note
    Original Publication: Annika Lenz and Lars Ojamäe, Computational studies of the stability of the (H2O)100 nanodrop, 2010, Journal of Molecular Structure: THEOCHEM, (944), 1-3, 163-167. http://dx.doi.org/10.1016/j.theochem.2009.12.033 Copyright: Elsevier Science B.V., Amsterdam http://www.elsevier.com/ Available from: 2010-01-18 Created: 2010-01-18 Last updated: 2017-12-12
    6. Structures of the I-, II- and H-Methane Clathrates and the Ice−Methane Clathrate Phase Transition from Quantum-Chemical Modeling with Force-Field Thermal Corrections
    Open this publication in new window or tab >>Structures of the I-, II- and H-Methane Clathrates and the Ice−Methane Clathrate Phase Transition from Quantum-Chemical Modeling with Force-Field Thermal Corrections
    2011 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, no 23, p. 6169-6176Article in journal (Refereed) Published
    Abstract [en]

    Methane hydrates with the three clathrate structures I, II and H are studied by quantumchemicalmethods. The periodic B3LYP computations are combined with force-field methodsfor the thermal energy corrections. The pressure dependencies for the crystal structures, latticeenergies and guest molecule interactions are derived. Quantum-chemical geometryoptimizations predict too small cell volumes compared to experimental data, but includingzero-point energy and thermal energy the cell volume increases and the correct densities areobtained. Phase diagram for the three structures are investigated, and phase transitions werefound at 5 GPa for the MH-I–MH-II transition and at 10 GPa for the MH-II–MH-H transition.

    Place, publisher, year, edition, pages
    ACS Publications, 2011
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-53177 (URN)10.1021/jp111328v (DOI)
    Note
    The original title of this article was: "Structure and phase transitions of I-, II- and H- methane clathrates and ice from quantum-chemical B3LYP computations with corrections for thermal effects".Available from: 2010-01-18 Created: 2010-01-18 Last updated: 2017-12-12Bibliographically approved
    7. ZnO Nanoparticles Functionalized with Organic Acids: An Experimental and Quantum-Chemical Study
    Open this publication in new window or tab >>ZnO Nanoparticles Functionalized with Organic Acids: An Experimental and Quantum-Chemical Study
    Show others...
    2009 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 113, no 40, p. 17332-17341Article in journal (Refereed) Published
    Abstract [en]

    Electrochemical synthesis and physical characterization of ZnO nanoparticles functionalized with four different organic acids, three aromatic (benzoic, nicotinic, and trans-cinnamic acid) and one nonaromatic (formic acid), are reported. The functionalized nanoparticles have been characterized by X-ray powder diffraction, transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, UV−vis, and photoluminescence spectroscopy. The adsorption of the organic acids at ZnO nanoparticles was further analyzed and interpreted using quantum-chemical density-functional theory computations. Successful functionalization of the nanoparticles was confirmed experimentally by the measured splitting of the carboxylic group stretching vibrations as well as by the N(1s) and C(1s) peaks from XPS. From a comparison between computed and experimental IR spectra, a bridging mode adsorption geometry was inferred. PL spectra exhibited a remarkably stronger near band edge emission for nanoparticles functionalized with formic acid as compared to the larger aromatic acids. From the quantum-chemical computations, this was interpreted to be due to the absence of aromatic adsorbate or surface states in the band gap of ZnO, caused by the formation of a complete monolayer of HCOOH. In the UV−vis spectra, strong charge-transfer transitions were observed.

    Keywords
    nanoparticles, ZnO, organic acids, adsorption, synthesis, XPS, UV-vis, quantum chemical calculations
    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-50783 (URN)10.1021/jp905481v (DOI)
    Available from: 2009-10-14 Created: 2009-10-14 Last updated: 2017-12-12
    8. Quantum-chemical investigations of phenol and larger aromatic molecules at the TiO2 anatase (101) surface
    Open this publication in new window or tab >>Quantum-chemical investigations of phenol and larger aromatic molecules at the TiO2 anatase (101) surface
    2008 (English)In: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 117, p. 012020-(8 pp)Article in journal (Refereed) Published
    Abstract [en]

