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  • 1.
    Ardabili, Sahar
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Microfluidic bases sample preparation for blood stream infections2014Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Microfluidics promises to re-shape the current health-care system by transferring diagnostic tools from central laboratories to close vicinity of the patient (point-of-care). One of the most important operational steps in any diagnostic platform is sample preparation, which is the main subject in this thesis. The goal of sample preparation is to isolate targets of interest from their surroundings. The work in this thesis is based on three ways to isolate bacteria:  immune-based isolation, selective cell lysis, size-based separation.

    The first sample-preparation approach uses antibodies against lipopolysaccharides (LPS), which are surface molecules found on all gram-negative bacteria. There are two characteristics that make this surface molecule interesting. First, it is highly abundant: one bacterium has approximately a million LPS molecules on its cell-wall. Second, the molecule has a conserved region within all gram-negative bacteria, so using one affinity molecule to isolate disease-causing gram-negative bacteria is an attractive option, particularly from the point of view of sample preparation. The main challenge, however, is antigen accessibility. To address this, we have developed a treatment protocol that improves the capturing efficiency.

    The strategy behind selective cell lysis takes advantage of the differences between the blood-cell membrane and the bacterial cell-wall. These fundamental differences make it possible to lyse (destroy) blood-cells selectively while keeping the target of interest, here the bacteria, intact and, what is more important alive. Viability plays an important role in determining antibiotic susceptibility.

    Difference in size is another well-used characteristic for sample- separation. Inertial microfluidics can focus size-dependent particle at high flow-rates. Thus, particles of 10 µm diameter were positioned in precise streamlines within a curved channel.  The focused particles can then be collected at defined outlets.  This approach was then used to isolate white blood cells, which account for approximately 1% of the whole blood.  In such a device particles of 2µm diameter (size of bacteria) would not be focused and thereby present at every outlet. To separate bacteria from blood elasto-inertial microfluidics was used. Here, e blood components are diverted to center of the channels while smaller bacteria remain in the side streams and can subsequently be separated.

  • 2.
    Ardabili, Sahar
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Gantelius, Jesper
    KTH, Skolan för bioteknologi (BIO), Nanobioteknologi (stängd 20130101).
    Kowalewski, Jacob
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Brismar, Hjalmar
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Russom, Aman
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Dean flow-coupled inertial focusing for ultra-high-throughput particle filtration2010Inngår i: 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2010, MicroTAS 2010: Volume 3, 2010, s. 1586-1588Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Particle manipulation represents an important and fundamental step prior to counting, sorting and detecting bio-particles. In this study, we report dean-coupled inertial focusing of particles in flows through a single curve microchannel at extremely high channel Reynold numbers (∼325). We found the lateral particle focusing position, xf to be fixed and largely independent of radius of curvature and whether particles are pre-focused (at equilibrium) entering the curvature or randomly distributed. Finally, using a single inlet, u-shaped, microchannel we demonstrate filtration of 10μm particles from 2 μm particles at throughputs several orders of magnitude higher than previously shown.

  • 3.
    Ardabili, Sahar
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Zelenin, Sergey
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Ramachandraiah, Harisha
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Russom, Aman
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Epitope unmasking for improved immuno-magnetic isolation of Gram-negative bacteriaManuskript (preprint) (Annet vitenskapelig)
  • 4.
    Faridi, Muhammad Asim
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Ramachandraiah, Harisha
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Ardabili, Sahar
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Zelenin, Sergey
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Russom, Aman
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Elasto-Inertial microfluidics for bacteria separation from whole blood for sepsis diagnosticsManuskript (preprint) (Annet vitenskapelig)
  • 5. Pavankumar, A. R.
    et al.
    Zelenin, Sergey
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lundin, A.
    Schulte, T.
    Rajarathinam, K.
    Rebellato, P.
    Ardabili, Sahar
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Salas, J.
    Achour, A.
    Russom, Aman
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Bioanalytical advantages of a novel recombinant apyrase enzyme in ATP-based bioluminescence methods2018Inngår i: Analytica Chimica Acta, ISSN 0003-2670, E-ISSN 1873-4324, Vol. 1025, s. 118-123Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ultrasensitive measurements of intracellular ATP (intATP) based on the firefly luciferase reactions are frequently used to enumerate bacterial or mammalian cells. During clinical applications, extracellular ATP (extATP) should be depleted in biological samples since it interferes with intATP and affects the quantification of bacteria. The extATP can be eliminated by ATP-degrading enzymes but complete hydrolysis of extATP remains a challenge for today's commercial enzymes. The catalytic efficiency of ATP-degrading enzymes depends on enzyme characteristics, sample composition and the ability to deplete diphosphates, triphosphates and their complexes generated during the reaction. This phenomenon restricts the usage of bioluminescence-based ATP methods in clinical diagnostics. In light of this, we have developed a recombinant Shigella flexneri apyrase (RSFA) enzyme and analysed its ATP depletion potential with five commercial biochemical sources including potato apyrase, acid phosphatase, alkaline phosphatase, hexokinase and glycerol kinase. The RSFA revealed superior activity by completely eliminating the extracellular ATP and ATP-complexes, even in biological samples like urine and serum. Therefore, our results can potentially unwrap the chemical and bio-analytical applications of ATP-based bioluminescence tests to develop highly sensitive point-of-care diagnostics.

