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  • 1.
    Abbasi Aval, Negar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Khati, Vamakshi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Pettersson, Torbjörn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Layer-by-Layer cellulose nanofibril coating for spheroid formation combined with decellularized extracellular matrix for 3D tumor modelingManuscript (preprint) (Other academic)
  • 2.
    Abbasi Aval, Negar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Khati, Vamakshi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Pettersson, Torbjörn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Influence of Decellularized Extra Cellular Matrix on 3D spheroids formed on Layer-by-Layer cellulose nanofibril/Polyelectrolytes coating as an in-vitro model for Hepatocellular CarcinomaManuscript (preprint) (Other academic)
  • 3.
    Abbasi Aval, Negar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Lahchaichi, Ekeram
    Fayazbakhsh, Farzaneh
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Tudoran, Oana
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Pettersson, Torbjörn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Evaluating the Impact of Positively Charged Polyelectrolyte Molecular Weightand Bilayer Number on Tumor Spheroid Formation in the Interaction with Negatively Charged Cellulose Nanofibrils in layer by layer assembly2023Manuscript (preprint) (Other academic)
  • 4.
    Abbasi Aval, Negar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Lahchaichi, Ekeram
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Tudoran, Oana
    Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. I. Chiricuta”, 400015 Cluj-Napoca, Romania.
    Fayazbakhsh, Farzaneh
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Heuchel, Rainer
    Pancreas Cancer Research Lab, Department of Clinical Science, Intervention and Technology, (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden.
    Löhr, Matthias
    Pancreas Cancer Research Lab, Department of Clinical Science, Intervention and Technology, (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden.
    Pettersson, Torbjörn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Assessing the Layer-by-Layer Assembly of Cellulose Nanofibrils and Polyelectrolytes in Pancreatic Tumor Spheroid Formation2023In: Biomedicines, E-ISSN 2227-9059, Vol. 11, no 11Article in journal (Refereed)
    Abstract [en]

    Three-dimensional (3D) tumor spheroids are regarded as promising models for utilization as preclinical assessments of chemo-sensitivity. However, the creation of these tumor spheroids presents challenges, given that not all tumor cell lines are able to form consistent and regular spheroids. In this context, we have developed a novel layer-by-layer coating of cellulose nanofibril–polyelectrolyte bilayers for the generation of spheroids. This technique builds bilayers of cellulose nanofibrils and polyelectrolytes and is used here to coat two distinct 96-well plate types: nontreated/non-sterilized and Nunclon Delta. In this work, we optimized the protocol aimed at generating and characterizing spheroids on difficult-to-grow pancreatic tumor cell lines. Here, diverse parameters were explored, encompassing the bilayer count (five and ten) and multiple cell-seeding concentrations (10, 100, 200, 500, and 1000 cells per well), using four pancreatic tumor cell lines—KPCT, PANC-1, MiaPaCa-2, and CFPAC-I. The evaluation includes the quantification (number of spheroids, size, and morphology) and proliferation of the produced spheroids, as well as an assessment of their viability. Notably, our findings reveal a significant influence from both the number of bilayers and the plate type used on the successful formation of spheroids. The novel and simple layer-by-layer-based coating method has the potential to offer the large-scale production of spheroids across a spectrum of tumor cell lines.

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  • 5.
    Akhtar, Ahmad Saleem
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Centrifugal microfluidics-based point of care diagnostics at resource limited settings2023Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Advancements in medical diagnostics have allowed us to understand the underlying mechanism and treat the root cause for many diseases which had been causing morbidity and mortality up until this point in human history. Furthermore, many of the standard diagnostic procedures have now been transformed to provide answers at or near the point-of-care. However, the effects of these positive developments have not trickled down to the parts of our society which are considered underdeveloped and lack the necessary infrastructure and facilities. Diagnostics in such resource limited settings still lag behind and fail to provide the requisite healthcare. 

    In order to translate the diagnostic solutions designed for central laboratories to resource limited settings, there are certain challenges that need to be addressed, such as portability, reduction in cost and ease-of-use, while keeping the sensitivity and specificity at the required level. The work presented in this thesis focuses on addressing some of these issues by using microfluidics to develop diagnostic platforms that are suitable to be used in resource limited settings. 

    In paper I, a very low-cost and simple centrifugal microfluidic platform was developed to be used in settings which do not have a reliable supply of electricity. The platform uses a smartphone as a source of power and the sensors of the phone for speed control.

    In paper II, a portable and low-cost diagnostic platform was developed for multiplexed detection of biomarkers based on centrifugal microfluidics. The platform uses colorimetric detection and a simple readout method which does not require a spectrophotometer for quantification.

    In paper III, a platform was developed for COVID-19 diagnostics which combines centrifugal microfluidics with a novel bead-based strategy for signal enhancement. The platform uses fluorescent detection with a smartphone readout and has the capability to process up to 20 samples at the same time.

    In paper IV, as a follow up of paper III, a more advanced platform was developed for COVID-19 diagnostics which allows the operator to carry out nucleic acid amplification in a completely automated manner, from adding the sample to getting the final result.

    In paper V, an alternative method for detection of SARS-CoV-2 was developed using electrochemical biosensing. This work combines the electrochemical technique with a flexible printed circuit board for a rapid, amplification-free and label-free detection of target SARS-CoV-2 sequences.

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    Ahmad_Thesis
  • 6.
    Akhtar, Ahmad Saleem
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lapins, Noa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Moura, João Martinho
    International Iberian Nanotechnology Laboratory.
    Paula, Luis
    International Iberian Nanotechnology Laboratory.
    Pedro, Adriano
    International Iberian Nanotechnology Laboratory.
    Martins, Fabio
    International Iberian Nanotechnology Laboratory.
    Mota, Duarte
    International Iberian Nanotechnology Laboratory.
    Pinto, Ines Fernandes
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Martins, Marco
    International Iberian Nanotechnology Laboratory.
    Russom, Aman
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Fully automated centrifugal microfluidic platform for COVID-19 detection using computer vision-based readoutManuscript (preprint) (Other academic)
    Abstract [en]

    COVID-19 pandemic made it evident that the world is unprepared for effectively tackling a pandemic resulting from an infectious disease. The conventional diagnostic methods for detection of infectious diseases were limited to centralized laboratories. As the burden of testing increased with the spread of the disease, the centralized testing facilities were strained for resources and personnel. These problems were further exacerbated in low- and middle-income countries where the health and transport infrastructure are not very well developed. To overcome this reliance on centralized testing and to facilitate decentralized testing, focus was shifted towards development of novel point-of-care diagnostic methods. We report the development of a fully automated centrifugal microfluidic platform that uses loop mediated isothermal amplification (LAMP) combined with computer vision-based readout for COVID-19 detection. The integrated platform allows sample to answer analysis at the push of a single button and can process 26 samples in 40 minutes. The platform performs a completely automated assay protocol involving heating, rotation and detection without the need for user intervention. A limit of detection of approximately 100 RNA copies in 10 µL reaction was achieved using RNA fragments spiked in water and similar results were obtained for artificial saliva samples. 

  • 7.
    Akhtar, Ahmad Saleem
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pinto, Ines Fernandes
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Soares, Ruben R. G.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Russom, Aman
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    An integrated centrifugal microfluidic platform for multiplexed colorimetric immunodetection of protein biomarkers in resource-limited settings2021In: Proceedings MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, Chemical and Biological Microsystems Society , 2021, p. 947-948Conference paper (Refereed)
    Abstract [en]

    The up- and down- regulation of inflammatory biomarkers such as cytokines can be indicative of several diseases such as primary cancers and/or metastatic tumors, as well as less serious conditions. For point-of-care clinical applications, the detection of these biomarkers requires a combination of a sensitive assay and multiplexing capabilities, together with fit-for-purpose signal transduction strategies. Here, we report the development of a versatile and cost-effective integrated centrifugal microfluidic platform compatible with resource-limited settings using nanoporous microbeads for immunoaffinity-based profiling of cytokines. With an automated colorimetric readout at the end, the platform allows for profiling of cytokines in < 30 mins.

  • 8.
    Akhtar, Ahmad Saleem
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pinto, Ines Fernandes
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Soares, Ruben R. G.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Russom, Aman
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Centrifugal microfluidic platform comprising an array of bead microcolumns for the multiplexed colorimetric quantification of inflammatory biomarkers at the point-of-care2019In: 23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2019, Chemical and Biological Microsystems Society , 2019, p. 1230-1231Conference paper (Refereed)
    Abstract [en]

    The detection of panels of inflammatory biomarkers such as cytokines has potential for the rapid and specific diagnostic of several devastating diseases such as primary cancers and/or metastatic tumors, as opposed to less serious conditions. For point-of-care clinical applications, the detection of these biomarkers requires a combination of pg/mL sensitivities and multiplexing capabilities, coupled with fit-for-purpose signal transduction strategies. Here, we report the development of a versatile centrifugal microfluidic platform combined with nanoporous microbeads for immunoaffinity-based profiling of cytokines. The device allows sample and analyte multiplexing and detection limits below 1 ng/mL were achieved within 30 minutes, using colorimetric detection.

  • 9.
    Akhtar, Ahmad Saleem
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Soares, Ruben R. G.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Pinto, Ines Fernandes
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Russom, Aman
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Center for the Advancement of Integrated Medical and Engineering Sciences, AIMES.
    A portable and low-cost centrifugal microfluidic platform for multiplexed colorimetric detection of protein biomarkers2023In: Analytica Chimica Acta, ISSN 0003-2670, E-ISSN 1873-4324, Vol. 1245, article id 340823Article in journal (Refereed)
    Abstract [en]

    Cytokines play a very important role in our immune system by acting as mediators to put up a coordinated defense against foreign elements in our body. Elevated levels of cytokines in the body can signal to an ongoing response of the immune system to some abnormality. Thus, the quantification of a panel of cytokines can provide valuable information regarding the diagnosis of specific diseases and state of overall health of an individual. Conventional Enzyme Linked Immunosorbent Assay (ELISA) is the gold-standard for quantification of cytokines, however the need for trained personnel and expensive equipment limits its application to centralized laboratories only. In this context, there is a lack of simple, low-cost and portable devices which can allow for quantification of panels of cytokines at point-of-care and/or resource limited settings.

    Here, we report the development of a versatile, low-cost and portable bead-based centrifugal microfluidic platform allowing for multiplexed detection of cytokines with minimal hands-on time and an integrated colorimetric signal readout without the need for any external equipment. As a model, multiplexed colorimetric quantification of three target cytokines i.e., Tumor necrosis factor alpha (TNF-α), Interferon gamma (IFN-γ) and Interleukin-2 (IL-2) was achieved in less than 30 min with limits of detection in ng/mL range. The developed platform was further evaluated using spiked-in plasma samples to test for matrix interference. The ease of use, low-cost and portability of the developed platform highlight its potential to serve as a sample-to-answer solution for detection of cytokine panels in resource limited settings.

