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  • 1.
    Anlind, Nils
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Eriksson, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Gromova, Arina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hong, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ljungström, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Markstedt, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Marknadsanalys av proteinstandarder för kvantitativ masspektrometri2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    QPrEST är en ny intern standard för absolut kvantifiering av proteiner utvecklat av företaget Atlas Antibodies AB. I en marknad där det redan finns etablerade standarder kan det vara svårt att konkurrera ut de nuvarande produkterna. Därför har denna rapport gjorts vilken består av en marknadsanalys av nuvarande standarder, statistisk undersökning av publicerade artiklar inom absolut kvantitativ proteomik samt en global kundundersökning med 35 svarande. Resultaten har legat till grund för förbättringsförslag till Atlas Antibodies AB för bättre marknadsföring och lansering av sin nya produkt, QPrEST. Slutsatsen från denna rapport är att Atlas Antibodies AB måste nischa in sin produkt till kvantifiering av ett målprotein då det är där standarden presterar bäst.

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  • 2.
    Bagge, Joakim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Hedman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Smedsrud, Sabina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Svärdström, Cornelia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Söderberg, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Valdés, Fernando
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Utveckling av metodik för påvisning och typning av Listeria i livsmedelskedjan2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
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  • 3.
    Crialesi-Esposito, Marco
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Engineering Mechanics.
    Gonzalez-Montero, L. A.
    Univ Politecn Valencia, CMT Motores Term, Valencia, Spain..
    Salvador, F. J.
    Univ Politecn Valencia, CMT Motores Term, Valencia, Spain..
    Effects of isotropic and anisotropic turbulent structures over spray atomization in the near field2022In: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 150, article id 103891Article in journal (Refereed)
    Abstract [en]

    Sprays and atomization processes are extremely diffused both in nature and in industrial applications. In this paper we analyze the influence of the nozzle turbulence on primary atomization, focusing on the resulting turbulent field and atomization patterns in the Near Field (NF). In order to do so, a Synthetic Boundary Condition (SBC) and a Mapped Boundary Condition (MBC), producing respectively isotropic and anisotropic turbulent fields, have been generated as inflow conditions for the spray Direct Numerical Simulations (DNS). We present a specific methodology to ensure consistency on turbulence intensity and integral lengthscale between the two inflows. The analysis performed on the turbulent field (using one-point statistics and spectrum analysis) reveals a significantly stronger turbulent field generated by the inflow boundary conditions with anisotropic structures. While the increased turbulence field generated in the MBC case results in a higher number of droplets generated, the probability functions of both cases are extremely similar, leading to the non-obvious conclusion that the atomization patterns are only slightly affected by the inflow condition. These considerations are supported by the analysis of droplet size distributions, radial distribution functions, axial and radial distributions, highlighting extremely similar behaviors between the MBC and the SBC cases. Finally, these analyses and their computations are presented in detail, underlining how this type of point-process characterization shows interesting potential in future studies on sprays.

  • 4.
    Iyengar, Sharath Narayana
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Isotachophoretically-driven rolling circle amplification unit for nucleic acid detectionManuscript (preprint) (Other academic)
  • 5.
    Kostines, Reneh
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Validation of anti-cytokeratin antibodies used in rapid cancer diagnostics by isoelectric focusing and QCM technology2021Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Antibodies are Y-shaped proteins. In the human body, antibodies areproduced by plasma cells, mainly T and B cells which are included inthe adaptive immune system. The production of antibodies is stimulatedby antigens. The binding between an antigen-specific antibody and itsantigen can be like the interconnect between a lock and a key.Therefore, antibodies are widely used as diagnostic tools for avariety of diseases but most importantly cancer. Some rapid diagnostictests are completely dependent on the specificity and reactivity ofantibodies such as UBC® Rapid produced by IDL Biotech AB. Therefore,the quality of these antibodies is important.