  • 6. Pavankumar, A.M.
    et al.
    Ardabili, Sahar
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Zelenin, Sergey
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Shulte, T.
    Lundin, A.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Russom, Aman
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Recombinant Shigella flexneri apyrase enzyme for bioluminescence based diagnostic applicationsManuskript (preprint) (Annet vitenskapelig)
  • 7.
    Periyannan Rajeswari, Prem Kumar
    et al.
    KTH, Skolan för bioteknologi (BIO), Bioprocessteknik (stängd 20130101). KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Ramachandraiah, Harisha
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Hansson, Jonas
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Ardabili, Sahar
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Veide, Andres
    KTH, Skolan för bioteknologi (BIO), Bioprocessteknik (stängd 20130101).
    Russom, Aman
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Development of microfluidic aqueous two-phase system for continuous partitioning of E. coli strains2011Inngår i: 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011, 2011, s. 1329-1331Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The interaction of bacterial cells with surrounding environment depends on its surface characteristics such as hydrophobicity, hydrophilicity balance and net charge. In this paper, aqueous two-phase system partitioning of Escherichia coli strains based on their difference in surface properties is introduced in a microfluidic system. While aqueous two-phase system is widely use to separate biomolecules on macroscale, the method has not been adapted in microfluidic system. The bacterial cells are partitioned based on their affinity for streams formed by aqueous polymers polyethylene glycol (PEG) and dextran (Dex). Partitioning efficiency of two Escherichia coli strains is currently being optimized.

  • 8.
    Ramachandraiah, Harisha
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ardabili, Sahar
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Faridi, Asim M.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Gantelius, Jesper
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Kowalewski, Jacob M.
    Mårtensson, Gustaf
    Russom, Aman
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Dean flow-coupled inertial focusing in curved channels2014Inngår i: Biomicrofluidics, ISSN 1932-1058, E-ISSN 1932-1058, Vol. 8, nr 3, s. 034117-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Passive particle focusing based on inertial microfluidics was recently introduced as a high-throughput alternative to active focusing methods that require an external force field to manipulate particles. In inertial microfluidics, dominant inertial forces cause particles to move across streamlines and occupy equilibrium positions along the faces of walls in flows through straight micro channels. In this study, we systematically analyzed the addition of secondary Dean forces by introducing curvature and show how randomly distributed particles entering a simple u-shaped curved channel are focused to a fixed lateral position exiting the curvature. We found the lateral particle focusing position to be fixed and largely independent of radius of curvature and whether particles entering the curvature are pre-focused (at equilibrium) or randomly distributed. Unlike focusing in straight channels, where focusing typically is limited to channel cross-sections in the range of particle size to create single focusing point, we report here particle focusing in a large cross-section area (channel aspect ratio 1: 10). Furthermore, we describe a simple u-shaped curved channel, with single inlet and four outlets, for filtration applications. We demonstrate continuous focusing and filtration of 10 mu m particles (with > 90% filtration efficiency) from a suspension mixture at throughputs several orders of magnitude higher than flow through straight channels (volume flow rate of 4.25ml/min). Finally, as an example of high throughput cell processing application, white blood cells were continuously processed with a filtration efficiency of 78% with maintained high viability. We expect the study will aid in the fundamental understanding of flow through curved channels and open the door for the development of a whole set of bio-analytical applications.

  • 9. Zelenin, S.
    et al.
    Ramachandraiah, Harisha
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Hansson, Jonas
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Ardabili, Sahar
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Brismar, Hjalmar
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik. Karolinska Institutet, Sweden.
    Russom, Aman
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Bacteria isolation from whole blood for sepsis diagnostics2011Inngår i: 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011, 2011, s. 518-520Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Rapid and reliable detection of bloodstream infections would gain a lot from improved and straightforward isolation of highly purified bacteria from whole blood. Here, we report a microfluidics-based sample preparation strategy to continuously isolate microorganisms from whole blood for downstream analysis. The continuous-flow method takes advantage of the fact that bacteria cells have rigid cell wall enables selective and complete blood cell lysis while ~ 100% of bacteria are readily recovered. The method as a sample preparation unit offers opportunities to develop molecular based POC for sepsis diagnostics.

  • 10.
    Zelenin, Sergey
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Hansson, Jonas
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ardabili, Sahar
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ramachandraiah, Harisha
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Brismar, Hjalmar
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Russom, Aman
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Microfluidic-based isolation of bacteria from whole blood for sepsis diagnostics2015Inngår i: Biotechnology letters, ISSN 0141-5492, E-ISSN 1573-6776, Vol. 37, nr 4, s. 825-830Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Blood-stream infections (BSI) remain a major health challenge, with an increasing incidence worldwide and a high mortality rate. Early treatment with appropriate antibiotics can reduce BSI-related morbidity and mortality, but success requires rapid identification of the infecting organisms. The rapid, culture-independent diagnosis of BSI could be significantly facilitated by straightforward isolation of highly purified bacteria from whole blood. We present a microfluidic-based, sample-preparation system that rapidly and selectively lyses all blood cells while it extracts intact bacteria for downstream analysis. Whole blood is exposed to a mild detergent, which lyses most blood cells, and then to osmotic shock using deionized water, which eliminates the remaining white blood cells. The recovered bacteria are 100 % viable, which opens up possibilities for performing drug susceptibility tests and for nucleic-acid-based molecular identification.

  • 11. Zelenin, Sergey
    et al.
    Hansson, Jonas
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Ramachandraiah, Harisha
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Ardabili, Sahar
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Brismar, Hjalmar
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Russom, Aman
    KTH, Skolan för bioteknologi (BIO), Nanobioteknologi (stängd 20130101).
    Microfluidic selective cell lysis for bacteria isolation from whole bloodManuskript (preprint) (Annet vitenskapelig)
1 - 11 of 11
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