  • 10.
    Aljadi, Zenib
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Abbasi Aval, Negar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Kumar, Tharagan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Qin, Taoyu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Ramachandraiah, Harisha
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pettersson, Torbjörn
    KTH, School of Engineering Sciences (SCI), Centres, VinnExcellence Center BiMaC Innovation. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Russom, Aman
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Layer-by-Layer Cellulose Nanofibrils: A New Coating Strategy for Development and Characterization of Tumor Spheroids as a Model for In Vitro Anticancer Drug Screening2022In: Macromolecular Bioscience, ISSN 1616-5187, E-ISSN 1616-5195, Vol. 22, no 10, article id 2200137Article in journal (Refereed)
    Abstract [en]

    Three-dimensional multicellular spheroids (MCSs) are complex structure of cellular aggregates and cell-to-matrix interaction that emulates the in-vivo microenvironment. This research field has grown to develop and improve spheroid generation techniques. Here, we present a new platform for spheroid generation using Layer-by-Layer (LbL) technology. Layer-by-Layer (LbL) containing cellulose nanofibrils (CNF) assemble on a standard 96 well plate. Various bi-layer numbers, multiple cell seeding concentration, and two tumor cell lines (HEK 293 T, HCT 116) are utilized to generate and characterize spheroids. The number and proliferation of generated spheroids, the viability, and the response to the anti-cancer drug are examined. The spheroids are formed and proliferated on the LbL-CNF coated wells with no significant difference in connection to the number of LbL-CNF bi-layers; however, the number of formed spheroids correlates positively with the cell seeding concentration (122 ± 17) and (42 ± 8) for HCT 116 and HEK 293T respectively at 700 cells ml−1. The spheroids proliferate progressively up to (309, 663) µm of HCT 116 and HEK 293T respectively on 5 bi-layers coated wells with maintaining viability. The (HCT 116) spheroids react to the anti-cancer drug. We demonstrate a new (LbL-CNF) coating strategy for spheroids generation, with high performance and efficiency to test anti-cancer drugs.

  • 11.
    Aljadi, Zenib
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Department of Clinical Science and Education, Karolinska Institutet, Stockholm, Sweden.
    Kalm, Frida
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Department of Clinical Science and Education, Karolinska Institutet, Stockholm, Sweden;Sachs´ Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden.
    Nilsson, Caroline
    Karolinska Inst, Dept Clin Sci & Educ, Stockholm, Sweden.;Soder Sjukhuset, Sachs Children & Youth Hosp, Stockholm, Sweden..
    Winqvist, Ola
    Karolinska Univ Hosp, Dept Clin Immunol, Stockholm, Sweden..
    Russom, Aman
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Lundahl, Joachim
    Karolinska Inst, Dept Clin Sci & Educ, Stockholm, Sweden.;Soder Sjukhuset, Sachs Children & Youth Hosp, Stockholm, Sweden..
    Nopp, Anna
    Karolinska Inst, Dept Clin Sci & Educ, Stockholm, Sweden.;Soder Sjukhuset, Sachs Children & Youth Hosp, Stockholm, Sweden..
    A novel tool for clinical diagnosis of allergy operating a microfluidic immunoaffinity basophil activation test technique2019In: Clinical Immunology, ISSN 1521-6616, E-ISSN 1521-7035, Vol. 209, article id UNSP 108268Article in journal (Refereed)
    Abstract [en]

    The Basophil Activation Test (BAT) is a valuable allergy diagnostic tool but is time-consuming and requires skilled personnel and cumbersome processing, which has limited its clinical use. We therefore investigated if a microfluidic immunoaffinity BAT (miBAT) technique can be a reliable diagnostic method. Blood was collected from allergic patients and healthy controls. Basophils were challenged with negative control, positive control (anti-FccRI), and two concentrations of a relevant and non-relevant allergen. CD203c and CD63 expression was detected by fluorescent microscopy and flow cytometry. In basophils from allergic patients the CD63% was significantly higher after allergen activation as compared to the negative control (p < .0001-p = .0004). Activation with non-relevant allergen showed equivalent CD63% expression as the negative control. Further, the miBAT data were comparable to flow cytometry. Our results demonstrate the capacity of the miBAT technology to measure different degrees of basophil allergen activation by quantifying the CD63% expression on captured basophils.

  • 12.
    Aljadi, Zenib
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska Inst, Dept Clin Sci & Educ, Stockholm, Sweden; Soder Sjukhuset, Stockholm, Sweden .
    Kalm, Frida
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska Inst, Dept Clin Sci & Educ, Stockholm, Sweden; Soder Sjukhuset, Stockholm, Sweden.
    Ramachandraiah, Harisha
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nopp, Anna
    Karolinska Inst, Dept Clin Sci & Educ, Stockholm, Sweden.;Soder Sjukhuset, Stockholm, Sweden..
    Lundahl, Joachim
    Karolinska Inst, Dept Clin Sci & Educ, Stockholm, Sweden.;Soder Sjukhuset, Stockholm, Sweden..
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Microfluidic Immunoaffinity Basophil Activation Test for Point-of-Care Allergy Diagnosis2019In: Journal of Applied Laboratory Medicine (JALM), ISSN 2475-7241, Vol. 4, no 2, p. 152-163Article in journal (Refereed)
    Abstract [en]

    Background: The flow cytometry-based basophil activation test (BAT) is used for the diagnosis of allergic response. However, flow cytometry is time-consuming, requiring skilled personnel and cumbersome processing, which has limited its use in the clinic. Here, we introduce a novel microfluidic-based immunoaffinity BAT (miBAT) method. Methods: The microfluidic device, coated with anti-CD203c, was designed to capture basophils directly from whole blood. The captured basophils are activated by anti-FceRI antibody followed by optical detection of CD63 expression (degranulation marker). The device was first characterized using a basophil cell line followed by whole blood experiments. Weevaluated the device with ex vivo stimulation of basophils in whole blood from healthy controls and patients with allergies and compared it with flow cytometry. Results: The microfluidic device was capable of capturing basophils directly from whole blood followed by in vitro activation and quantification of CD63 expression. CD63 expression was significantly higher (P = 0.0002) in on-chip activated basophils compared with nonactivated cells. The difference in CD63 expression on anti-FceRI-activated captured basophils in microfluidic chip was significantly higher (P = 0.03) in patients with allergies compared with healthy controls, and the results were comparable with flow cytometry analysis (P = 0.04). Furthermore, there was no significant difference of CD63% expression in anti-FceRI-activated captured basophils in microfluidic chip compared with flow cytometry. Conclusions: We report on the miBAT. This device is capable of isolating basophils directly from whole blood for on-chip activation and detection. The new miBAT method awaits validation in larger patient populations to assess performance in diagnosis and monitoring of patients with allergies at the point of care.

  • 13.
    Antypas, H.
    et al.
    Karolinska Inst, Dept Neurosci, Swedish Med Nanosci Ctr, Stockholm, Sweden..
    Veses-Garcia, M.
    Karolinska Inst, Dept Neurosci, Swedish Med Nanosci Ctr, Stockholm, Sweden..
    Weibull, Emelie
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Svahn Andersson, Helene
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Richter-Dahlfors, A.
    Karolinska Inst, Dept Neurosci, Swedish Med Nanosci Ctr, Stockholm, Sweden..
    A universal platform for selection and high-resolution phenotypic screening of bacterial mutants using the nanowell slide2018In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 18, no 12, p. 1767-1777Article in journal (Refereed)
    Abstract [en]

    The Petri dish and microtiter plate are the golden standard for selection and screening of bacteria in microbiological research. To improve on the limited resolution and throughput of these methods, we developed a universal, user-friendly platform for selection and high-resolution phenotypic screening based on the nanowell slide. This miniaturized platform has an optimal ratio between throughput and assay complexity, holding 672 nanowells of 500 nl each. As monoclonality is essential in bacterial genetics, we used FACS to inoculate each nanowell with a single bacterium in 15 min. We further extended the protocol to select and sort only bacteria of interest from a mixed culture. We demonstrated this by isolating single transposon mutants generated by a custom-made transposon with dual selection for GFP fluorescence and kanamycin resistance. Optical compatibility of the nanowell slide enabled phenotypic screening of sorted mutants by spectrophotometric recording during incubation. By processing the absorbance data with our custom algorithm, a phenotypic screen for growth-associated mutations was performed. Alternatively, by processing fluorescence data, we detected metabolism-associated mutations, exemplified by a screen for -galactosidase activity. Besides spectrophotometry, optical compatibility enabled us to perform microscopic analysis directly in the nanowells to screen for mutants with altered morphologies. Despite the miniaturized format, easy transition from nano- to macroscale cultures allowed retrieval of bacterial mutants for downstream genetic analysis, demonstrated here by a cloning-free single-primer PCR protocol. Taken together, our FACS-linked nanowell slide replaces manual selection of mutants on agar plates, and enables combined selection and phenotypic screening in a one-step process. The versatility of the nanowell slide, and the modular workflow built on mainstream technologies, makes our universal platform widely applicable in microbiological research.

  • 14.
    Ashammakhi, Nureddin
    et al.
    Institute for Quantitative Health Science and Engineering (IQ) and Department of Biomedical Engineering (BME); Department of Microbiology and Molecular Genetics Michigan State University East Lansing MI.
    Nasiri, Rohollah
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Contag, Christopher H.
    Institute for Quantitative Health Science and Engineering (IQ) and Department of Biomedical Engineering (BME); Department of Microbiology and Molecular Genetics Michigan State University East Lansing MI.
    Herland, Anna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Modelling Brain in a Chip2023In: The Journal of Craniofacial Surgery, ISSN 1049-2275, E-ISSN 1536-3732, Vol. 34, no 3, p. 845-847Article in journal (Other academic)
  • 15.
    Azizian, Parnian
    et al.
    Sharif Univ Technol, Dept Mech Engn, Tehran, Iran..
    Mohammadrashidi, Mahbod
    Sharif Univ Technol, Dept Mech Engn, Tehran, Iran..
    Abbas Azimi, Ali
    Sharif Univ Technol, Dept Mech Engn, Tehran, Iran..
    Bijarchi, Mohamad Ali
    Sharif Univ Technol, Dept Mech Engn, Tehran, Iran..
    Shafii, Mohammad Behshad
    Sharif Univ Technol, Dept Mech Engn, Tehran, Iran..
    Nasiri, Rohollah
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Magnetically Driven Manipulation of Nonmagnetic Liquid Marbles: Billiards with Liquid Marbles2023In: Micromachines, E-ISSN 2072-666X, Vol. 14, no 1, article id 49Article in journal (Refereed)
    Abstract [en]

    Liquid marbles are droplets encapsulated by a layer of hydrophobic nanoparticles and have been extensively employed in digital microfluidics and lab-on-a-chip systems in recent years. In this study, magnetic liquid marbles were used to manipulate nonmagnetic liquid marbles. To achieve this purpose, a ferrofluid liquid marble (FLM) was employed and attracted toward an electromagnet, resulting in an impulse to a water liquid marble (WLM) on its way to the electromagnet. It was observed that the manipulation of the WLM by the FLM was similar to the collision of billiard balls except that the liquid marbles exhibited an inelastic collision. Taking the FLM as the projectile ball and the WLM as the other target balls, one can adjust the displacement and direction of the WLM precisely, similar to an expert billiard player. Firstly, the WLM displacement can be adjusted by altering the liquid marble volumes, the initial distances from the electromagnet, and the coil current. Secondly, the WLM direction can be adjusted by changing the position of the WLM relative to the connecting line between the FLM center and the electromagnet. Results show that when the FLM or WLM volume increases by five times, the WLM shooting distance approximately increases by 200% and decreases by 75%, respectively.