    Adsorption of aromatic molecules at the (101) surface of titanium dioxide anatase is studied by quantum-chemical B3LYP computations, where both cluster and periodic calculations were performed and compared. For phenol different adsorption modes at a TiO2 cluster were mapped out and the energetically most favourable conformation was used for investigation of the electronic structure, for periodic calculations, and as a mould for the adsorption modes of phenylmethanol, phenylethanol, naphthalen-2-ol, phenanthren-2-ol, pyren-2-ol and perylen-2-ol. The alcohols form a H-bond to a surface O and a O(molecule)-Ti bond. For the larger aromatic molecules their increasingly higher HOMO levels decrease the effective bad gap of the system. Inclusion of spacer groups as in phenylmethanol and phenylethanol results in higher adsorption energies and larger band gaps. The LUMOs for the adsorbates help visualize the electronic coupling to the surface. Comparison of the cluster with the periodic model indicates that the former describes the electronic coupling in a similar manner as the latter, although the former lacks in the description of the anatase substrate.

    Keywords
    TiO2, anatase, phenol, adsorption, nanoparticles
    National Category
    Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-50664 (URN)10.1088/1742-6596/117/1/012020 (DOI)
    Available from: 2009-10-13 Created: 2009-10-13 Last updated: 2017-12-12
  • 21.
    Ljunggren, Stefan A
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Inflammation Medicine. Linköping University, Faculty of Health Sciences.
    Helmfrid, Ingela
    Linköping University, Department of Clinical and Experimental Medicine, Division of Inflammation Medicine. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart and Medicine Center, Occupational and Environmental Medicine Center.
    Salihovic, Samira
    Örebro University, Sweden.
    van Bavel, Bert
    Örebro University, Sweden.
    Wingren, Gun
    Linköping University, Department of Clinical and Experimental Medicine, Division of Inflammation Medicine. Linköping University, Faculty of Health Sciences.
    Lindahl, Mats
    Linköping University, Department of Clinical and Experimental Medicine, Division of Inflammation Medicine. Linköping University, Faculty of Health Sciences.
    Karlsson, Helen
    Linköping University, Department of Clinical and Experimental Medicine, Division of Inflammation Medicine. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart and Medicine Center, Occupational and Environmental Medicine Center.
    Persistent organic pollutants distribution in lipoprotein fractions in relation to cardiovascular disease and cancer.2014In: Environment International, ISSN 0160-4120, E-ISSN 1873-6750, Vol. 65, p. 93-9Article in journal (Refereed)
    Abstract [en]

    Persistent organic pollutants (POPs) are lipophilic environmental toxins that have been associated with cardiovascular disease (CVD) and cancer. The aim of this study was to investigate the concentrations of POPs in human high and low/very low-density lipoproteins (HDL and LDL/VLDL) and the possible association with CVD and cancer occurrence in individuals living in a contaminated area. Lipoproteins from 28 individuals (7 healthy controls, 8 subjects with cancer, 13 subjects with CVD) were isolated and the fraction-specific concentration of 20 different POPs was analyzed by high resolution gas chromatography/high resolution mass spectrometry. The activity of Paraoxonase 1 (PON1), an anti-oxidant in HDL, was determined in plasma of these 28 subjects and additional 50 subjects from the same area excluding diseases other than cancer or CVD. Fourteen polychlorinated biphenyls (PCBs) and three organochlorine pesticides were detected, and especially highly chlorinated PCBs were enriched in lipoproteins. Significantly higher concentrations of POPs were found among individuals with CVD or cancer compared to controls. Principal component analyses showed that POP concentrations in HDL were more associated with CVD, while POP concentrations in LDL/VLDL were more associated with cancer. PON1 activity was negatively correlated to sumPCB and a co-variation between decreased arylesterase-activity, increased PCB concentrations and CVD was found. This study shows that POPs are present in lipoproteins and were more abundant in individuals with CVD or cancer compared to healthy controls. The results also indicate that PCB exposure is accompanied by reduced PON1 activity that could impair the HDL function to protect against oxidation.