    This master thesis at IDL Biotech aimed to validate six anticytokeratinantibodies that are currently used in several rapid cancerdiagnostic tests produced by IDL. Antibody validation is a processwhere specificity, selectivity and reproductivity of an antibody isdemonstrated through specific laboratory investigations. During thisthesis, two laboratory methods were used to validate antibodies,namely, isoelectric focusing electrophoresis and the Attana QuartzCrystal Microbalance based biosensor.

    Isoelectric focusing electrophoresis (IEF) is a method that determinesproteins pI-values which can then reveal information about posttranslationalmodifications and protein sustainability during storage.IEF revealed changes in pI-values in two antibodies: AB2 and AB4.

    Attana biosensor analysis on AB1-5 showed that all antibodies havehigh specificity, reactivity and relatively high affinity to theircytokeratin targets. It also revealed that 4 antibodies (AB1 and AB3-5) have lower cross-reactivity with other cytokeratins than theirtarget cytokeratins compared to AB2.

    Keywords: Antibody validation, Isoelectric focusing, QCM, Attanabiosensor, biosensors, rapid diagnostics, epithelial carcinomas.

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  • 6.
    Ladhani, Laila
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    An electrostatic sampling device for point-of-care detection of bioaerosols2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Bioaerosols are not only a significant factor of air quality but contribute greatly to the spread of infectious diseases, specifically through expired pathogen-laden aerosols. Clear examples of airborne transmission include: the recent influenza pandemic of 2009, the ongoing tuberculosis epidemic, and yearly norovirus out- breaks, which affect millions of people worldwide and pose serious threats to public healthcare systems. Given these acute concerns and the critical lack of knowledge of the field, it is important to develop methods for sampling and detecting these air- borne pathogens. Specifically, detection at the point-of-care can play an important role in improving the outcome of patient care by providing rapid and convenient diagnostics.

    Electrostatic precipitation has emerged as a promising sampling tool for bio- aerosols, which together with a rapid analysis technique, can provide a powerful and integrated approach to pathogen detection or disease diagnosis at the point- of-care. Moreover, such a sampling-detection scheme could be a potentialy non- invasive breath sampling tool for diagnosis of respiratory infectious diseases.

    This thesis presents a sampling device based on electrostatic precipitation, for capture of bioaerosols, and designed for use at point-of-care settings. A multi-point- to-plane electrode configuration allows charging of aerosol particles and direct air- to-liquid capture within a miniaturized volume with potentential for concatenation with on-site detection methods. Performance of the device was evaluated, using non-biological aerosols, for geometric (inter-electrode distance), electrical (inter- electrode potential and corona current), and aerosol parameters (particle size and gas velocity). Moreover, four different collector designs were investigated for im- proved collection efficiency and other features suitable for point-of-care settings (e.g. easy sample extraction and minimized volume).

    The device was then validated, using bioaerosols, both in vitro and in vivo. In vitro validation was performed by capturing aerosolized influenza virus and analyz- ing the device collection efficiency. Lastly, prototype devices, designed for point- of-care, were validated in vivo with patients at the clinical setting. A pilot study was performed to capture exhaled pathogens from infected patients, with success- ful capture of exhaled bacteria.

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    KTH_Ladhani
  • 7.
    Ladhani, Laila
    et al.
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Pardon, Gaspard
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Meeuws, Hanne
    Janssen Diagnostics.
    van Wesenbeeck, Liesbeth
    Janssen Diagnostics.
    Schmidt, Kristiane
    Janssen Diagnostics.
    Stuyver, Lieven
    Janssen Diagnostics .
    van der Wijngaart, Wouter
    KTH, School of Electrical Engineering (EES), Micro and Nanosystems.
    Sampling and detection of airborne influenza virus towards point-of-care applications2017In: PLOS ONE, E-ISSN 1932-6203, PlosONEArticle in journal (Refereed)
    Abstract [en]