  • 16.
    Bachmann, Till T.
    et al.
    Center for Inflammation Research, University of Edinburgh, Edinburgh, UK.
    Mitsakakis, Konstantinos
    Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany; Hahn-Schickard, Freiburg, Germany.
    Hays, John P.
    Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Centre (Erasmus MC), Rotterdam, Netherlands.
    van Belkum, Alex
    BioMérieux Open Innovation & Partnerships, La Balme Les Grottes, France.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. Division of Nanobiotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.
    Luedke, Gerd
    Curetis GmbH, Holzgerlingen, Germany.
    Simonsen, Gunnar Skov
    Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway.
    Abel, Gyorgy
    Division of Pathology and Laboratory Medicine, Lahey Hospital & Medical Center, Burlington, Massachusetts, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.
    Peter, Harald
    Branch Bioanalytics and Bioprocesses, Fraunhofer Institute for Cell Therapy and Immunology, Potsdam, Germany, Branch Bioanalytics and Bioprocesses.
    Goossens, Herman
    Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Department of Medical Microbiology, Antwerp University Hospital, Antwerp, Belgium.
    Moran-Gilad, Jacob
    Department of Health Policy and Management, School of Public Health, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
    Vila, Jordi
    Department of Clinical Microbiology, Biomedical Diagnostic Centre (CDB), Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain.
    Becker, Karsten
    University Hospital Münster, Münster, Germany.
    Moons, Pieter
    Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Department of Medical Microbiology, Antwerp University Hospital, Antwerp, Belgium.
    Sampath, Rangarajan
    Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland.
    Peeling, Rosanna W.
    Department of Clinical Research, London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases, London, UK.
    Luz, Saturnino
    Usher Institute, University of Edinburgh, Edinburgh, UK.
    van Staa, Tjeerd
    Health eResearch Centre, Farr Institute for Health Informatics Research, University of Manchester, Manchester, UK.
    Di Gregori, Valentina
    San Pier Damiano Hospital GVM Care and Research, Ravenna, Italy.
    Expert guidance on target product profile development for AMR diagnostic tests2023In: BMJ Global Health, E-ISSN 2059-7908, Vol. 8, no 12, article id e012319Article in journal (Refereed)
    Abstract [en]

    Diagnostics are widely considered crucial in the fight against antimicrobial resistance (AMR), which is expected to kill 10 million people annually by 2030. Nevertheless, there remains a substantial gap between the need for AMR diagnostics versus their development and implementation. To help address this problem, target product profiles (TPP) have been developed to focus developers’ attention on the key aspects of AMR diagnostic tests. However, during discussion between a multisectoral working group of 51 international experts from industry, academia and healthcare, it was noted that specific AMR-related TPPs could be extended by incorporating the interdependencies between the key characteristics associated with the development of such TPPs. Subsequently, the working group identified 46 characteristics associated with six main categories (ie, Intended Use, Diagnostic Question, Test Description, Assay Protocol, Performance and Commercial). The interdependencies of these characteristics were then identified and mapped against each other to generate new insights for use by stakeholders. Specifically, it may not be possible for diagnostics developers to achieve all of the recommendations in every category of a TPP and this publication indicates how prioritising specific TPP characteristics during diagnostics development may influence (or not) a range of other TPP characteristics associated with the diagnostic. The use of such guidance, in conjunction with specific TPPs, could lead to more efficient AMR diagnostics development.

  • 17.
    Banerjee, Indradumna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Point of care microfluidic tool development for resource limited settings2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The development of point of care diagnostics using recent advances in microfluidics have the potential to transform health care in several ways, especially in resource limited settings with limited access to advanced health care infrastructure. However, translating a point of care device to reality is often a challenging task because of the complexities involved in integrating a number of diverse engineering concepts into an easy to use, accurate and portable device. This thesis focuses on miniaturization of crucial diagnostic laboratory tools, that can be used in a portable point of care format without compromising on the accuracy or performance. The first part of the thesis (Paper I-III) focuses on understanding and applying elasto-inertial microfluidics, which is a label-free and passive bio-particle sorting and separation method. A basic understanding of particle trajectories in both inertial (Paper I) and visco-elastic flows (Paper II) is established, followed by an investigation on the combined effects of inertia and elasticity (Paper III). The second part of the thesis (Paper IV-VI) focuses on developing integrated microfluidic platforms, each of which addresses different aspects of point of care diagnostic applications. The applications include neonatal diagnostics using a hand-driven Slipdisc technique (Paper IV), rapid nucleic acid quantification using a novel precipitate-based detection on a centrifugal microfluidics platform (Paper V), and hematocrit level measurement in blood using a portable lab-on- Disc platform operated by a mobile phone (Paper VI). The proof of concept microfluidic tools presented in the scope of this thesis have the potential to replace a number of functions of standard laboratory equipment, at a fraction of the price and without compromising performance. Hence, the different methods developed should contribute towards decentralization of medical testing laboratories, making healthcare accessible to one and all.

    Download full text (pdf)
    fulltext
  • 18.
    Banerjee, Indradumna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Aralaguppe, S. P. G.
    Lapins, Noa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Kazemzadeh, Amin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Sönneborg, A.
    Neogi, U.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    MicroCap: Microfluidic centrifuge assisted precipitation for DNA quantification on lab-on-DVD2018In: 22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018, Chemical and Biological Microsystems Society , 2018, p. 1802-1805Conference paper (Refereed)
    Abstract [en]

    We report for the first time the MicroCAP technique, for rapid DNA detection and quantification, that does not require any purification or fluorescent labelling of DNA. The invention is based on DNA interacting with a detection dye (Gelred) to form a complex, that forms a visible precipitate within seconds of centrifugation. MicroCAP can be used for DNA quantification, when combined with the Lab-on-DVD with inbuilt centrifugation and sub-micron imaging resolution. We quantify PCR and LAMP assay products using MicroCAP on the integrated Lab-on-DVD platform, and demonstrate a detection limit of 10 ng/μl. Copyright 

  • 19.
    Banerjee, Indradumna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Aralaguppe, Shambhu Prasad
    Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Sweden.
    Lapins, Noa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Kazemzadeh, Amin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Sönneborg, Anders
    Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Sweden.
    Neogi, Ujjwal
    Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Sweden.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    MicroCAP: Microfluidic Centrifuge Assisted Precipitation for DNA Quantification on Lab-on-DVD2018Conference paper (Refereed)
    Abstract [en]

    We report for the first time the MicroCAP technique, for rapid DNA detection and quantification, that does not require any purification or fluorescent labelling of DNA. The invention is based on DNA interacting with a detection dye (Gelred) to form a complex, that forms a visible precipitate within seconds of centrifugation. MicroCAP can be used for DNA quantification, when combined with the Lab-on-DVD with inbuilt centrifugation and sub- micron imaging resolution. We quantify PCR and LAMP assay products using MicroCAP on the integrated Lab-on- DVD platform, and demonstrate a detection limit of 10 ng/!".

    KEYWORDS: MicroCAP, DNA detection, Centrifuge,Precipitate, LAMP, PCR.

    INTRODUCTION

    Detection of amplified DNA is often based on measurement of turbidity, fluorescence (after staining with a detec- tion dye) or absorbance. Commercially available instruments for DNA quantitation can be broadly divided into two categories: UV instruments based on absorbance (such as spectrophotometers, e.g. Nanodrop or Nanophotometer) and instruments based on measurement of a fluorescent dye (such as plate readers). One bottleneck in quantifying amplified DNA in a nucleic acid amplification test (NAAT) reaction, based on absorbance measurement technique, is the bias introduced due to the presence of the isothermal amplification buffer, dNTPs and other reagents. Each reagent or buffer may have an absorbance density at around 260 nm, elevating the apparent concentration measured by the device compared to the actual value. Hence, for most quantitation based NAATs, it is important to include an extra DNA purification step, which may result in non-negligible loss of the amplified product and increases the cost of the purification kit. Measurements based on fluorescence mostly use fluorescent dyes that are potentially hazardous for handling. In addition, fluorescence based quantitation methods require time consuming labelling and washing steps.

    In this report, we describe a new method, termed microfluidic centrifugation assisted precipitation (microCAP), involving quantification and detection of DNA based on precipitation of nucleic acids. The basis of the method is formation of a visible precipitate when GelRed, a nucleic acid intercalacting dye commonly used in gel electropho- resis, is mixed with DNA and centrifuged. A visible precipitate is formed after just a few seconds of centrifugation and enables rapid detection of the presence of DNA in a sample. To the best of our knowledge, the visible precipitate formed as a product of centrifuging GelRed mixed with DNA has not been reported before. We showed that the DNA GelRed complex is dense enough compared to water to precipitate upon centrifugation. Further, we extended the μCAP method to the Lab-on-DVD platform1 to quantify the DNA concentration from images generated using the optical DVD reader instrument. The modified DVD player was able to image the precipitate formed up to a detection limit of 10 ng/μl of DNA. For calibration of the images, known quantities of a purified PCR product were used to identify the relationship between the amounts of DNA and precipitate formed. We applied the method to quantify an unknown quantity of LAMP amplicons from a LAMP assay for a HIV-1B type genome containing plasmid on the Lab-on-DVD platform. A sensitivity limit of 10 ng/μl of DNA was achieved, comparable with that of a Nanophotometer.18 The results demonstrated that the method is able to quantitatively detect the presence of DNA in a sample in a few seconds without any purification step.

    EXPERIMENTAL

    The Lab-on-DVD system was employed for spinning and imaging the precipitate product using a modified DVD drive, as mentioned in our previous report.1 We began by dispensing the sample in the design chamber, adding GelRed dye (at a concentration of 4000X in water) and centrifuging the mixture at 1200 rpm. Figure 1a and 1b

    show schematics of the DNA sample precipitation process conducted in test tubes and the DVD platform, respec- tively. We used known amounts of a PCR product to calibrate the quantity of precipitate to the DNA concentration. We used a HIV genome amplified from 50 ng of plasmid pNL4.3 using the primers 0776F and 6231R.2 To evaluate the sensitivity of DNA detection of our system, we used the amplified products from a LAMP assay. The sensitivity of LAMP primers was tested on DNA from pNL4.3 (a HIV-1B genome containing plasmid). A 25X LAMP primer mix was prepared according to Curtis et al.,3 using the same template DNA sequence, set of primers and DNA polymerase. Eight concentrations (each being 5 μl volume) of the HIV-1B genome containing plasmid (pNL4.3) were tested, starting from 1 ng/!" serially diluted to 1 fg/!". Two negative controls were also prepared, one without DNA and primers and one without primers. The total reaction volume was increased to 30 μl (instead of 25 μl used in Curtis et al.3) by multiplying every component volume in the reaction by a factor of 1.2. Fabrication of the multi- layer microfluidic Disc followed the same procedure as described in our previous report.1 The Lab-on-DVD system was used to generate images of the precipitation zone. To quantify the amount of precipitate, an image processing script was written in MATLAB software (Mathworks, USA).