  • 22.
    Mantz, Amy
    et al.
    Univ Nebraska, NE 68588 USA.
    Rosenthal, Alice
    Leibniz Inst Polymerforsch Dresden eV, Germany; Tech Univ Dresden, Germany.
    Farris, Eric
    Univ Nebraska, NE 68588 USA.
    Kozisek, Tyler
    Univ Nebraska, NE 68588 USA.
    Bittrich, Eva
    Leibniz Inst Polymerforsch Dresden eV, Germany.
    Nazari, Saghar
    Leibniz Inst Polymerforsch Dresden eV, Germany.
    Schubert, Eva
    Univ Nebraska, NE USA.
    Schubert, Mathias
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering. Univ Nebraska, NE 68588 USA; Leibniz Inst Polymerforsch Dresden eV, Germany; Univ Nebraska, NE USA.
    Stamm, Manfred
    Leibniz Inst Polymerforsch Dresden eV, Germany; Tech Univ Dresden, Germany.
    Uhlmann, Petra
    Leibniz Inst Polymerforsch Dresden eV, Germany; Univ Nebraska, NE 68588 USA.
    Pannier, Angela K.
    Univ Nebraska, NE 68588 USA.
    Free Polyethylenimine Enhances Substrate-Mediated Gene Delivery on Titanium Substrates Modified With RGD-Functionalized Poly(acrylic acid) Brushes2019In: Frontiers in Chemistry, E-ISSN 2296-2646, Vol. 7, article id 51Article in journal (Refereed)
    Abstract [en]

    Substrate mediated gene delivery (SMD) is a method of immobilizing DNA complexes to a substrate via covalent attachment or nonspecific adsorption, which allows for increased transgene expression with less DNA compared to traditional bolus delivery. It may also increase cells receptivity to transfection via cell-material interactions. Substrate modifications with poly(acrylic) acid (PM) brushes may improve SMD by enhancing substrate interactions with DNA complexes via tailored surface chemistry and increasing cellular adhesion via moieties covalently bound to the brushes. Previously, we described a simple method to graft PM brushes to Ti and further demonstrated conjugation of cell adhesion peptides (i.e., RGD) to the PM brushes to improve biocompatibility. The objective of this work was to investigate the ability of Ti substrates modified with PM-RGD brushes (PM-RGD) to immobilize complexes composed of branched polyethyleneimine and DNA plasmids (bPEI-DNA) and support SMD in NIH/3T3 fibroblasts. Transfection in NIH/3T3 cells cultured on bPEI-DNA complexes immobilized onto PM-RGD substrates was measured and compared to transfection in cells cultured on control surfaces with immobilized complexes including Flat Ti, PM brushes modified with a control peptide (RGE), and unmodified PM. Transfection was two-fold higher in cells cultured on PM-RGD compared to those cultured on all control substrates. While DNA immobilization measured with radiolabeled DNA indicated that all substrates (PM-RGD, unmodified PM, Flat Ti) contained nearly equivalent amounts of loaded DNA, ellipsometric measurements showed that more total mass (i.e., DNA and bPEI, both complexed and free) was immobilized to PM and PM-RGD compared to Flat Ti. The increase in adsorbed mass may be attributed to free bPEI, which has been shown to improve transfection. Further transfection investigations showed that removing free bPEI from the immobilized complexes decreased SMD transfection and negated any differences in transfection success between cells cultured on PM-RGD and on control substrates, suggesting that free bPEI may be beneficial for SMD in cells cultured on bPEI-DNA complexes immobilized on PM-RGD grafted to Ti. This work demonstrates that substrate modification with PM-RGD is a feasible method to enhance SMD outcomes on Ti and may be used for future applications such as tissue engineering, gene therapy, and diagnostics.

  • 23.
    Nygren, Patrik
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Lundqvist, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Biotechnology . Linköping University, The Institute of Technology.
    Broo, Klas
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Jonsson, Bengt-Harald
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Biotechnology . Linköping University, The Institute of Technology.
    Fundamental Design Principles That Guide Induction of Helix upon Formation of Stable Peptide−Nanoparticle Complexes2008In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 8, no 7, p. 1844-1852Article in journal (Refereed)
    Abstract [en]

    We have shown that it is possible to design a peptide that has a very low helical content when free in solution but that adopts a well-defined helix when interacting with silica nanoparticles. From a systematic variation of the amino acid composition and distribution in designed peptides, it has been shown that the ability to form helical structure upon binding to the silica surface is dominated by two factors. First, the helical content is strongly correlated with the net positive charge on the side of the helix that interacts with the silica, and arginine residues are strongly favored over lysine residues in these positions. The second important factor is to have a high net negative charge on the side of the helix that faces the solution. Apparently, both attractive and repulsive electrostatic forces dominate the induction and stabilization of a bound helix. It is also evident that using amino acids that have high propensity to form helix in solution are also advantageous for the formation of helix on surfaces.