    Airborne transmission of the influenza virus contributes significantly to the spread of this infectious pathogen, particularly over large distances when carried by aerosol droplets with long survival times. Efficient sampling of virus-loaded aerosol in combination with a low limit of detection of the collected virus could enable rapid and early detection of airborne influenza virus at the point-of-care setting. Here, we demonstrate a successful sampling and detection of airborne influenza virus using a system specifically developed for such applications. Our system consists of a custom-made electrostatic precipitation (ESP)-based bioaerosol sampler that is coupled with downstream quantitative polymerase chain reaction (qPCR) analysis. Aerosolized viruses are sampled directly into a miniaturized collector with liquid volume of 150 μL, which constitutes a simple and direct interface with subsequent biological assays. This approach reduces sample dilution by at least one order of magnitude when compared to other liquid-based aerosol bio-samplers. Performance of our ESP-based sampler was evaluated using influenza virus-loaded sub-micron aerosols generated from both cultured and clinical samples. Despite the miniaturized collection volume, we demonstrate a collection efficiency of at least 10% and sensitive detection of a minimum of 3721 RNA copies. Furthermore, we show that an improved extraction protocol can allow viral recovery of down to 303 RNA copies and a maximum sampler collection efficiency of 47%. A device with such a performance would reduce sampling times dramatically, from a few hours with current sampling methods down to a couple of minutes with our ESP-based bioaerosol sampler.

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  • 8.
    Lindmark, Manfred
    Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF). Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Optimization of quality assured dataflow from biosensors: Time series analysis of plankton respiration by oxygen optode2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Data analysis can be a time consuming part of an experimental method, especially when the method is used frequently and large amounts of data are produced each time. In this study, an application software was developed to improve work flow and data management for respiration rate measurements using an optical oxygen sensor. The application was used to analyze data files from the oxygen sensor without the need to manually enter and analyze the data in a spreadsheet application. The software was written in the Python programming language and utilized available scientific computing packages as well as a graphical user interface framework to provide user friendly access to all functions. Any number of files with experimental data were imported into the program and a linear regression analysis was done for each file and viewed to verify the quality of the data. Tables and summarizing graphs were used to display the key information and statistical results. The final results were exported for use in other applications. Data processing that used to take an hour to complete was done with the new application in five to ten minutes and the risk of introducing human errors in the data was simultaneously reduced. User tests indicated that learning the basics of the program was easy. This study shows the usefulness of a bioinformatics approach and the tools provided by Python and its related software to solve problems that arise with managing large volumes of numerical data.

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    Lindmark2015SensorDataFlow
  • 9.
    Lundstedt, Erik Torbjörn
    et al.
    AcureOmics AB.
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gabrielsson, Jon Robert
    AcureOmics AB.
    Ekström, Gunilla
    Anamar AB.
    Metabolic profiles2012Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    The invention relates to the use of endogenous metabolites to produce a metabolic profile of a disorder or disease in a subject, e.g. an autoimmune disease, in particular rheumatoid arthritis, and the analysis of such metabolic profiles in order to find disturbances in such profiles in a subject which are caused by or correlated with the said diseases or disorders. Such disturbances can be normalised by treatment of the subject with specified compounds, particularly N-(2-chloro-3,4-dimethoxybenzylideneamino)guanidine or an aminoguanidine.