    RESULTS AND DISCUSSION

    MicroCAP was found to be suitable for determining the presence of DNA in a sample, We carried out the LAMP assay in Eppendorf tubes in an oven set at 65°C. After 45 minutes, 3 μl of 10,000X GelRed in water was added to two tubes of 30 μl volume each, one having an unknown concentration of LAMP amplified DNA and the other one with no DNA template as a control. After centrifugation for approximately 5 seconds, a visible precipitate was formed in the tube containing amplified DNA, whereas no precipitate was formed in the control tube (Fig. 2a). 10 μl volume of DNA was inserted into a U shaped channel of the DVD alongwith 1 μl of 10,000X GelRed in water, which was the same ratio of DNA sample to Gelred as used in the test tube. An imageable precipitate was observed in the Lab on DVD custom imaging software (fig.2b).

    A Matlab script was used for image analysis in which an original image(fig.3a) was transformed into a binary image (fig.3b) by defining a threshold pixel value, exploiting the difference in intensity of the precipitate from its background. The entire area to the left of the threshold line in the histogram (Fig. 3c), i.e. from value 0 to the threshold value (normally 90), was summed to estimate the total area of the precipitate.

    For DNA quantification, known concentrations of a PCR product was used for calibration. The initial concentration of purified PCR product was 129 ng/μl, measured with a Nanophotometer (in triplicates) after purification with a GeneJet PCR purification kit. The purified PCR product was subsequently diluted serially several times and each diluted concentration was measured again with the Nanophotometer (in triplicate). The measurements were then repeated with the Lab-on-DVD method. Fig. 4a shows four images recorded at four known concentrations together with their binary threshold images. Fig. 4b shows the precipitation area calculated from the images plotted against the known DNA concentrations, showing a linear relationship. 10 ng/μl was the lowest concentration detectable in the DVD images.

    For quantification of unknown quantities of nucleic acids, we carried out the LAMP assay on HIV-1B genome containing plasmid DNA using serial dilutions (10-fold dilutions from 1 ng/μl to 0.1 fg/μl) to evaluate the limit of detection (Fig.5). Two negative controls were also prepared, one comprising primers and no DNA template and second, no DNA template and no primers.

    Fig. 6 shows the precipitation area plotted against the starting concentration of DNA template. It shows that the amplification in the LAMP assay is not linear for all the starting concentrations of DNA template. The error bars in the figure show the standard deviation for a particular concentration. For a LAMP assay, which fluctuates somewhat in its yield of amplified prod- ucts, we believe that this error range is acceptable.

    The precipitation area was converted to an actual yield of DNA products for each of the concentrations. This conversion was based on the linear empirical equation generated from the calibration curve presented earlier in Fig. 4b, given by:

    y= 9.61x – 4.05 (1) Here, y denotes the precipitation area in arbitrary units while x denotes the DNA concentration.

    CONCLUSION

    We demonstrated an extremely fast visual DNA quantification method (μCAP) that can be made quantifiable on a Lab-on-DVD platform. The approach was based on DNA forming a precipitate upon centrifugation when in contact with the GelRed dye. Results using HIV-1B genome containing plasmid DNA revealed a detection limit of 0.01 pg/μl or total amount of 0.1 pg of starting DNA template, which is an acceptable standard for resource limited settings. The limit of detection of DNA with the Lab-on-DVD platform was found to be 10 ng/μl, which is almost comparable to the detection limits reported by commercially available instruments, such as the Nanophotometer. However, the μCAP method offers a distinct advantage over other state-of-the-art techniques as it does not require additional purification of the DNA. We believe the μCAP technique combined with the Lab-on-DVD platform provides a simple and low cost technology that can fulfil the need for a point-of-care device for DNA quantification.

    REFERENCES

    1. [1]  H. Ramachandraiah, M. Amasia, J. Cole, P. Sheard, S. Pickhaver, C. Walker, V. Wirta, P. Lexow, R. Lione and A. Russom, "Lab-on-DVD: standard DVD drives as a novel laser scanning microscope for image based point of care diagnostics."Lab. Chip, 2013, 13, 1578–1585.

    2. [2]  S. Grossmann, P. Nowak, and U. Neogi, “ Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical man- agement.” Journal of the International AIDS Society, 2015,18(1), 20035.

    3. [3]  K. A. Curtis, D. L. Rudolph, I. Nejad, J. Singleton, A. Beddoe, B. Weigl, P. LaBarre and S. M. Owen, "Rapid detection of HIV-1 by reverse-transcription, loop-mediated isothermal amplification (RT- LAMP)." PLoS ONE, , DOI:10.1371/journal.pone.0031432.

    CONTACT

    *A. Russom; phone: +46-87909863; aman@kth.se

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    MicroCAP
  • 20.
    Banerjee, Indradumna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Ganeshappa Aralaguppe, Shambhu Prasad
    Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Sweden..
    Lapins, Noa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Zhang, Wang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Sweden..
    Kazemzadeh, Amin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Sönnerborg, Anders
    Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Sweden..
    Neogi, Ujjwal
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Sweden..
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Microfluidic Centrifugation Assisted Precipitation based DNA QuantificationManuscript (preprint) (Other academic)
    Abstract [en]

    Nucleic acid amplification methods are increasingly being used to detect trace quantities of DNA in samples for various diagnostic applications. However, quantifying the amount of DNA from such methods often require time consuming purification, washing or labeling step. Here, we report a novel microfluidic centrifugation assisted precipitation (uCAP) method for single-step DNA quantification. The method is based on formation of a visible precipitate, that can be quantified, when an intercalating dye (GelRed) is added to DNA sample and centrifuged for few seconds. We describe the mechanism leading to the precipitation phenomenon. We utilize centrifugal microfluidics to precisely control the formation of visible and quantifiable mass. Using a standard CMOS sensor for imaging, we report a detection limit of 45 ng/ul. Furthermore, using an integrated Lab-on-DVD platform we recently developed, the detection limit was lowered to 10 ng/ul, which is comparable to current commercially available instruments for DNA quantification. As a proof of principle, we demonstrate the quantification of LAMP products for a HIV-1B type genome containing plasmid on the Lab-on-DVD platform. The simple DNA quantification system could facilitate advanced molecular diagnosis at point of care.

  • 21.
    Banerjee, Indradumna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Rosti, M. E.
    Kumar, Tharagan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Russom, Aman
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Analogue tuning of particle focusing in elasto-inertial flow2021In: Meccanica (Milano. Print), ISSN 0025-6455, E-ISSN 1572-9648, Vol. 56, no 7, p. 1739-1749Article in journal (Refereed)
    Abstract [en]

    We report a unique tuneable analogue trend in particle focusing in the laminar and weak viscoelastic regime of elasto-inertial flows. We observe experimentally that particles in circular cross-section microchannels can be tuned to any focusing bandwidths that lie between the “Segre-Silberberg annulus” and the centre of a circular microcapillary. We use direct numerical simulations to investigate this phenomenon and to understand how minute amounts of elasticity affect the focussing of particles at increasing flow rates. An Immersed Boundary Method is used to account for the presence of the particles and a FENE-P model is used to simulate the presence of polymers in a Non-Newtonian fluid. The numerical simulations study the dynamics and stability of finite size particles and are further used to analyse the particle behaviour at Reynolds numbers higher than what is allowed by the experimental setup. In particular, we are able to report the entire migration trajectories of the particles as they reach their final focussing positions and extend our predictions to other geometries such as the square cross section. We believe complex effects originate due to a combination of inertia and elasticity in the weakly viscoelastic regime, where neither inertia nor elasticity are able to mask each other’s effect completely, leading to a number of intermediate focusing positions. The present study provides a fundamental new understanding of particle focusing in weakly elastic and strongly inertial flows, whose findings can be exploited for potentially multiple microfluidics-based biological sorting applications. 

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    fulltext
  • 22.
    Banerjee, Indradumna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Rosti, Marco E.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Kumar, Tharagan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Particle focusing dynamics in extended elasto inertial flow2018In: 22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018, Chemical and Biological Microsystems Society , 2018, p. 472-475Conference paper (Refereed)
    Abstract [en]

    We report the decoupled effects of inertial and viscous forces on particle focusing, the stability of particles, and particle trajectories to reach equilibrium position in an extended elasto inertial pressure driven flow, in a circular micro-capillary. We report numerically and experimentally for the first time, the existence of multiple stable equilibrium positions in the EEI regime, which was unobserved for flows previously studied at lower Reynolds number viscoelastic flows. 

  • 23.
    Banerjee, Indradumna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Rosti, Marco Edoardo
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Kumar, Tharagan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Analog particle position tuning in Elasto-inertial microfluidic flowsManuscript (preprint) (Other academic)
    Abstract [en]

    We observe for the first time an analog trend in particle focusing in a high throughput weakly viscoelastic regime, where it is possible to tune particles into multiple intermediate focusing positions that lie between the "Segre-Silberberg annulus" and the center of a circular microcapillary. The "Segre-Silberberg annulus" (0.6 times the pipe radius), that describes particle equilibrium in a predominantly inertial flow, shrinks consistently closer to the center for increasing elasticity in extremely dilute PEO concentrations (ranging from 0.001 wt% to 0.05wt%). The experimental observations are supported by direct numerical simulations, where an Immersed Boundary Method is used to account for the presence of particles and a FENE-P model is used to simulate the presence of polymers in a Non-Newtonian fluid. The numerical simulations study the dynamics and stability of finite size particles and are further used to analyze particle behavior at Reynolds number higher than what is allowed by the present experimental setup. In particular, we are able to report the entire migration trajectories of the particles as they reach their final equilibrium positions and extend our predictions to other geometries such as the square cross-section. We believe complex effects originate due to a combination of inertia and elasticity in a weakly viscoelastic regime, where neither inertia nor elasticity are able to mask each other's effect completely, thus leading to a number of intermediate focusing positions. The present study provides a new understanding into the mechanism of particle focusing in elasto-inertial flows and opens up new possibilities for exercising analog control in tuning the particle focusing positions.

  • 24.
    Banerjee, Indradumna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Russom, Aman
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Lab-on-DVD: Optical Disk Drive-Based Platforms for Point-of-Care Diagnostics2018In: Frugal Innovation in Bioengineering for the Detection of Infectious Diseases / [ed] AK Chavali, R Ramji, Switzerland: Springer, 2018, 2, p. 23-38Chapter in book (Refereed)
    Abstract [en]

    There is a growing demand for simple, affordable, reliable and quality-assured point-of-care (POC) diagnostics for use in resource-limited settings. Among the top ten leading causes of death worldwide, three are infectious diseases, namely, respiratory infections, HIV/AIDS and diarrheal diseases (World Health Organization 2012). Although high-quality diagnostic tests are available, these are often not available to patients in developing countries. While recent development in microfluidics and “lab-on-a-chip” devices has the potential to spur the development of protocols and affordable instruments for diagnosis of infectious disease at POC, integration of complex sample preparation and detection into automated molecular and cellular systems remain a bottleneck for implementation of these systems at resource-limited settings. Towards this, we describe here how low-cost optical drives can, with minor modifications, be turned into POC diagnostic platforms. A DVD drive is essentially a highly advanced and low-cost optical laser-scanning microscope, with the capability to deliver high-resolution images for biological applications. Furthermore, the inherent centrifugal force on rotational discs is elegantly used for sample preparation and integration. Hence, the merging of low-cost optical disc drives with centrifugal microfluidics is feasible concept for POC diagnostics, specifically designed to meet the needs at resource-limited settings.