  • 24.
    Olofsson, Evelina
    Linköping University, The Department of Physics, Chemistry and Biology.
    Bronopol - ett miljöproblem i Sverige?2008Independent thesis Advanced level (degree of Magister), 20 points / 30 hpStudent thesis
    Abstract [en]

    Bronopol (2-brom-2nitropropan-1,3-diol) occurs in many products, for example cosmetics, medicines and industrial water systems. In this thesis Bronopol was investigated to see if it is an environmental problem in Sweden.

    As a starting point two existing analysis methods was used to combine to one. The first one was suited for phenol analysis and the other one for Bronopol analysis. The combined method was optimized as far as possible, although this wasn’t achieved as hoped. The cause of this was due to errors beyond our explanation. Because of this problem the yield couldn’t be determined.

    The water samples were taken from Tekniska Verken in Linköping, Sweden. It was two samples, one incoming and one outgoing sample from the waste water treatment plant. The samples were filtered and then they were passed through SPE columns. The samples were evaporated to dryness with N2. After this the samples were derivatizised with TMS and the following step was GC analysis with EC – detector.

    Bronopol was detected in the incoming water sample.

  • 25.
    Patra, Hirak Kumar
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Imani, Roghayeh
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering. Univ,of Ljubljana, Slovenia; University of Ljubljana, Slovenia.
    Jangamreddy, Jaganmohan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Pazoki, Meysam
    Uppsala University, Sweden.
    Iglic, Ales
    University of Ljubljana, Slovenia.
    Turner, Anthony
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
    Tiwari, Ashutosh
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. Tekidag AB, SE-58330 Linkoping, Sweden.
    On/off-switchable anti-neoplastic nanoarchitecture2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, no 14571, p. 1-9Article in journal (Refereed)
    Abstract [en]

    Throughout the world, there are increasing demands for alternate approaches to advanced cancer therapeutics. Numerous potentially chemotherapeutic compounds are developed every year for clinical trial and some of them are considered as potential drug candidates. Nanotechnology-based approaches have accelerated the discovery process, but the key challenge still remains to develop therapeutically viable and physiologically safe materials suitable for cancer therapy. Here, we report a high turnover, on/off-switchable functionally popping reactive oxygen species (ROS) generator using a smart mesoporous titanium dioxide popcorn (TiO2 Pops) nanoarchitecture. The resulting TiO2 Pops, unlike TiO2 nanoparticles (TiO2 NPs), are exceptionally biocompatible with normal cells. Under identical conditions, TiO2 Pops show very high photocatalytic activity compared to TiO2 NPs. Upon on/off-switchable photo activation, the TiO2 Pops can trigger the generation of high-turnover flash ROS and can deliver their potential anticancer effect by enhancing the intracellular ROS level until it crosses the threshold to open the death gate, thus reducing the survival of cancer cells by at least six times in comparison with TiO2 NPs without affecting the normal cells.

  • 26.
    Sandin, Emma
    Linköping University, Department of Physics, Chemistry and Biology.
    Optimization of the In vitro Pyrogen Test (IPT) Regarding Detection of Pyrogens in Air Samples2010Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Pyrogens are substances that may induce fever in the human body. They can be parts of bacteria, virus or fungi and due to the reaction they may cause in the body, they are routinely looked for in the medical technology industries. A method called in vitro pyrogen test (IPT) has been developed to detect these pyrogens. It is based on the fever reaction in the human body and only requires blood in combination with a solution believed to contain pyrogens. If the result is positive, the production of cytokines is started. The cytokines of interest in the IPT method are those involved in the fever process and two of them are IL-1β and TNF-α, which are the cytokines used as markers of infection in this study. Since the production of cytokines is in proportion to the amount of pyrogens, the inflammation-inducing potential of the sample can be decided. Due to problems in standardizing the method, mainly because it handles with living blood cells, focus is still pointed at improving it. The aim of this study was to optimize parameters within the IPT method by analysing air samples taken in indoor surroundings believed to contain pyrogens. The different parameters included extraction of the filter from the air sampling, incubation of whole blood and sample extract and analysis of the incubation with ELISA (enzyme linked immunosorbent assay). More specific, some of the issues concerned extraction media, time and shaking intensity for the extraction, blood ratio for the whole blood incubation and cytokines suitable for the method.

    A possible approach for the IPT method, when analysing air samples containing pyrogens, was reached.