  • 10.
    Narmack, Samuel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Functionalization and Evaluation of Nanoparticle Probes for the Development of a 14-Plex Diagnostic assay2021Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This work was a collaboration between Aplex Bio AB and Scilifelab with the aim of developing a molecular assay capable of detecting and discriminating between 14 different pathogenic targets. There are 4 chapters with focus on different goals. In chapter one a method of evaluating emissions of fluorescent nanoparticle clusters was developed. The first approach of evaluating nanoparticle emissions was to utilize click chemistry to bind nanoparticles to macroscale structures of amplified DNA targets. The second evaluated approach was the formation of aggregated complexes of nanoparticles and amplified DNA targets. The second chapter of the thesis used azide functionalized nanoparticles supplied by Aplex Bio AB to utilize azide groups as crosslinkers and use them to functionalize the nanoparticles with DBCO oligos. A hybridization-based method was then developed to quantify relative oligo densities on the nanoparticles, enabling reproducible oligo functionalization of nanoparticles, producing nanoparticle probes that can bind to DNA. The final task of chapter 2 was evaluating the binding efficiency and specificity of the developed nanoparticle probes. The third chapter of the thesis evaluated amplification of synthetic ssDNA sequences corresponding to genetic markers of 14 pathogenic targets using RCA. The goal was to confirm specificity of chosen padlock probes and corresponding synthetic targets for each pathogen. Specific amplification of each target was a prerequisite to enable detecting and discriminating between the 14 pathogenic targets. In chapter 4 the goal was to develop a cost-effective method of oligo functionalization for nanoparticles. This chapter evaluated two main approaches of using DBCO-NHS-ester reagents to perform DBCO modification of amine-oligos. The realization of this work would develop an assay that has the potential to impact the field of diagnostics on a global scale. When fully developed, the molecular assay can be modified to detect any RNA/DNA targets which enables numerous applications, making the assay a competitive diagnostic tool which can be implemented in existing microscopy systems.

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  • 11.
    Nordesjö, Olle
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Pontén, Victor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Herman, Stephanie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ås, Joel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Jamal, Sabri
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Nyberg, Alona
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Ett sannolikhetsbaserat kvalitetsmått förbättrar klassificeringen av oförväntade sekvenser i in situ sekvensering2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In situ sequencing is a method that can be used to localize differential expression of mRNA directly in tissue sections, something that can give valuable insights to many statest of disease. Today, many of the registered sequences from in situ sequencing are lost due to a conservative quality measure used to filter out incorrect sequencing reads. There is room for improvement in the performance of the current method for base calling since the technology is in an early stage of development. We have performed exploratory data analysis to investigate occurrence of systematic errors, and corrected for these by using various statistical methods. The primary methods that have been investigated are the following:

    I) Correction of emission spectra overlap resulting in spillover between channels.

    II) A probability-based interpretation of intensity data, resulting in a novel quality measure and an alternative classifier based on supervised learning.

    III) Analysis of occurrence of cycle dependent effects, e.g. incomplete dehybridization of fluorescent probes.

    We suggest the following:

    • Implementation and evaluation of the probability-based quality measure
    • Development and implementation of the proposed classifier
    • Additional experiments to investigate the possible occurrence of incomplete dehybridization
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    Ett_sannolikhetsbaserat_kvalitetsmått_förbättrar_klassificeringen_av_oförväntade_sekvenser_i_in_situ_sekvensering
  • 12.
    Oresic, Matej
    Örebro University, School of Medical Sciences. Systems Biology and Bioinformatics, VTT Technical Research Centre of Finland, Espoo, Finland.
    Obesity and psychotic disorders: uncovering common mechanisms through metabolomics2012In: Disease Models and Mechanisms, ISSN 1754-8403, E-ISSN 1754-8411, Vol. 5, no 5, p. 614-620Article in journal (Refereed)
    Abstract [en]

    Primary obesity and psychotic disorders are similar with respect to the associated changes in energy balance and co-morbidities, including metabolic syndrome. Such similarities do not necessarily demonstrate causal links, but instead suggest that specific causes of and metabolic disturbances associated with obesity play a pathogenic role in the development of co-morbid disorders, potentially even before obesity develops. Metabolomics - the systematic study of metabolites, which are small molecules generated by the process of metabolism - has been important in elucidating the pathways underlying obesity-associated co-morbidities. This review covers how recent metabolomic studies have advanced biomarker discovery and the elucidation of mechanisms underlying obesity and its co-morbidities, with a specific focus on metabolic syndrome and psychotic disorders. The importance of identifying metabolic markers of disease-associated intermediate phenotypes - traits modulated but not encoded by the DNA sequence - is emphasized. Such markers would be applicable as diagnostic tools in a personalized healthcare setting and might also open up novel therapeutic avenues.