  • 25.
    Banerjee, Indradumna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    MicroCAP2018Patent (Other (popular science, discussion, etc.))
    Abstract [en]

  • 26.
    Battisti, Umberto Maria
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Scilifelab Univ Gothenburg, Dept Chem & Mol Biol.
    Gao, Chunxia
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Univ Gothenburg, Dept Chem & Mol Biol, S-41296 Gothenburg, Sweden.;KTH Royal Inst Technol, Sci Life Lab, S-10450 Stockholm, Sweden..
    Akladios, Fady
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. Univ Gothenburg, Dept Chem & Mol Biol, S-41296 Gothenburg, Sweden.;KTH Royal Inst Technol, Sci Life Lab, S-10450 Stockholm, Sweden..
    Kim, Woonghee
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Yang, Hong
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Bayram, Cemil
    Ataturk Univ, Fac Med, Dept Med Pharmacol, TR-25240 Erzurum, Turkiye..
    Bolat, Ismail
    Ataturk Univ, Fac Vet, Dept Pathol, TR-25240 Erzurum, Turkiye..
    Kiliclioglu, Metin
    Ataturk Univ, Fac Vet, Dept Pathol, TR-25240 Erzurum, Turkiye..
    Yuksel, Nursena
    Erzurum Tech Univ, Fac Sci, Dept Mol Biol & Genet, TR-25050 Erzurum, Turkiye..
    Tozlu, Ozlem Ozdemir
    Erzurum Tech Univ, Fac Sci, Dept Mol Biol & Genet, TR-25050 Erzurum, Turkiye..
    Zhang, Cheng
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Zhengzhou Univ, Sch Pharmaceut Sci, Zhengzhou 450001, Peoples R China..
    Sebhaoui, Jihad
    Trustlife Labs, Drug Res & Dev Ctr, TR-34774 Istanbul, Turkiye..
    Iqbal, Shazia
    Trustlife Labs, Drug Res & Dev Ctr, TR-34774 Istanbul, Turkiye..
    Shoaie, Saeed
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England..
    Hacimuftuoglu, Ahmet
    Ataturk Univ, Fac Med, Dept Med Pharmacol, TR-25240 Erzurum, Turkiye..
    Yildirim, Serkan
    Ataturk Univ, Fac Vet, Dept Pathol, TR-25240 Erzurum, Turkiye..
    Turkez, Hasan
    Ataturk Univ, Fac Med, Dept Med Biol, TR-25240 Erzurum, Turkiye..
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Boren, Jan
    Univ Gothenburg, Dept Mol & Clin Med, S-40530 Gothenburg, Sweden.;Sahlgrens Univ Hosp, S-40530 Gothenburg, Sweden..
    Mardinoglu, Adil
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England..
    Grotli, Morten
    Univ Gothenburg, Dept Chem & Mol Biol, S-41296 Gothenburg, Sweden..
    Ellagic Acid and Its Metabolites as Potent and Selective Allosteric Inhibitors of Liver Pyruvate Kinase2023In: Nutrients, E-ISSN 2072-6643, Vol. 15, no 3, p. 577-, article id 577Article in journal (Refereed)
    Abstract [en]

    Liver pyruvate kinase (PKL) has recently emerged as a new target for non-alcoholic fatty liver disease (NAFLD), and inhibitors of this enzyme could represent a new therapeutic option. However, this breakthrough is complicated by selectivity issues since pyruvate kinase exists in four different isoforms. In this work, we report that ellagic acid (EA) and its derivatives, present in numerous fruits and vegetables, can inhibit PKL potently and selectively. Several polyphenolic analogues of EA were synthesized and tested to identify the chemical features responsible for the desired activity. Molecular modelling studies suggested that this inhibition is related to the stabilization of the PKL inactive state. This unique inhibition mechanism could potentially herald the development of new therapeutics for NAFLD.

  • 27.
    Battisti, Umberto Maria
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Monjas, Leticia
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Akladios, Fady
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Matic, Josipa
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Andresen, Eric
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Nagel, Carolin H.
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Hagkvist, Malin
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Haversen, Liliana
    Univ Gothenburg, Dept Mol & Clin Med, SE-41345 Gothenburg, Sweden.;Sahlgrens Univ Hosp, SE-41345 Gothenburg, Sweden..
    Kim, Woonghee
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Boren, Jan
    Univ Gothenburg, Dept Mol & Clin Med, SE-41345 Gothenburg, Sweden.;Sahlgrens Univ Hosp, SE-41345 Gothenburg, Sweden..
    Mardinoglu, Adil
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England..
    Grotli, Morten
    Univ Gothenburg, Dept Chem & Mol Biol, SE-41296 Gothenburg, Sweden..
    Exploration of Novel Urolithin C Derivatives as Non-Competitive Inhibitors of Liver Pyruvate Kinase2023In: Pharmaceuticals, E-ISSN 1424-8247, Vol. 16, no 5, article id 668Article in journal (Refereed)
    Abstract [en]

    The inhibition of liver pyruvate kinase could be beneficial to halt or reverse non-alcoholic fatty liver disease (NAFLD), a progressive accumulation of fat in the liver that can lead eventually to cirrhosis. Recently, urolithin C has been reported as a new scaffold for the development of allosteric inhibitors of liver pyruvate kinase (PKL). In this work, a comprehensive structure-activity analysis of urolithin C was carried out. More than 50 analogues were synthesized and tested regarding the chemical features responsible for the desired activity. These data could pave the way to the development of more potent and selective PKL allosteric inhibitors.

  • 28.
    Björk, Sara
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Droplet microfluidics for screening and sorting of microbial cell factories2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Cell factories are cells that have been engineered to produce a compound of interest, ranging from biopharmaceuticals to biofuels. With advances in metabolic engineering, the number of cell factory variants to evaluate has increased dramatically, necessitating screening methods with increased throughput. Microfluidic droplets, which can be generated, manipulated and interrogated at very high throughput, are isolated reaction vessels at the single cell scale. Compartmentalization maintains the genotype-phenotype link, making droplet microfluidics suitable for screening of extracellular traits such as secreted products and for screening of microcolonies originating from single cells.

     

    In Paper I, we investigated the impact of droplet microfluidic incubation formats on cell culture conditions and found that syringe and semi open incubation resulted in different metabolic profiles. Controlling culture conditions is key to cell factory screening, as product formation is influenced by the state of the cell.

     

    In Paper II and III, we used droplet microfluidics to perform screening campaigns of interference based cell factory variant libraries. In Paper II, two S. cerevisiae RNAi libraries were screened based on amylase secretion, and from the sorted fraction genes linked to improved protein secretion could be identified. In paper III, we screened a Synecosystis sp. CRISPRi library based on lactate secretion. The library was sorted at different time points after induction, followed by sequencing to reveal genes enriched by droplet sorting.

     

    In Paper IV, we developed a droplet microcolony-based assay for screening intracellular triacylglycerol (TAG) in S. cerevisiae, and showed improved strain separation compared to flow cytometry in a hypothetical sorting scenario. By screening microcolonies compartmentalized in droplets, we combine the throughput of single cell screening methods with the reduced impact of cell-to-cell noise in cell ensemble analysis.

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  • 29.
    Björk, Sara
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Jönsson, Håkan
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Microfluidics for cell factory and bioprocess development2019In: Current Opinion in Biotechnology, ISSN 0958-1669, E-ISSN 1879-0429, Vol. 55, p. 95-102Article in journal (Refereed)
    Abstract [en]

    Bioindustry is expanding to an increasing variety of food, chemical and pharmaceutical products, each requiring rapid development of a dedicated cell factory and bioprocess. Microfluidic tools are, together with tools from synthetic biology and metabolic modeling, being employed in cell factory and bioprocess development to speed up development and address new products. Recent examples of microfluidics for bioprocess development range from integrated devices for DNA assembly and transformation, to high throughput screening of cell factory libraries, and micron scale bioreactors for process optimization. These improvements act to improve the biotechnological engineering cycle with tools for building, testing and evaluating cell factories and bioprocesses by increasing throughput, parallelization and automation.

  • 30.
    Björk, Sara M.
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Sjostrom, Staffan L.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson-Svahn, Helene
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Jönsson, Håkan N.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Metabolite profiling of microfluidic cell culture conditions for droplet based screening2015In: Biomicrofluidics, E-ISSN 1932-1058, Vol. 9, no 4, article id 044128Article in journal (Refereed)
    Abstract [en]

    We investigate the impact of droplet culture conditions on cell metabolic state by determining key metabolite concentrations in S. cerevisiae cultures in different microfluidic droplet culture formats. Control of culture conditions is critical for single cell/clone screening in droplets, such as directed evolution of yeast, as cell metabolic state directly affects production yields from cell factories. Here, we analyze glucose, pyruvate, ethanol, and glycerol, central metabolites in yeast glucose dissimilation to establish culture formats for screening of respiring as well as fermenting yeast. Metabolite profiling provides a more nuanced estimate of cell state compared to proliferation studies alone. We show that the choice of droplet incubation format impacts cell proliferation and metabolite production. The standard syringe incubation of droplets exhibited metabolite profiles similar to oxygen limited cultures, whereas the metabolite profiles of cells cultured in the alternative wide tube droplet incubation format resemble those from aerobic culture. Furthermore, we demonstrate retained droplet stability and size in the new better oxygenated droplet incubation format.

  • 31.
    Björk, Sara
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Schappert, Martin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Jönsson, Håkan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Droplet microfluidic microcolony analysis of triacylglycerol yields in S. cerevisiae for high throughput screeningManuscript (preprint) (Other academic)
  • 32.
    Björk, Sara
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schappert, Martin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Jönsson, Håkan
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Engineering.
    Droplet microfluidic microcolony sorting by fluorescence area for high throughput, yield-based screening of triacyl glycerides in S. Cerevisiae2020In: MicroTAS 2020 - 24th International Conference on Miniaturized Systems for Chemistry and Life Sciences, Chemical and Biological Microsystems Society , 2020, p. 1015-1016Conference paper (Refereed)
    Abstract [en]

    Here we present a droplet microfluidics workflow for cell factory screening by yield of an intracellular product from isogenic microcolonies, i.e. minimal cell populations, encapsulated in picoliter droplets. This allows us to utilize all the benefits of droplet microfluidic screening in terms of throughput, but based on the signal from a population average, rather than the noisy single cell signal. We demonstrate microcolony sorting by integrated droplet fluorescence area of encapsulated E. coli, optimize triglyceride (TG) microcolony assay in droplets and apply the microcolony screening concept to analyze triglyceride (TG) production in S. cerevisiae.

