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  • 1.
    Golabi, Mohsen
    Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology.
    Functionalised surfaces for bacterial discrimination2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Bacterial detection and identification is a critical step in many arenas, including food and water safety, clinical diagnostics, bioprocess control and biosecurity. Social hygiene has a direct correlation with the strict control of microorganisms in these fields. The worldwide cases of bacterial infectious disease is assessed to be 1-2 billion annually, and these have a massive negative effect on the global economy. Although many precise techniques are currently available, a huge mortality and morbidity related to bacterial infection disease continues to be reported annually due to misdiagnosis or delay in diagnosis. Increasing efficiency and reliability of pathogen detection methods will potentially improve social health and protect society against pathogenic diseases.

    The development of culture media for selective isolation and differentiation of bacteria started in the late 19th century. Immunological assays and then genotyping techniques were developed in 20th century, in addition to many less commonly used techniques for bacterial detection. Each of the currently used methods has its advantages and weaknesses in terms of speed, cost and accuracy. Much effort has recently been devoted to developing biosensors for bacterial detection for simpler and more rapid use.

    This thesis is focused on functionalised surfaces for the development of biosensors for bacterial discrimination and detection, and is divided in three subsections. First, we explored a new approach for bacterial discrimination based on pattern recognition. Traditional culturing methods discriminate bacteria based on their metabolic activity pattern. Taking inspiration from the extensive body of work that reports the use of electronic-noses to differentiate bacteria based on the volatiles patterns they produce, we explored the possibility of bacteria differentiation based on adhesion patterns. By altering the electropolymerisation conditions, the physicalchemical surface properties of polypyrrole (PPy) can be tuned to fabricate a range of dissimilar surfaces. The adhesion of different bacteria on a series of polymers was measured. Data analysis of the adhesion patterns proved that bacteria can be discriminated by examining their adhesion to dissimilar surfaces. Next, we developed a new functionalisation of PPy by doping PPy with 4-N-Pentylphenylboronic Acid and investigated the modulation of bacteria binding to those surfaces. In this second section, a new electropolymerisation technique for whole-cell imprinting was developed based on different functional monomers. 3-Aminophenyl boronic acid was shown to be a good monomer to produce whole-cell imprinted polymers (CIP) with high affinity for bacterial cells with improved releasing ability. Finally, in the third section aptamers, which are promising synthetic recognition elements, were explored for bacterial detection testing. A specific aptamer was used to fabricate of a prototype of label-free aptasensor for bacterial detection. Also, the SELEX process was used to produce a pool of aptamers, or “polyclonal” aptamers, which targeted a group of bacteria species. Using polyclonal aptamers as a recognition element enables biosensors to enhance their resolution to detect broader types of bacterial species using a single serological-like test.

    List of papers
    1. Tuning the surface properties of polypyrrole films for modulating bacterial adhesion.
    Open this publication in new window or tab >>Tuning the surface properties of polypyrrole films for modulating bacterial adhesion.
    2016 (English)In: Macromolecular Chemistry and Physics, ISSN 1022-1352, E-ISSN 1521-3935, Vol. 217, no 10, p. 1128-1135Article in journal (Refereed) Published
    Abstract [en]

    Tuning the physical–chemical properties of polypyrrole (PPy) opens up potentially exciting new applications, especially in the area of bacterial adhesion. Polypyrrole is electrochemically synthesized under various conditions and the physical properties of the films and their effects on bacterial adhesion are characterized. Five types of dopants—chloride (Cl), perchlorate (ClO4), p-toluene-sulfonate (ToS), dodecylbenzene sulfonate (DBS), and poly sodium styrene sulfonate (PSS)—are used to fabricate PPy films at two different constant potentials (0.500 and 0.850 V) with and without Fe3+. Their thickness, roughness, and wettability are measured. The adhesion tendency of Escherichia coli, as a model bacterium, to the four polymers is studied. E. coli shows greater adhesion tendency to the hydrophobic, rough surface of PPy-DBS, and less adhesion tendency to the smooth and hydrophilic surface of PPy-PSS. The results facilitate the choice of appropriate electropolymerization conditions to modulate bacterial adhesion.