  • 13.
    Pechsiri, Joseph Santhi
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Water and Environmental Engineering.
    Thomas, Jean-Baptiste
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Water and Environmental Engineering.
    El Bahraoui, Naoufel
    Mines ParisTech, Ctr Energy Efficiency & Syst, 60 Bd St Michel, F-75272 Paris, France.;Setec Energie Environm, 42-52 Quai Rapee, F-75012 Paris, France..
    Acien Fernandez, Francisco Gabriel
    Univ Almeria, Dept Chem Engn, Canda San Urbano S-N, Almeria 04120, Spain..
    Chaouki, Jamal
    Polytech Montreal, 2500 Chem Polytech, Montreal, PQ H3T 1J4, Canada..
    Chidami, Saad
    Polytech Montreal, 2500 Chem Polytech, Montreal, PQ H3T 1J4, Canada..
    Tinoco, Rodrigo Rivera
    Mines ParisTech, Ctr Energy Efficiency & Syst, 60 Bd St Michel, F-75272 Paris, France..
    Pena Martin, Jose
    Univ Almeria, Dept Chem Engn, Canda San Urbano S-N, Almeria 04120, Spain..
    Gomez, Cintia
    Univ Almeria, Dept Chem Engn, Canda San Urbano S-N, Almeria 04120, Spain..
    Combe, Michel
    Setec Energie Environm, 42-52 Quai Rapee, F-75012 Paris, France..
    Gröndahl, Fredrik
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Water and Environmental Engineering.
    Comparative life cycle assessment of conventional and novel microalgae production systems and environmental impact mitigation in urban-industrial symbiosis2023In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 854, article id 158445Article in journal (Refereed)
    Abstract [en]

    The versatility of microalgae biomass as candidates for various products and bioremediation needs motivates interests towards design and implementation of novel microalgae bioreactors. Conventional open-reactors are reliant on large quantities of sunlight and space while yields are constrained by outdoor environment conditions. Conversely, closed-reactor systems like bubble columns reduces these constrains on microalgae growth while occupying far less space at the expense of high energy demands, notably from lighting systems. A novel patented closed reactor design has recently been proposed that improves the bubble column concept with an efficient and effective lighting system. The present study uses Life Cycle Assessment approach to compare the environmental performance of conventional reactors and the proposed internally luminated novel closed reactor design, expressing impacts per kg biostimulant for the Scenedesmus almeriensis harvest from such units. All performance data was collected from a pilot facility in Almeria, Spain. Urban-industrial symbiosis scenarios are also portrayed in the study using wastewater and incinerator flue gas. Results show that under synthetic nutrient and carbon inputs in Spanish pilot operations, the cumulative energy demand for the novel photobioreactors is similar to conventional vertically-stacked horizon bioreactors but are substantially more demanding than conventional open reactors. However, when leveraging renewable energy sources and the photosynthesis process to consume wastestreams in urban-industrial symbiosis scenarios, the novel photobioreactor was able to achieve up to 80 % improvements in several impact categories e.g. eutrophication and climate change. Impact mitigation credits per kg dwt biomass across all energy scenarios in symbiosis amount to asymptotic to 1.8 kg CO(2)eq and asymptotic to 0.09 kg PO4 eq. This highlights that such closed and internally illuminated photobioreactors can be competitive with conventional reactors, and have potential to harness photosynthesis to reduce environmental burdens in an urban-industrial symbiosis setting. Possible economies of scale and the associated potential gains in efficiencies are further discussed.