  • 33.
    Breideband, Louise
    et al.
    Goethe Univ Frankfurt, Phys Biol Grp, BMLS, Frankfurt, Germany..
    Pampaloni, Francesco
    Goethe Univ Frankfurt, Phys Biol Grp, BMLS, Frankfurt, Germany..
    Mårtensson, Gustaf
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. Mycronic AB, Täby, Sweden.
    Eklund, Robert
    Mycronic AB, Taby, Sweden..
    Wurst, Helmut
    Cellendes GmbH, Reutlingen, Germany..
    Angres, Brigitte
    Cellendes GmbH, Reutlingen, Germany..
    Torras, Nuria
    Barcelona Inst Sci & Technol BIST, Inst Bioengn Catalonia IBEC, Barcelona, Spain..
    Martinez, Elena
    Barcelona Inst Sci & Technol BIST, Inst Bioengn Catalonia IBEC, Barcelona, Spain..
    Shalom-Feuerstein, Ruby
    Technion Israel Inst Technol, Dept Genet & Dev Biol, Ruth & Bruce Rappaport Fac Med, Haifa, Israel..
    BIOPRINTING BY LIGHT SHEET LITHOGRAPHY: ENGINEERING COMPLEX TISSUES WITH HIGH RESOLUTION AT HIGH SPEED2022In: Tissue Engineering. Part A, ISSN 1937-3341, E-ISSN 1937-335X, Vol. 28, p. S443-S443Article in journal (Other academic)
  • 34.
    Buchmann, Sebastian
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences at KI and KTH/ 3 Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Organic Electronics and Microphysiological Systems to Interface, Monitor, and Model Biology2024Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biological processes in the human body are regulated through complex and precise arrangements of cell structures and their interactions. In vivo models serve as the most accurate choice for biological studies to understand these processes. However, they are costly, time-consuming, and raise ethical issues. Microphysiological systems have been developed to create advanced in vitro models that mimic in vivo-like microenvironments. They are often combined with integrated sensing technologies to perform real-time measurements to gain additional information. However, conventional sensing electrodes, made of inorganic materials such as gold or platinum, differ fundamentally from biological materials. Organic bioelectronic devices made from conjugated polymers are promising alternatives for biological sensing applications and aim to improve the interconnection between abiotic electronics and biotic materials. The widespread use of these devices is partly hindered by the limited availability of materials and low-cost fabrication methods. In this thesis, we provide new tools and materials that facilitate the use of organic bioelectronic devices for in vitro sensing applications. We developed a method to pattern the conducting polymer poly(3,4‑ethylenedioxythiophene) polystyrene sulfonate and to fabricate organic microelectronic devices using wax printing, filtering, and tape transfer. The method is low-cost, time-effective, and compatible with in vitro cell culture models. To achieve higher resolution, we further developed a patterning method using femtosecond laser ablation to fabricate organic electronic devices such as complementary inverters or biosensors. The method is maskless and independent of the type of conjugated polymer. Besides fabrication processes, we introduced a newly synthesized material, the semiconducting conjugated polymer p(g42T‑T)‑8%OH. This polymer contains hydroxylated side chains that enable surface modifications, allowing control of cell adhesion. Using the new femtosecond laser-based patterning method, we could fabricate p(g42T‑T)‑8%OH‑based organic electrochemical transistors to monitor cell barrier formations in vitro. Microphysological systems are further dependent on precise compartmentalization to study cellular interaction. We used femtosecond laser 3D printing to develop a co-culture neurite guidance platform to control placement and interactions between different types of brain cells. In summary, the thesis provides new tools to facilitate the fabrication of organic electronic devices and microphysiological systems. This increases their accessibility and widespread use to interface, monitor, and model biological systems. 

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    fulltext
  • 35.
    Buchmann, Sebastian
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Enrico, Alessandro
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Holzreuter, Muriel Alexandra
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Reid, Michael S.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Zeglio, Erica
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Niklaus, Frank
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Stemme, Göran
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Herland, Anna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Probabilistic cell seeding and non-autofluorescent 3D-printed structures as scalable approach for multi-level co-culture modeling2023In: Materials Today Bio, ISSN 2590-0064, Vol. 21, p. 100706-100706, article id 100706Article in journal (Refereed)
    Abstract [en]

    To model complex biological tissue in vitro, a specific layout for the position and numbers of each cell type isnecessary. Establishing such a layout requires manual cell placement in three dimensions (3D) with micrometricprecision, which is complicated and time-consuming. Moreover, 3D printed materials used in compartmentalizedmicrofluidic models are opaque or autofluorescent, hindering parallel optical readout and forcing serial charac-terization methods, such as patch-clamp probing. To address these limitations, we introduce a multi-level co-culture model realized using a parallel cell seeding strategy of human neurons and astrocytes on 3D structuresprinted with a commercially available non-autofluorescent resin at micrometer resolution. Using a two-stepstrategy based on probabilistic cell seeding, we demonstrate a human neuronal monoculture that forms net-works on the 3D printed structure and can establish cell-projection contacts with an astrocytic-neuronal co-cultureseeded on the glass substrate. The transparent and non-autofluorescent printed platform allows fluorescence-based immunocytochemistry and calcium imaging. This approach provides facile multi-level compartmentaliza-tion of different cell types and routes for pre-designed cell projection contacts, instrumental in studying complextissue, such as the human brain.

  • 36.
    Buchmann, Sebastian
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden/ Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Stoop, Pepijn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden/ Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Roekevisch, Kim
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden/ Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Jain, Saumey
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Kroon, Renee
    Department of Science and Technology, Laboratory of Organic Electronics, Linköping University, Norrköping, Sweden.
    Müller, Christian
    Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Hamedi, Mahiar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Zeglio, Erica
    AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden/ Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden/ Wallenberg Initiative Materials Science for Sustainability, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
    Herland, Anna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden/ Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    In situ functionalization of polar polythiophene based organic electrochemical transistor to interface in vitro modelsManuscript (preprint) (Other academic)
  • 37.
    Campinoti, Sara
    et al.
    Fdn Liver Res, Roger Williams Inst Hepatol, London, England.;Kings Coll London, Fac Life Sci & Med, London, England..
    Almeida, Bruna
    Fdn Liver Res, Roger Williams Inst Hepatol, London, England..
    Bencina, Stefan
    Karolinska Inst, Dept Lab Med, Div Pathol, Stockholm, Sweden..
    Goudarzi, Negin
    Fdn Liver Res, Roger Williams Inst Hepatol, London, England.;Kings Coll London, Fac Life Sci & Med, London, England..
    Cox, Jane
    Fdn Liver Res, Roger Williams Inst Hepatol, London, England.;Kings Coll London, Fac Life Sci & Med, London, England..
    Khati, Vamakshi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Gaudenzi, Giulia
    Karolinska Inst, Dept Global Publ Hlth, Stockholm, Sweden..
    Urbani, Luca
    Fdn Liver Res, Roger Williams Inst Hepatol, London, England.;Kings Coll London, Fac Life Sci & Med, London, England..
    Gramignoli, Roberto
    Karolinska Inst, Dept Lab Med, Div Pathol, Stockholm, Sweden..
    Perfusion bioreactor and decellularized liver matrix in support of human amnion epithelial cell maturation into functional hepatocyte-like cells2023In: Transplantation, ISSN 0041-1337, E-ISSN 1534-6080, Vol. 107, no 10, p. 133-133Article in journal (Other academic)
  • 38.
    Campinoti, Sara
    et al.
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Almeida, Bruna
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Goudarzi, Negin
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Bencina, Stefan
    Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Solna, Sweden.
    Grundland Freile, Fabio
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Department of Medical and Molecular Genetics, School of Basic and Medical Bioscience, Faculty of Life Science and Medicine, King’s College London, London, UK.
    McQuitty, Claire
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Natarajan, Dipa
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Cox, I. Jane
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Le Guennec, Adrien
    Centre for Biomolecular Spectroscopy, Randall Centre for Cell and Molecular Biophysics, Kings College London, London, UK.
    Khati, Vamakshi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gaudenzi, Giulia
    Department of Global Public Health, Karolinska Institutet, Solna, Sweden.
    Gramignoli, Roberto
    Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Solna, Sweden; Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Huddinge, Sweden.
    Urbani, Luca
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Rat liver extracellular matrix and perfusion bioreactor culture promote human amnion epithelial cell differentiation towards hepatocyte-like cells2023In: Journal of Tissue Engineering, ISSN 2041-7314, Vol. 14Article in journal (Refereed)
    Abstract [en]

    Congenital and chronic liver diseases have a substantial health burden worldwide. The most effective treatment available for these patients is whole organ transplantation; however, due to the severely limited supply of donor livers and the side effects associated with the immunosuppressive regimen required to accept allograft, the mortality rate in patients with end-stage liver disease is annually rising. Stem cell-based therapy aims to provide alternative treatments by either cell transplantation or bioengineered construct transplantation. Human amnion epithelial cells (AEC) are a widely available, ethically neutral source of cells with the plasticity and potential of multipotent stem cells and immunomodulatory properties of perinatal cells. AEC have been proven to be able to achieve functional improvement towards hepatocyte-like cells, capable of rescuing animals with metabolic disorders; however, they showed limited metabolic activities in vitro. Decellularised extracellular matrix (ECM) scaffolds have gained recognition as adjunct biological support. Decellularised scaffolds maintain native ECM components and the 3D architecture instrumental of the organ, necessary to support cells’ maturation and function. We combined ECM-scaffold technology with primary human AEC, which we demonstrated being equipped with essential ECM-adhesion proteins, and evaluated the effects on AEC differentiation into functional hepatocyte-like cells (HLC). This novel approach included the use of a custom 4D bioreactor to provide constant oxygenation and media perfusion to cells in 3D cultures over time. We successfully generated HLC positive for hepatic markers such as ALB, CYP3A4 and CK18. AEC-derived HLC displayed early signs of hepatocyte phenotype, secreted albumin and urea, and expressed Phase-1 and -2 enzymes. The combination of liver-specific ECM and bioreactor provides a system able to aid differentiation into HLC, indicating that the innovative perfusion ECM-scaffold technology may support the functional improvement of multipotent and pluripotent stem cells, with important repercussions in the bioengineering of constructs for transplantation.