    Place, publisher, year, edition, pages
    John Wiley & Sons, 2016
    Keywords
    Biopolymer surface, modulating bacterial adhesion, polymer thickness, polypyrrole roughness, wettability
    National Category
    Polymer Technologies
    Identifiers
    urn:nbn:se:liu:diva-128197 (URN)10.1002/macp.201500445 (DOI)000380018100004 ()
    Note

    Funding agencies:  Iranian Ministry of Science, Research and Technology; Linkoping University; Swedish Research Council [VR-2014-3079]

    Available from: 2016-05-20 Created: 2016-05-20 Last updated: 2019-10-09
    2. Tunable conjugated polymers for bacterial differentiation
    Open this publication in new window or tab >>Tunable conjugated polymers for bacterial differentiation
    2016 (English)In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 222, p. 839-848Article in journal (Refereed) Published
    Abstract [en]

    A novel rapid method for bacterial differentiation is explored based on the specific adhesion pattern of bacterial strains to tunable polymer surfaces. Different types of counter ions were used to electrochemically fabricate dissimilar polypyrrole (PPy) films with diverse physicochemical properties such as hydrophobicity, thickness and roughness. These were then modulated into three different oxidation states in each case. The dissimilar sets of conducting polymers were exposed to five different bacterial strains, Deinococcus proteolyticus, Serratia marcescens, Pseudomonas fluorescens, Alcaligenes faecalis and Staphylococcus epidermidis. By analysis of the fluorescent microscope images, the number of bacterial cells adhered to each surface were evaluated. Generally, the number of cells of a particular bacterial strain that adhered varied when exposed to dissimilar polymer surfaces, due to the effects of the surface properties of the polymer on bacterial attachment. Similarly, the number of cells that adhered varied with different bacterial strains exposed to the same surface, reflecting the different surface properties of the bacteria. Principal component analysis showed that each strain of bacteria had its own specific adhesion pattern. Hence, they could be discriminated by this simple, label-free method based on tunable polymer arrays combined with pattern recognition. (C) 2015 Elsevier B.V. All rights reserved.

    Place, publisher, year, edition, pages
    ELSEVIER SCIENCE SA, 2016
    Keywords
    Conducting polymer; Polypyrrole; Rapid microbial detection; Bacterial adhesion; Pattern recognition; Principal component analysis (PCA)
    National Category
    Polymer Chemistry Textile, Rubber and Polymeric Materials
    Identifiers
    urn:nbn:se:liu:diva-122780 (URN)10.1016/j.snb.2015.09.033 (DOI)000363815800109 ()
    Note

    Funding Agencies|Iranian Ministry of Science, Research and Technology; Linkoping University; Swedish Research Council [VR-2014-3079]

    Available from: 2015-11-23 Created: 2015-11-23 Last updated: 2019-10-09
    3. Doping Polypyrrole Films with 4-N-Pentylphenylboronic Acid to Enhance Affinity towards Bacteria and Dopamine
    Open this publication in new window or tab >>Doping Polypyrrole Films with 4-N-Pentylphenylboronic Acid to Enhance Affinity towards Bacteria and Dopamine
    Show others...
    2016 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 11, article id e0166548Article in journal (Refereed) Published
    Abstract [en]

    Here we demonstrate the use of a functional dopant as a fast and simple way to tune the chemical affinity and selectivity of polypyrrole films. More specifically, a boronic-functionalised dopant, 4-N-Pentylphenylboronic Acid (PBA), was used to provide to polypyrrole films with enhanced affinity towards diols. In order to prove the proposed concept, two model systems were explored: (i) the capture and the electrochemical detection of dopamine and (ii) the adhesion of bacteria onto surfaces. The chemisensor, based on overoxidised polypyrrole boronic doped film, was shown to have the ability to capture and retain dopamine, thus improving its detection; furthermore the chemisensor showed better sensitivity in comparison with overoxidised perchlorate doped films. The adhesion of bacteria, Deinococcus proteolyticus, Escherichia coli, Streptococcus pneumoniae and Klebsiella pneumoniae, onto the boric doped polypyrrole film was also tested. The presence of the boronic group in the polypyrrole film was shown to favour the adhesion of sugar-rich bacterial cells when compared with a control film (Dodecyl benzenesulfonate (DBS) doped film) with similar morphological and physical properties. The presented single step synthesis approach is simple and fast, does not require the development and synthesis of functional monomers, and can be easily expanded to the electrochemical, and possibly chemical, fabrication of novel functional surfaces and interfaces with inherent pre-defined sensing and chemical properties.