  • 27.
    Storr, Tim
    et al.
    Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
    Dyrager, Christine
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
    Pinto Vieira, Rafael
    Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada(1);Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil(3);CAPES Foundation, Ministry of Education of Brazil, 70040-020 Brasília, DF, Brazil.
    Nyström, Sofie
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Nilsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Synthesis and evaluation of benzothiazole-triazole and benzothiadiazole-triazole scaffolds as potential molecular probes for amyloid-β aggregation.2017In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 41, no 4, p. 8p. 1566-1573Article in journal (Refereed)
    Abstract [en]

    Small-molecule ligands that bind to misfolded protein aggregates are essential tools for the study and detection of pathological hallmarks in neurodegenerative disorders, such as Alzheimer's disease (AD). In the present study, three compounds (one benzothiazole-triazole, L1, and two benzothiadiazole-triazoles, L2 and L3) were synthesized via a modular approach (azide–alkyne cycloaddition) and evaluated as potential ligands for amyloid-β (Aβ) aggregates. The binding to amyloid-like fibrils, generated from recombinant Aβ1–42, were studied and the binding specificity to amyloid deposits was evaluated in brain sections from transgenic mice with AD pathology. All three derivatives showed significant reduced emission in the presence of recombinant Aβ1–42 amyloid fibrils. In addition, the observed binding to Aβ deposits in tissue sections suggests that the benzothiazole-triazole and benzothiadiazole-triazole structures are promising molecular scaffolds that can be modified for binding to specific protein aggregates. [ABSTRACT FROM AUTHOR]

  • 28.
    Strömdahl, Helge
    Linköping University, Department of Social and Welfare Studies, Learning, Aesthetics, Natural science. Linköping University, Faculty of Educational Sciences.
    Teaching chemistry in Sweden2010In: Teaching Chemistry around the World / [ed] Björn Risch (Ed.), Münster: Waxman Verlag GmbH , 2010, 1, p. 343-356Chapter in book (Other (popular science, discussion, etc.))
    Abstract [en]

    A description of the Swedish educational system about chemistry and its challenges.

  • 29.
    Syväjärvi, Mikael
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Materials Science . Linköping University, The Institute of Technology.
    Ciechonski, Rafal R.
    Linköping University, Department of Physics, Chemistry and Biology, Materials Science . Linköping University, The Institute of Technology.
    Yazdi, Gholamreza R.
    Linköping University, Department of Physics, Chemistry and Biology, Materials Science . Linköping University, The Institute of Technology.
    Yakimova, Rositsa
    Linköping University, Department of Physics, Chemistry and Biology, Materials Science . Linköping University, The Institute of Technology.
    Fast epitaxy by PVT of SiC in hydrogen atmosphere2005In: Journal of Crystal Growth, ISSN 0022-0248, E-ISSN 1873-5002, Vol. 275, no 1-2, p. e1103-e1107 Article in journal (Refereed)
    Abstract [en]

    Epitaxial growth in hydrogen atmosphere has been studied in relation to sublimation epitaxial growth. A new type of features with a hexagonal shape are observed in the layers grown in hydrogen atmosphere. The morphological details of the features have been studied with optical microscopy and atomic force microscopy. An interactive relation of the defect appearance with the step flow growth mode seems to be present. The results are compared with growth in vacuum, argon, and helium conditions. The possible influence of thermal component to a reactive one in hydrogen etching is discussed.

  • 30.
    Zhou, Ye
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Andersson, Olof
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Lindberg, Peter
    Biacore AB, Rapsgatan 7, S-754 50, Uppsala, Sweden.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Protein Microarrays on Carboxymethylated Dextran Hydrogels: Immobilization, Characterization and Application2004In: Microchimica Acta, ISSN 0026-3672, E-ISSN 1436-5073, Vol. 147, no 1-2, p. 21-30Article in journal (Refereed)
    Abstract [en]