  • 39.
    Campinoti, Sara
    et al.
    Kings College London, UK.
    Almeida, Bruna
    Kings College London, UK.
    Goudarzi, Negin
    Kings College London, UK.
    Cox, Jane
    Kings College London, UK.
    Khati, Vamakshi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Gaudenzi, Giulia
    Karolinska Institute.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Urbani, Luca
    Kings College London, UK.
    Gramignoli, Roberto
    Karolinska Institutet.
    Liver extracellular matrix and perfusion bioreactor culture promoting human amnion epithelial cell differentiation towards hepatocyte-like cellsManuscript (preprint) (Other academic)
  • 40. da Silva, P. G.
    et al.
    Nascimento, M. S. J.
    Soares, Ruben R. G.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
    Sousa, S. I. V.
    Mesquita, J. R.
    Airborne spread of infectious SARS-CoV-2: Moving forward using lessons from SARS-CoV and MERS-CoV2021In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 764, article id 142802Article in journal (Refereed)
    Abstract [en]

    Background: Although an increasing body of data reports the detection of SARS-CoV-2 RNA in air, this does not correlate to the presence of infectious viruses, thus not evaluating the risk for airborne COVID-19. Hence there is a marked knowledge gap that requires urgent attention. Therefore, in this systematic review, viability/stability of airborne SARS-CoV-2, SARS-CoV and MERS-CoV viruses is discussed. Methods: A systematic literature review was performed on PubMed/MEDLINE, Web of Science and Scopus to assess the stability and viability of SARS-CoV, MERS-CoV and SARS-CoV-2 on air samples. Results and discussion: The initial search identified 27 articles. Following screening of titles and abstracts and removing duplicates, 11 articles were considered relevant. Temperatures ranging from 20 °C to 25 °C and relative humidity ranging from 40% to 50% were reported to have a protective effect on viral viability for airborne SARS-CoV and MERS-CoV. As no data is yet available on the conditions influencing viability for airborne SARS-CoV-2, and given the genetic similarity to SARS-CoV and MERS-CoV, one could extrapolate that the same conditions would apply. Nonetheless, the effect of these conditions seems to be residual considering the increasing number of cases in the south of USA, Brazil and India, where high temperatures and humidities have been observed. Conclusion: Higher temperatures and high relative humidity can have a modest effect on SARS-CoV-2 viability in the environment, as reported in previous studies to this date. However, these studies are experimental, and do not support the fact that the virus has efficiently spread in the tropical regions of the globe, with other transmission routes such as the contact and droplet ones probably being responsible for the majority of cases reported in these regions, along with other factors such as human mobility patterns and contact rates. Further studies are needed to investigate the extent of aerosol transmission of SARS-CoV-2 as this would have important implications for public health and infection-control policies.

  • 41.
    Damiati, Laila A.
    et al.
    Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia;Centre for the Cellular Microenvironment, University of Glasgow, Glasgow, United Kingdom.
    Damiati, Safa A.
    Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia.
    Damiati, Samar
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
    Developments in the use of microfluidics in synthetic biology2022In: New Frontiers and Applications of Synthetic Biology, Elsevier BV , 2022, p. 423-435Chapter in book (Other academic)
    Abstract [en]

    Biomimetics aims to copy and imitate natural elements and systems in a simpler form to overcome the limitations of complex biological elements and systems. The construction of biomimetic platforms to investigate physiological conditions requires an understanding of the native structure of cells and tissues and their interactions. Thus synthetic biology effectively connects biology and engineering. The engineering of custom cells/organs involves the construction of seminatural models that either perform existing functions in a modified manner or perform functions that do not exist naturally. In addition to providing an understanding of biological approaches, artificial models allow the mimicking of human physiology and diseases, facilitating the discovery of new drugs. Microfluidics is one of the most advanced technologies that allow the studying, mimicking, and manipulation of biological behaviors. Microfluidic devices are miniaturized devices that are functionally integrated on a single platform. The continuous development of microfluidic technology has led to the generation of artificial cells/organs that are based on in vivo mimetic models. Hence, it offers promising approaches for drug analysis, investigation of diseases and toxicity pathways, and construction of artificial models and even synthetic cell/organ chassis. This chapter presents microfluidic innovations for cell-like and organ-like architectures that were developed to simplify the complex networks of cells and organs. The merging of synthetic biology and microfluidics has led to the successful generation of artificial cells and organ-on-a-chip models. These biomimetic microfluidic environments have reduced the technical difficulties that acted as obstacles to studying cellular biology, have allowed the investigation of cell-cell, cell-tissue, and organ-like interfaces, and have aided the discovery of new therapeutic agents. 

  • 42.
    Damiati, Samar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia; Institute for Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
    Acoustic Biosensors for Cell Research2021In: Handbook of Cell Biosensors, Springer Nature , 2021, p. 537-568Chapter in book (Other academic)
    Abstract [en]

    Drawing inspiration from nature and applying natural principles can support the continuous improvement of sensing technologies in various fields, such as medicine, pharmacy, and environmental applications. It is difficult to directly connect a sensing system to a complex biological system. Thus, finding a suitable technique that simplifies and interprets complicated biological information to generate readable signals is in high demand. Acoustic technology appears to be a promising sensing model. The monitoring of the biochemical processes or the quantification of a captured analyte can be performed utilizing acoustic wave devices that rely on gravimetric sensing of materials adsorbed onto the sensor surface. Considering nature as a toolkit that provides individual puzzle pieces that can be assembled carefully into a sensory system offers a rich source to build selective and sensitive biosensors. The natural toolbox includes biological components such as DNA, RNA, sugar, amino acids, proteins, and lipids, in addition to nonbiological components such as graphene, carbon nanotubes, and metals. These molecules can be assembled together onto piezoelectric substrates to enhance the functionality of fabricated acoustic devices. This chapter has classified acoustic biosensors into four classes for various cell applications. First, lipid membrane-based biosensors are biomimetic models constructed by natural biological materials to simplify the complexity of biological cell membranes and enable investigations of membrane proteins in a native-like environment. These bioarchitectures also offer a good opportunity to investigate the interactions of lipids and proteins under controlled conditions. Second, whole cell-based biosensors are fabricated to enable investigations of cellular behaviors such as cell adhesion and cell-substrate interactions. Third, detection biosensors are also attracting attention due to their high sensitivity, ability to track cells in real time without labeling, and ability to differentiate between viable and nonviable cells. Finally, recent advancements in the fabrication of acoustic biosensors have enabled cells themselves to act as biosensors to detect analytes. All designed acoustic platforms are aimed at studying the cell, the basic unit of life, from different perspectives. The facts discussed in this chapter are based on phenomena that cannot be visualized by the eye, such as cellular interactions, or factors present in such small quantities, but they can be heard by tracking their acoustic sounds.

  • 43.
    Damiati, Samar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KAU, Dept Biochem, Fac Sci, Jeddah 21589, Saudi Arabia.;BOKU Univ Nat Resources & Life Sci, Inst Synthet Bioarchitectures, Dept NanoBiotechnol, Muthgasse 11, A-1190 Vienna, Austria..
    Schuster, Bernhard
    BOKU Univ Nat Resources & Life Sci, Inst Synthet Bioarchitectures, Dept NanoBiotechnol, Muthgasse 11, A-1190 Vienna, Austria..
    Electrochemical Biosensors Based on S-Layer Proteins2020In: Sensors, E-ISSN 1424-8220, Vol. 20, no 6, article id 1721Article, review/survey (Refereed)
    Abstract [en]

    Designing and development of electrochemical biosensors enable molecule sensing and quantification of biochemical compositions with multitudinous benefits such as monitoring, detection, and feedback for medical and biotechnological applications. Integrating bioinspired materials and electrochemical techniques promote specific, rapid, sensitive, and inexpensive biosensing platforms for (e.g., point-of-care testing). The selection of biomaterials to decorate a biosensor surface is a critical issue as it strongly affects selectivity and sensitivity. In this context, smart biomaterials with the intrinsic self-assemble capability like bacterial surface (S-) layer proteins are of paramount importance. Indeed, by forming a crystalline two-dimensional protein lattice on many sensors surfaces and interfaces, the S-layer lattice constitutes an immobilization matrix for small biomolecules and lipid membranes and a patterning structure with unsurpassed spatial distribution for sensing elements and bioreceptors. This review aims to highlight on exploiting S-layer proteins in biosensor technology for various applications ranging from detection of metal ions over small organic compounds to cells. Furthermore, enzymes immobilized on the S-layer proteins allow specific detection of several vital biomolecules. The special features of the S-layer protein lattice as part of the sensor architecture enhances surface functionalization and thus may feature an innovative class of electrochemical biosensors.

  • 44.
    Damiati, Samar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. King Abdulaziz Univ, Dept Biochem, Fac Sci, Jeddah 21589, Saudi Arabia.;KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Div Nanobiotechnol, S-17121 Stockholm, Sweden..
    Sopstad, Sindre
    Univ South Eastern Norway, Fac Technol Nat Sci & Maritime, Dept Microsyst, N-3184 Borre, Norway..
    Peacock, Martin
    Zimmer & Peacock Ltd, Royston SG8 9JL, England..
    Akhtar, Ahmad Saleem
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pinto, Ines Fernandes
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Soares, Ruben R. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Flex Printed Circuit Board Implemented Grapene-Based DNA Sensor for Detection of SARS-CoV-22021In: IEEE Sensors Journal, ISSN 1530-437X, E-ISSN 1558-1748, Vol. 21, no 12, p. 13060-13067Article in journal (Refereed)
    Abstract [en]

    Since the COVID-19 outbreak was declared a pandemic by the World Health Organization (WHO) in March 2020, ongoing efforts have been made to develop sensitive diagnostic platforms. Detection of viral RNA provides the highest sensitivity and specificity for detection of early and asymptomatic infections. Thus, this work aimed at developing a label-free genosensor composed of graphene as a working electrode that could be embedded into a flex printed circuit board (FPCB) for the rapid, sensitive, amplification-free and label-free detection of SARS-CoV-2. To facilitate liquid handling and ease of use, the developed biosensor was embedded with a user-friendly reservoir chamber. As a proof-of-concept, detection of a synthetic DNA strand matching the sequence of ORF1ab was performed as a two-step strategy involving the immobilization of a biotinylated complementary sequence on a streptavidin-modified surface, followed by hybridization with the target sequence recorded by the differential pulse voltammetric (DPV) technique in the presence of a ferro/ferricyanide redox couple. The effective design of the sensing platform improved its selectivity and sensitivity and allowed DNA quantification ranging from 100 fg/mL to 1 mu g/mL. Combining the electrochemical technique with FPCB enabled rapid detection of the target sequence using a small volume of the sample (5-20 mu L). We achieved a limit-of-detection of 100 fg/mL, whereas the predicted value was similar to 33 fg/mL, equivalent to approximately 5 x 10(5) copies/mL and comparable to sensitivities provided by isothermal nucleic acid amplification tests. We believe that the developed approach proves the ability of an FPCB-implemented DNA sensor to act as a potentially simpler and more affordable diagnostic assay for viral infections in Point-Of-Care (POC) applications.