    Place, publisher, year, edition, pages
    PUBLIC LIBRARY SCIENCE, 2016
    National Category
    Other Chemistry Topics
    Identifiers
    urn:nbn:se:liu:diva-133388 (URN)10.1371/journal.pone.0166548 (DOI)000388886000017 ()27875555 (PubMedID)
    Note

    Funding Agencies|Ministry of Science Research and Technology of Iran; Linkoping University; Swedish Research Council [VR-2014-3079]; Erasmus exchange program of the European Commission

    Available from: 2016-12-27 Created: 2016-12-22 Last updated: 2019-10-09
    4. Electrochemical bacterial detection using poly(3-aminophenylboronic acid)-based imprinted polymer.
    Open this publication in new window or tab >>Electrochemical bacterial detection using poly(3-aminophenylboronic acid)-based imprinted polymer.
    Show others...
    2017 (English)In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 93, p. 87-93Article in journal (Refereed) Published
    Abstract [en]

    Biosensors can deliver the rapid bacterial detection that is needed in many fields including food safety, clinical diagnostics, biosafety and biosecurity. Whole-cell imprinted polymers have the potential to be applied as recognition elements in biosensors for selective bacterial detection. In this paper, we report on the use of 3-aminophenylboronic acid (3-APBA) for the electrochemical fabrication of a cell-imprinted polymer (CIP). The use of a monomer bearing a boronic acid group, with its ability to specifically interact with cis-diol, allowed the formation of a polymeric network presenting both morphological and chemical recognition abilities. A particularly beneficial feature of the proposed approach is the reversibility of the cis-diol-boronic group complex, which facilitates easy release of the captured bacterial cells and subsequent regeneration of the CIP. Staphylococcus epidermidis was used as the model target bacteria for the CIP and electrochemical impedance spectroscopy (EIS) was explored for the label-free detection of the target bacteria. The modified electrodes showed a linear response over the range of 103–107 cfu/mL. A selectivity study also showed that the CIP could discriminate its target from non-target bacteria having similar shape. The CIPs had high affinity and specificity for bacterial detection and provided a switchable interface for easy removal of bacterial cell.

    Place, publisher, year, edition, pages
    Elsevier, 2017
    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-133647 (URN)10.1016/j.bios.2016.09.088 (DOI)000399259000013 ()27751788 (PubMedID)
    Note

    Funding agencies: Ministry of Science Research and Technology of Iran [MSRT 89100094]; Linkoping University [1259 00 0200]; Swedish Research Council [VR-2014-3079]

    Available from: 2017-01-05 Created: 2017-01-05 Last updated: 2019-10-09
    5. Diazonium-based impedimetric aptasensor for the rapid label-free detection of Salmonella typhimurium in food sample
    Open this publication in new window or tab >>Diazonium-based impedimetric aptasensor for the rapid label-free detection of Salmonella typhimurium in food sample
    Show others...
    2016 (English)In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 80, p. 566-573Article in journal (Refereed) Published
    Abstract [en]

    Fast and accurate detection of microorganisms is of key importance in clinical analysis and in food and water quality monitoring. Salmonella typhimurium is responsible for about a third of all cases of food borne diseases and consequently, its fast detection is of great importance for ensuring the safety of foodstuffs. We report the development of a label-free impedimetric aptamer-based biosensor for S. typhimurium detection. The aptamer biosensor was fabricated by grafting a diazonium-supporting layer onto screen printed carbon electrodes (SPEs), via electrochemical or chemical approaches, followed by chemical immobilisation of aminated-aptamer. FTIR-ATR, contact angle and electrochemical measurements were used to monitor the fabrication process. Results showed that electrochemical immobilisation of the diazonium-grafting layer allowed the formation of a denser aptamer layer, which resulted in higher sensitivity. The developed aptamer-biosensor responded linearly, on a logarithm scale, over the concentration range 1 x 10(1) to 1 x 10(8) CFU mL(-1), with a limit of quantification (LOQ) of 1 x 10(1) CFU mL(-1) and a limit of detection (LOD) of 6 CFU mL(-1). Selectivity studies showed that the aptamer biosensor could discriminate S. typhimurium from 6 other model bacteria strains. Finally, recovery studies demonstrated its suitability for the detection of S. typhimurium in spiked (1 x 10(2), 1 x 10(4) and 1 x 10(6) CFU mL(-1)) apple juice samples. (C) 2016 Elsevier B.V. All rights reserved.