  • 14.
    Periyannan Rajeswari, Prem Kumar
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Soderberg, Lovisa M
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Andersson Svahn, Helene
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Jönsson, Håkan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Color-coded bead based readout from droplet PCR for the detection of pathogen biomarkersManuscript (preprint) (Other academic)
    Abstract [en]

    We present a workflow using fluorescent color-coded Luminex beads to detect the

    outcome of droplet PCR assay. The assay was performed to detect three important

    poultry pathogens: avian influenza, infectious laryngotracheitis virus and

    campylobacter. Droplet-based TaqMan PCR has been commonly used for detection

    of rare and significant biomarkers in clinical samples. However, the spectral overlap

    of fluorescent TaqMan probes limits the detection to 5 different targets in a single

    assay. The color codes of the Luminex detection beads allowed accurate classification

    of the different bead sets used in this assay concurrently. The target-specific capture

    probes coupled to distinct bead sets enabled capture and detection of target DNA in

    the droplet. The capture assay detected target DNA of all three poultry pathogens with

    high specificity, from samples with average target concentration of 1 template per

    droplet. This workflow demonstrates that the detection panel of droplet PCR assay

    can be increased to potentially detect multiple targets in a sample by utilizing the

    scalability offered by the color-coded detection beads.

  • 15.
    Rivas, Lourdes
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Reuterswärd, Philippa
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Rasti, Reza
    Herrmann, Björn
    Mårtensson, Andreas
    Alfvén, Tobias
    Gantelius, Jesper
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Svahn Andersson, Helene
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    A vertical flow paper-microarray assay with isothermal DNA amplification for detection of Neisseria meningitidis2018In: Talanta: The International Journal of Pure and Applied Analytical Chemistry, ISSN 0039-9140, E-ISSN 1873-3573, Vol. 183, p. 192-200Article in journal (Refereed)
    Abstract [en]

    Paper-based biosensors offer a promising technology to be used at the point of care, enabled by good performance, convenience and low-cost. In this article, we describe a colorimetric vertical-flow DNA microarray (DNA-VFM) that takes advantage of the screening capability of DNA microarrays in a paper format together with isothermal amplification by means of Recombinase Polymerase Amplification (RPA). Different assay parameters such as hybridization buffer, flow rate, printing buffer and capture probe concentration were optimized. A limit of detection (LOD) of 4.4 nM was achieved as determined by tabletop scanning. The DNA-VFM was applied as a proof of concept for detection of Neisseria meningitidis, a primary cause of bacterial meningitis. The LOD was determined to be between 38 and 2.1Å~106 copies/VFM assay, depending on the choice of DNA capture probes. The presented approach provides multiplex capabilities of DNA microarrays in a paper-based format for future point-of-care applications.

  • 16.
    Svahn, Leo
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Bestämning och jämförelse av helblodspåsars leukocyt-innehåll: vid tre olika vilotider efter blodgivning, analyserat med flödescytometri2021Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    During blood donation, blood donors donate blood voluntarily. The blood can then be used in healthcare for, for example, blood transfusions, which requires blood products compatible with the patient. The presence of leukocytes in blood products increases the risk of febrile transfusion reactions in transfused patients. Therefore, leukocyte-reduction in blood products is necessary during production. Each blood center must perform quality control on produced blood products.

    With the analysis B-leukocyte particle concentration (LPK), the total number of leukocytes in whole blood can be calculated. Flow cytometry is a method that can analyze the optical and fluorescent properties of, for example, cells in a suspension, which can be used to quantify cell numbers. The BD Leucocount™-Kit (BD Biosciences) is intended for flow cytometric analysis of the number of leukocytes remaining in leukocyte-reduced blood products.

    When producing blood products, the whole blood bag should rest at room temperature for at least three hours after the donation. In Falun, either a day program is used where production takes place on the same day as the blood was donated, or an overnight program where production takes place the next day. Samples from 505 controlled erythrocyte units, collected in Falun, have shown a difference in leukocyte concentration depending on the program used.

    The reason why the leukocyte content of erythrocyte units differs is not known. The purpose of this study is therefore to investigate whether the resting period has any effect on the leukocyte concentration in whole blood bags.