  • 45.
    Dietvorst, Jiri
    et al.
    CSIC, Inst Microelect Barcelona IMB CNM, Bellaterra 08193, Barcelona, Spain.;CSIC, Inst Adv Chem Catalonia IQAC, Dept Chem & Biomol Nanotechnol, Nanobiotechnol Diagnost Nb4D, Barcelona 08034, Spain..
    Ferrer-Vilanova, Amparo
    CSIC, Inst Microelect Barcelona IMB CNM, Bellaterra 08193, Barcelona, Spain.;Univ Autonoma Barcelona, Dept Quim, Bellaterra 08193, Barcelona, Spain..
    Iyengar, Sharath Narayana
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Vigues, Nuria
    Univ Autonoma Barcelona, Dept Genet & Microbiol, Bellaterra 08193, Barcelona, Spain..
    Mas, Jordi
    Univ Autonoma Barcelona, Dept Genet & Microbiol, Bellaterra 08193, Barcelona, Spain..
    Vilaplana, Lluisa
    CSIC, Inst Adv Chem Catalonia IQAC, Dept Chem & Biomol Nanotechnol, Nanobiotechnol Diagnost Nb4D, Barcelona 08034, Spain..
    Marco, Maria-Pilar
    CSIC, Inst Adv Chem Catalonia IQAC, Dept Chem & Biomol Nanotechnol, Nanobiotechnol Diagnost Nb4D, Barcelona 08034, Spain.;CIBER Bioingn Biomat & Nanomed CIBER BBN, Barcelona 08034, Spain..
    Guirado, Gonzalo
    Univ Autonoma Barcelona, Dept Quim, Bellaterra 08193, Barcelona, Spain..
    Munoz-Berbel, Xavier
    CSIC, Inst Microelect Barcelona IMB CNM, Bellaterra 08193, Barcelona, Spain..
    Bacteria Detection at a Single-Cell Level through a Cyanotype-Based Photochemical Reaction2022In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 94, no 2, p. 787-792Article in journal (Refereed)
    Abstract [en]

    The detection of living organisms at very low concentrations is necessary for the early diagnosis of bacterial infections, but it is still challenging as there is a need for signal amplification. Cell culture, nucleic acid amplification, or nano-structure-based signal enhancement are the most common amplification methods, relying on long, tedious, complex, or expensive procedures. Here, we present a cyanotype-based photochemical amplification reaction enabling the detection of low bacterial concentrations up to a single-cell level. Photocatalysis is induced with visible light and requires bacterial metabolism of iron-based compounds to produce Prussian Blue. Bacterial activity is thus detected through the formation of an observable blue precipitate within 3 h of the reaction, which corresponds to the concentration of living organisms. The short time-to-result and simplicity of the reaction are expected to strongly impact the clinical diagnosis of infectious diseases.

  • 46.
    Eklundh, Annika
    et al.
    Sachs Children & Youth Hosp, Pediat Emergency Dept, S-11883 Stockholm, Sweden.;Karolinska Inst, Dept Global Publ Hlth, S-17177 Stockholm, Sweden..
    Rhedin, Samuel
    Sachs Children & Youth Hosp, Pediat Emergency Dept, S-11883 Stockholm, Sweden.;Karolinska Inst, Dept Med Epidemiol & Biostat, S-17177 Stockholm, Sweden..
    Ryd-Rinder, Malin
    Karolinska Univ Hosp, Astrid Lindgren Childrens Hosp, Pediat Emergency Dept, S-17164 Solna, Sweden.;Karolinska Inst, Dept Womens & Childrens Hlth, S-17177 Stockholm, Sweden..
    Andersson, Maria
    Univ Gothenburg, Dept Infect Dis, S-40530 Gothenburg, Sweden..
    Gantelius, Jesper
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gaudenzi, Giulia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska Inst, Dept Global Publ Hlth, S-17177 Stockholm, Sweden..
    Lindh, Magnus
    Univ Gothenburg, Dept Infect Dis, S-40530 Gothenburg, Sweden..
    Peltola, Ville
    Univ Turku, Turku Univ Hosp, Dept Paediat & Adolescent Med, FI-20521 Turku, Finland..
    Waris, Matti
    Univ Turku, Inst Biomed, FI-20521 Turku, Finland.;Turku Univ Hosp, Clin Microbiol, FI-20521 Turku, Finland..
    Naucler, Pontus
    Dept Med, Div Infect Dis, S-17176 Stockholm, Sweden.;Karolinska Inst, S-17164 Solna, Sweden.;Karolinska Univ Hosp, Dept Infect Dis, S-17164 Solna, Sweden..
    Martensson, Andreas
    Uppsala Univ, Dept Womens & Childrens Hlth, Int Maternal & Child Hlth IMCH, S-75237 Uppsala, Sweden..
    Alfven, Tobias
    Sachs Children & Youth Hosp, Pediat Emergency Dept, S-11883 Stockholm, Sweden.;Karolinska Inst, Dept Global Publ Hlth, S-17177 Stockholm, Sweden..
    Etiology of Clinical Community-Acquired Pneumonia in Swedish Children Aged 1-59 Months with High Pneumococcal Vaccine Coverage-The TREND Study2021In: Vaccines, E-ISSN 2076-393X, Vol. 9, no 4, article id 384Article in journal (Refereed)
    Abstract [en]

    (1) Immunization with pneumococcal conjugate vaccines has decreased the burden of community-acquired pneumonia (CAP) in children and likely led to a shift in CAP etiology. (2) The Trial of Respiratory infections in children for ENhanced Diagnostics (TREND) enrolled children 1-59 months with clinical CAP according to the World Health Organization (WHO) criteria at Sachs' Children and Youth Hospital, Stockholm, Sweden. Children with rhonchi and indrawing underwent "bronchodilator challenge". C-reactive protein and nasopharyngeal PCR detecting 20 respiratory pathogens, were collected from all children. Etiology was defined according to an a priori defined algorithm based on microbiological, biochemical, and radiological findings. (3) Of 327 enrolled children, 107 (32%) required hospitalization; 91 (28%) received antibiotic treatment; 77 (24%) had a chest X-ray performed; and 60 (18%) responded to bronchodilator challenge. 243 (74%) episodes were classified as viral, 11 (3%) as mixed viral-bacterial, five (2%) as bacterial, two (0.6%) as atypical bacterial and 66 (20%) as undetermined etiology. After exclusion of children responding to bronchodilator challenge, the proportion of bacterial and mixed viral-bacterial etiology was 1% and 4%, respectively. (4) The novel TREND etiology algorithm classified the majority of clinical CAP episodes as of viral etiology, whereas bacterial etiology was uncommon. Defining CAP in children <5 years is challenging, and the WHO definition of clinical CAP is not suitable for use in children immunized with pneumococcal conjugate vaccines.

  • 47.
    Enrico, Alessandro
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems. Synthetic Physiology lab, Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, Pavia, 27100 Italy.
    Buchmann, Sebastian
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, Center for the Advancement of Integrated Medical and Engineering Sciences, AIMES.
    De Ferrari, Fabio
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Lin, Yunfan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Wang, Yazhou
    Guangzhou Key Laboratory of Flexible Electronic Materials and Wearable Devices School of Materials Science and Engineering Sun Yat‐sen University Guangzhou 510275 P. R. China.
    Yue, Wan
    Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education School of Materials Science and Engineering Sun Yat‐sen University Guangzhou 510275 P. R. China.
    Mårtensson, Gustaf
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Mycronic AB Nytorpsvägen 9 Täby 183 53 Sweden.
    Stemme, Göran
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Hamedi, Mahiar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Niklaus, Frank
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Herland, Anna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, Center for the Advancement of Integrated Medical and Engineering Sciences, AIMES.
    Zeglio, Erica
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, Center for the Advancement of Integrated Medical and Engineering Sciences, AIMES. Wallenberg Initiative Materials Science for Sustainability, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, 114 18 Sweden.
    Cleanroom‐Free Direct Laser Micropatterning of Polymers for Organic Electrochemical Transistors in Logic Circuits and Glucose Biosensors2024In: Advanced Science, E-ISSN 2198-3844Article in journal (Refereed)
    Abstract [en]

    Organic electrochemical transistors (OECTs) are promising devices for bioelectronics, such as biosensors. However, current cleanroom-based microfabrication of OECTs hinders fast prototyping and widespread adoption of this technology for low-volume, low-cost applications. To address this limitation, a versatile and scalable approach for ultrafast laser microfabrication of OECTs is herein reported, where a femtosecond laser to pattern insulating polymers (such as parylene C or polyimide) is first used, exposing the underlying metal electrodes serving as transistor terminals (source, drain, or gate). After the first patterning step, conducting polymers, such as poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS), or semiconducting polymers, are spin-coated on the device surface. Another femtosecond laser patterning step subsequently defines the active polymer area contributing to the OECT performance by disconnecting the channel and gate from the surrounding spin-coated film. The effective OECT width can be defined with high resolution (down to 2 µm) in less than a second of exposure. Micropatterning the OECT channel area significantly improved the transistor switching performance in the case of PEDOT:PSS-based transistors, speeding up the devices by two orders of magnitude. The utility of this OECT manufacturing approach is demonstrated by fabricating complementary logic (inverters) and glucose biosensors, thereby showing its potential to accelerate OECT research.

  • 48.
    Etcheverry, Sebastián
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics.
    Russom, Aman
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Laurell, Fredrik
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics.
    Margulis, Walter
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics.
    Trapping and Optical Identification of Microparticles in a Liquid with a Functional Optical Fiber Probe2018In: 2018 conference on lasers and electro-optics (CLEO), IEEE , 2018Conference paper (Refereed)
    Abstract [en]

    A fiber probe traps single micrometer-particles by fluid suction into a hollow microstructure and enables optical identification by the fluorescence light collected in a fiber core. The probe finds applications in life-science and environmental monitoring.

  • 49.
    Faridi, Muhammad Asim
    et al.
    KTH.
    Shahzad, Adnan Faqui
    KTH.
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Wiklund, Martin
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Milliliter scale acoustophoresis based bioparticle processing platform2018In: ASME 2018 16th International Conference on Nanochannels, Microchannels, and Minichannels, ICNMM 2018, ASME Press, 2018Conference paper (Refereed)
    Abstract [en]

    Bioparticles such as mammalian cells and bacteria can be manipulated directly or indirectly for multiple applications such as sample preparation for diagnostic applications mainly up-concentration, enrichment & separation as well as immunoassay development. There are various active and passive microfluidic particle manipulation techniques where Acoustophoresis is a powerful technique showing high cell viability. The use of disposable glass capillaries for acoustophoresis, instead of cleanroom fabricated glass-silicon chip can potentially bring down the cost factor substantially, aiding the realization of this technique for real-world diagnostic devices. Unlike available chips and capillary-based microfluidic devices, we report milliliter-scale platform able to accommodate 1ml of a sample for acoustophoresis based processing on a market available glass capillary. Although it is presented as a generic platform but as a demonstration we have shown that polystyrene suspending medium sample can be processed with trapping efficiency of 87% and the up-concentration factor of 10 times in a flow through manner i.e., at 35µl/min. For stationary volume accommodation, this platform practically offers 50 times more sample handling capacity than most of the microfluidic setups. Furthermore, we have also shown that with diluted blood (0.6%) in a flow-through manner, 82% of the white blood cells (WBCs) per ml could be kept trapped. This milliliter platform could potentially be utilized for assisting in sample preparation, plasma separation as well as a flow-through immunoassay assay development for clinical diagnostic applications.

  • 50. Fornell, Anna
    et al.
    Nilsson, Johan
    Jonsson, Linus
    Periyannan Rajeswari, Prem Kumar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Jönsson, Håkan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Tenje, Maria
    Particle enrichment in droplet acoustofluidics2016In: Micronano System Workshop (MSW 2016), Lund, Sweden, May 17-18 2016, 2016Conference paper (Refereed)
123 1 - 50 of 148
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