    Place, publisher, year, edition, pages
    ELSEVIER ADVANCED TECHNOLOGY, 2016
    Keywords
    Diazonium grafting; Aptamer; S. typhimurium; Label-free detection; Electrochemical impedance spectroscopy; Food analysis
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-127249 (URN)10.1016/j.bios.2016.02.024 (DOI)000372558500079 ()26894987 (PubMedID)
    Note

    Funding Agencies|Vetenskapsradet (Pathoscreen project; Swedish Research Link) [D0675001]; Ministry of Science Research and Technology of Iran

    Available from: 2016-04-20 Created: 2016-04-19 Last updated: 2019-10-09Bibliographically approved
  • 2.
    Jullesson, David
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
    Wiring liposomes and chloroplasts to the grid with an electronic polymer.2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    We present a novel thylakoid based bio-solar cell capable of generating a photoelectric current of    0.7 µA/cm2. We have introduced an electro conductive polymer, PEDOT-S, to the thylakoid membrane. PEDOT-S intervenes in the photosynthesis, captures electrons from the electron transport chain and transfers them directly across the thylakoid membrane, thus generating a current. The incorporation of the electro conductive polymer into the thylakoid membrane is therefore vital for the function of the bio-solar cell. A liposomal model system based on liposomes formed by oleic acid was used to develop and study the incorporation of PEDOT-S to fatty acid membranes. The liposomes allow for a more controllable and easily manipulated system compared to the thylakoid membrane. In the model system, PEDOT-S could successfully be incorporated to the membrane, and the developed methods were applied to the real system of thylakoid membranes. We found that a bio-compatible electrolyte and redox couple was required for this system to function. The final thylakoid based bio-solar cell was evaluated according to performance and reproducibility. We found that this bio-solar system can generate a low but reproducible current.

     

     

  • 3.
    Kim, Nara
    et al.
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Petsagkourakis, Ioannis
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Chen, Shangzhi
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Berggren, Magnus
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Crispin, Xavier
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Jonsson, Magnus
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Zozoulenko, Igor
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Electric Transport Properties in PEDOT Thin Films2019In: Conjugated Polymers: Properties, Processing, and Applications / [ed] John R. Reynolds; Barry C. Thompson; Terje A. Skotheim, Boca Raton: CRC Press, 2019, p. 45-128Chapter in book (Refereed)
    Abstract [en]

    In this chapter, the authors summarize their understanding of Poly(3,4-ethylenedioxythiophene) (PEDOT), with respect to its chemical and physical fundamentals. They focus upon the structure of several PEDOT systems, from the angstrom level and up, and the impact on both electronic and ionic transport. The authors discuss the structural properties of PEDOT:X and PEDOT:poly(styrenesulfonate) based on experimental data probed at the scale ranging from angstrom to submicrometer. The morphology of PEDOT is influenced by the nature of counter-ions, especially at high oxidation levels. The doping anions intercalate between PEDOT chains to form a “sandwich” structure to screen the positive charges in PEDOT chains. The authors provide the main transport coefficients such as electrical conductivity s, Seebeck coefficient S, and Peltier coefficient σ, starting from a general thermodynamic consideration. The optical conductivity of PEDOT has also been examined based on the effective medium approximation, which is normally used to describe microscopic permittivity properties of composites made from several different constituents.

  • 4.
    Kleinhans, Henrik
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Evaluation of the Carbonization of Thermo-Stabilized Lignin Fibers into Carbon Fibers2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Thermo-stabilized lignin fibers from pH-fractionated softwood kraft lignin were carbonized to various temperatures during thermomechanical analysis (TMA) under static and increasing load and different rates of heating. The aim was to optimize the carbonization process to obtain suitable carbon fiber material with good mechanical strength potential (high tensile strength and high E-modulus). The carbon fibers were therefore mainly evaluated of mechanical strength in Dia-Stron uniaxial tensile testing.

    In addition, chemical composition, in terms of functional groups, and elemental (atomic) composition was studied in Fourier transform infrared spectroscopy (FTIR) and in energy-dispersive X-ray spectroscopy (EDS), respectively. The structure of carbon fibers was imaged in scanning electron microscope (SEM) and light microscopy. Thermogravimetrical analysis was performed on thermo-stabilized lignin fibers to evaluate the loss of mass and to calculate the stress-changes and diameter-changes that occur during carbonization.

    The TMA-analysis of the deformation showed, for thermo-stabilized lignin fibers, a characteristic behavior of contraction during carbonization. Carbonization temperatures above 1000°C seemed most efficient in terms of E-modulus and tensile strength whereas rate of heating did not matter considerably. The E-modulus for the fibers was improved significantly by slowly increasing the load during the carbonization. The tensile strength remained however unchanged.