    The LPK varied between the whole blood bags. An increasing leukocyte count was observed over time in most of the whole blood bags. However, hypothesis testing did not show statistical significance.

    The hypothesis that leukocyte counts increase goes against basic hematology. Based on the results of this study, the hypothesis cannot be proven. Further studies should be conducted.

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    Leo Svahn BMA-examensuppsats
  • 17. Sánchez Martín, Darío
    et al.
    Strømme, Maria
    Zardán Gómez de la Torre, Teresa
    Sensitive multiplex visual detection of DNA targets using colored polystyrene nanoparticles and circle-to-circle amplification.Manuscript (preprint) (Other academic)
    Abstract [en]

    Antibiotic resistance poses a significant threat to public health, acknowledged by the World Health Organization as a foremost global concern. The detection of pathogens and the determination of antibiotic resistance are critical for effective treatment. In a previous study, we introduced a DNA detection method capable of producing visible aggregates from DNA-amplified products and functionalized magnetic nanoparticles. This current research focuses on optimizing key parameters of the amplification protocol to develop a point-of-care detection method. Circle-to-circle amplification has been employed to enhance sensitivity. Through systematic adjustments to sample volumes, reaction times, padlock probe design and length, polymerase selection, and nanoparticle types, we achieved a visual limit of detection of 100 zeptomoles for a synthetic DNA target. This represents to a 10-fold improvement over our previously reported LOD.

    Noteworthy is the utilization of phi29-XT, a novel phi29 DNA polymerase mutant, for PLP amplification and diagnostic assay development. Additionally, we successfully demonstrated multiplexed detection of two DNA targets within a single sample, employing colored polystyrene nanoparticles. Each target was identified by a distinct nanoparticle color (red or blue), achieving an LOD of 500 zeptomoles.

    Lastly, we explored a method for end-point analysis of multiplexed samples using smartphone camera images and image analysis with ImageJ, albeit in an early development state. These advancements underscore the potential for our optimized methods to contribute significantly to the field of antibiotic resistance detection and diagnosis, paving the way for more effective and tailored treatments.

  • 18.
    Söderberg, Lovisa
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fonseca, Pedro
    Karolinska Intitutet, Department of Oncology and Pathology.
    Panaretakis, Theocharis
    Karolinska Intitutet, Department of Oncology and Pathology.
    Jönsson, Håkan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Detection of single exosomes in microfluidic droplets by RT-PCR amplification of 18S RNA contentManuscript (preprint) (Other academic)
    Abstract [en]

    We present a workflow for reverse transcription-PCR (RT-PCR) in microfluidic droplets to identify exosomes based on their RNA content. Available techniques for exosome detection have been limited to size or surface markers which limit their diagnostic capabilities. Exosome detection based on RNA content could be developed to be used as a diagnostic, prognostic or predictive tool for cancer based on specific RNA biomarkers in liquid biopsies. In this manuscript we demonstrate a high throughput method for the amplification of exosome derived 18S RNA in microfluidic droplets. Automated image analysis using open source software was applied to distinguish and count PCR-positive droplets with fluorescent intensity over a set threshold. We benchmark our workflow against picoliter scale RT-PCR on serially diluted exosome samples and demonstrate the ability of the droplet based workflow to correctly rank exosome samples based on exosome concentration.  This represents a key step towards a quantitative analysis of exosomal RNA content and the sorting of single exosomes by their RNA content.