    Tetraoctadecylammonium bromide (TOAB, (CH3(CH2)17)4N+Br) has been used to print temporary hydrophobic barriers on carboxymethylated dextran (CMD) hydrogels to create a generic platform for protein microarray applications. The primary reason for printing temporary hydrophobic barriers is to prevent cross-contamination and overflow during microdrop dispensing. Equally important is to eliminate the risk for non-specific binding to the barriers during analyte exposure. This has been accomplished by introducing a regeneration step that removes the barriers after ligand immobilization. The overall fabrication process was characterized by microscopic wetting, atomic force microscopy, imaging ellipsometry, fluorescence microscopy, surface plasmon microscopy and biospecific interaction analysis. A series of model proteins including transferrin, Protein A, anti-myoglobin and bovine serum albumin was spotted into the TOAB-defined areas under different experimental conditions, e.g. at increased humidity and reduced substrate temperature or with glycerol as an additive in the protein solution. Much emphasis was devoted to studies aiming at exploring the homogeneity and activity of the immobilized proteins. The printed barriers were removed after protein immobilization using tert-n-butyl alcohol (TBA). TBA was found to be a very efficient agent as compared to previously used salt regeneration solutions, and the regeneration time could be reduced from 30 to 10 minutes. Finally, the potential of using the well established CMD hydrogel chemistry as a platform for protein microarrays was exploited using surface plasmon microscopy.

  • 31.
    Zhybak, Mykhailo T.
    et al.
    Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology. Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, 03680, Ukraine .
    Vagin, Mikhail Yu.
    Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Beni, Valerio
    ACREO Swedish ICT, -601 74, Norrköping, SE, Sweden .
    Liu, Xianjie
    Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry. Linköping University, Faculty of Science & Engineering.
    Dempsey, Eithne
    Centre for Research in Electroanalytical Technologies, Department of Science, Institute of Technology Tallaght, Tallaght, Dublin, Ireland .
    Turner, Anthony P. F.
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
    Korpan, Yaroslav I.
    Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, 03680, Ukraine .
    Direct detection of ammonium ion by means of oxygen electrocatalysis at a copper-polyaniline composite on a screen-printed electrode.2016In: Microchimica Acta, ISSN 0026-3672, E-ISSN 1436-5073, Vol. 183, no 6, p. 1981-1987Article in journal (Refereed)
    Abstract [en]

    A novel electrocatalytic material for oxygen reduction, based on polyaniline in combinationwith copper, was developed and utilised for the direct voltammetric quantification of ammonium ions. Consecutive electrode modification by electrodeposited copper, a Nafion membrane and electropolymerised polyaniline resulted in an electrocatalytic composite material which the retained conductivity at neutral pH. Ammonia complex formation with Cu (I) caused the appearance of oxygen electrocatalysis, which was observed as an increase in cathodic current. This Faradaic phenomenon offered the advantage of direct voltammetric detection and was utilised for ammonium electroanalysis. The developed quantification protocol was applied for ammonium assay in human serum and compared with the routine approach for clinical analysis.

  • 32.
    Zweigel, Catarina
    Linköping University, Department of Physics, Chemistry and Biology.
    Validering av metoder för analys av Cu, Fe och Na i processvatten med AAS-grafitugn2009Independent thesis Basic level (university diploma), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Södra Cell Mörrum is one of the five paper pulp plants that are included in Södra Cell, and the paper pulp that is produced here is not only sold to Swedish paper mills. Most of the paper pulp is exported to different countries in Europe. In the manufacturing process the plant needs different kind of process water and there are guideline values for how much copper, iron and sodium this water is allowed to contain. Analyzes of this water is in the current situation done with an atomic absorption spectrometric instrument (AAS-instrument) with a flame.

     

    Measurements done with flame-AAS of samples that have concentrations near the guideline values for copper, iron and sodium, are not reliable. The reason for not being reliable is that the quantitation limits of these metals are higher than the limit values. An alternative method that should give more reliable values is to analyze with an AAS- instrument with a graphite furnace. The purpose of this project was to perform a method validation of the graphite furnace of the AAS-instrument in the analysis of Cu, Fe and Na. The focus of the project was to find the detection limits for each metal, study the variation and to see if it is possible to analyze these water samples with this technique.

     

    The concentrations of the calibration solutions is between 1-10 µg/l for Na, 5-25 µg/l for Cu and 2-20 µg/l for Fe.The detection limits for all metals were slightly below 1 µg/l and during the present circumstances in the laboratory; it would be difficult to get even lower detection limits. There are improvements that can be done to get to the even lower detection limits. The results from this work show that the variation in each sampling cup is very small but if you look at different sampling cups the variation could be large if the cups are not treated in the right way. Further validation analyzes like variation in between days needs to be done.

    It is possible to analyze these low concentrations of copper, iron and sodium in the water samples with the AAS- graphite furnace, but it is difficult because there are many factors that affect the results. Examples of such factors are the environment where the instrument is placed in the laboratory and the human factor. Further analyzes needs to be done to get a better view of how these factors affect the result.

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