    The FTIR-analysis indicated that many functional groups, mainly oxygen containing, dissociate from the lignin polymers during carbonization. The EDS supported this by showing that the oxygen content decreased. Accordingly, the relative carbon content increased passively to around 90% at 1000°C. Aromatic structures in the carbon fibers are thought to contribute to the mechanical strength and are likely formed during the carbonization. However, the FTIR result showed no evident signs that aromatic structures had been formed, possible due to some difficulties with the KBr-method.

    In the SEM and light microscopy imaging one could observe that porous formations on the surface of the fibers increased as the temperature increased in the carbonization. These formations may have affected the mechanical strength of the carbon fibers, mainly tensile strength.

    The carbonization process was optimized in the sense that any heating rate can be used. No restriction in production speed exists. The carbonization should be run to at least 1000°C to achieve maximum mechanical strength, both in E-modulus and tensile strength. To improve the E-modulus further, a slowly increasing load can be applied to the lignin fibers during carbonization. The earlier the force is applied, to counteract the lignin fiber contraction that occurs (namely around 300°C), the better. However, in terms of mechanical performance, the lignin carbon fibers are still far from practical use in the industry.

  • 5.
    Sandén, Camilla
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Nanostructures on a Vector: Enzymatic Oligo Production for DNA Nanotechnology2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The technique of DNA origami utilizes the specific and limited bonding properties of DNA to fold single stranded DNA sequences of various lengths to form a predesigned structure. One longer sequence is used as a scaffold and numerous shorter sequences called staples, which are all complementary to the scaffold sequence, are used to fold the scaffold into intricate shapes. The most commonly used scaffold is derived by extracting the genome of the M13 phage and the staples are usually chemically synthesized oligonucleotides. Longer single stranded sequences are difficult to synthesize with high specificity, which limits the choices of scaffold sequences available. In this project two main methods of single stranded amplification, Rolling Circle Amplification (RCA) and the usage of helper phages, were explored with the goal to produce both a 378 nt scaffold and staple sequences needed for folding a DNA origami structure. To facilitate imaging by Transmission Electron Microscopy (TEM) of this small structure, the DNA origami structure was created to form a polymer structure. Production of the scaffold sequence in high yield was unsuccessful and no well-defined polymers were found in the folded samples, though a few results showed promise for further studies and optimizations. Due to time constraints of this project, only production of the scaffold sequence was tested. Unfortunately the scaffold produced by the helper phages was of the complementary strand to that used to design the DNA origami structure, and could therefore not be used for folding. The correct strand was produced by the RCA where the yield was too low when using Phi29 DNA polymerase for proper folding to take place, though small scale RCA by Bst DNA polymerase on the other hand showed promising results. These results indicate that the scaffold production may not be far off but still more experience in producing intermediate size oligonucleotides may be necessary before succeeding in high yield production of this 378 nt long sequence. The promise given by this production is to enable high yield, high purity, low cost and also an easily scalable process set-up. This would be an important step in future DNA nanotechnology research when moving from small scale laboratory research to large scale applications such as targeted drug delivery systems.

  • 6.
    Westergren, Elisabeth
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology.
    Analysis of hydrogels for immobilisation of hepatocytes (HepG2) in 3D cell culturing systems2018Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In pharmaceutical development cell cultures are used as in vitro models to evaluate the function of drug candidates. In such research it is vital to have models that resemble the in vivo environment to get reliable results. In 3D models with hydrogels ECM like scaffolds are supporting the cells in a more in vivo like environment than flat 2D cultures.

    In this project PEG-peptide based hydrogels with cell binding RGD incorporated on one PEG-peptide type has been evaluated for culturing of HepG2 cells. Structure and viscoelastic properties were evaluated with techniques like circular dichroism spectroscopy, dynamic light scattering and rheology. Sterilisation impact was also evaluated for PEG-peptides. For cell culturing, observations in light microscope and evaluation with Live/Dead assay and albumin assay were performed. A few companies were interviewed regarding 3D culturing and interest in mechanically tuneable hydrogels.

    The HepG2 cells grows and forms spherical clusters in the 3D environment with hydrogels, percentage of RGD seems to not impact cell adhesion, growth or albumin secretion. UV irradiation was the most suitable sterilisation method for gel components. The most rigid gel combination formed had storage modulus of around 230 Pa.

    Mechanically tuneable hydrogels is interesting for the industry. The PEG-peptide based gels are suitable tor growing cells but too soft to closely resemble the in vivo rigidity of hepatocytes.

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