  • 19. Zambrano, Jesús
    et al.
    Krustok, Ivo
    Nehrenheim, Emma
    Carlsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    A simple model for algae-bacteria interaction in photo-bioreactors2016In: Algal Research, ISSN 2211-9264, Vol. 19, p. 155-161Article in journal (Refereed)
    Abstract [en]

    This work presents a simple model to describe the consortia of algae-bacteria in a photo-bioreactor. The model is inspired by the Activated Sludge Model (ASM) structure, which includes different process rates and stoichiometric parameters. The model comprises two main biomass populations (algae and bacteria), two dissolved substrates (ammonium and nitrate) and two dissolved gases (oxygen and carbon dioxide) in the reactor. The model was calibrated with data from batch experiments performed in two lab-scale photo-bioreactors. A sensitivity analysis was done to identify the parameters to be considered for the model calibration. Results indicate that the maximum algae and bacteria growth rate, bacteria growth yield and half-saturation constant for carbon were the most sensitive parameters. Moreover, the comparison between the experiments and the model shows good agreement in terms of predicting the ammonium, nitrate and oxygen concentrations in the photobioreactor.

  • 20.
    Öberg Månsson, Ingrid
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Electroanalytical devices with fluidic control using textile materials and methods2020Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis, written by Ingrid Öberg Månsson at KTH Royal Institute of Technology and entitled “Electroanalytical devices with fluidic control using textile materials and methods”, presents experimental studies on the development of textile based electronic devices and biosensors. One of the reasons why this is of interest is the growing demand for integrated smart products for wearable health monitoring or energy harvesting. To enable such products, new interdisciplinary fields arise combining traditional textile technology and electronics.

    Textile based devices have garnered much interest in recent years due to their innate ability to incorporate function directly into, for example, clothing or bandages by textile processes such as weaving, knitting or stitching. However, many modifications of yarns required for such applications are not available on an industrial scale. The major objective of this work has been to study how to achieve the performance necessary to create electronic textile devices by either coating yarns with conductive material or using commercially available conductive yarns that are functionalized to create sensing elements.

    Further, liquid transport within textile materials has been studied to be able to control the contact area between electrolyte and electrodes in electrochemical devices such as sensors and transistors. Yarns with specially designed cross-sections, traditionally used in sportswear to wick sweat away from the body and enhance evaporation, was used to transport electrolyte liquids to come in contact with yarn electrodes. The defined area of the junction where the fluidic yarn meets the conductive yarn was shown to increase stability of the measurements and the reproducibility between devices.

    The results presented in the two publications of this thesis as well as additional results presented in the thesis itself show the promising potential of using textile materials to integrate electronic and electrochemical functionality in our everyday life. This is shown by using basic textile materials and processing techniques to fabricate complex devices for various application areas such as sensors and diagnostics as well as electrical and energy harvesting components.

    Download full text (pdf)
    Lic thesis Ingrid Öberg Månsson
  • 21.
    Öberg Månsson, Ingrid
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Piper, Andrew
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Hamedi, Mahiar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Weaving Off-The-Shelf Yarns into Textile Micro Total Analysis Systems (μTAS)2020In: Macromolecular Bioscience, ISSN 1616-5187, E-ISSN 1616-5195, article id 2000150Article in journal (Refereed)
    Abstract [en]

    Textile based biosensors have garnered much interest in recent years. Devices woven out of yarns have the ability to be incorporated into clothing and bandages. Most woven devices reported in the literature require yarns that are not available on an industrial scale or that require modifications which are not possible in large scale manufacturing. In this work, commercially produced yarns are taken without any modification or cleaning, and developed woven textile diagnostic devices out of them. The yarn properties that are important to their function within the device have been characterised and discussed. The wicking ability and analyte retention of Coolmax yarns, developed to wick sweat in mass produced sportswear, are determined. The electrochemistry and functionalizability of Au coated multifilament yarns are investigated with no cleaning or treatment and are found to have as good a thiolate self‐assembled monolayer (SAM) coverage as cleaned Au disk electrodes. The feasibility of using these yarns is established off the shelf, with no cleaning, to make woven capillary force driven microfluidic devices and three electrode sensing devices. A proof of principle three electrode system capable of detecting clinically relevant concentrations of glucose in human sweat is reported.

    Download full text (pdf)
    mabi.202000150
1 - 21 of 21
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