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  • 1.
    Anlind, Nils
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Eriksson, Alexandra
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Gromova, Arina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Hong, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ljungström, Sara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Markstedt, Olof
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Marknadsanalys av proteinstandarder för kvantitativ masspektrometri2015Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    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.

    Fulltekst (pdf)
    fulltext
  • 2.
    Bagge, Joakim
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Hedman, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Smedsrud, Sabina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Svärdström, Cornelia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Söderberg, Elisabeth
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Valdés, Fernando
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Utveckling av metodik för påvisning och typning av Listeria i livsmedelskedjan2017Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Fulltekst (pdf)
    fulltext
  • 3.
    Crialesi-Esposito, Marco
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Teknisk mekanik.
    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 field2022Inngår i: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 150, artikkel-id 103891Artikkel i tidsskrift (Fagfellevurdert)
    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, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap, Nanobioteknologi.
    Isotachophoretically-driven rolling circle amplification unit for nucleic acid detectionManuskript (preprint) (Annet vitenskapelig)
  • 5.
    Kostines, Reneh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Validation of anti-cytokeratin antibodies used in rapid cancer diagnostics by isoelectric focusing and QCM technology2021Independent thesis Advanced level (professional degree), 20 poäng / 30 hpOppgave
    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.

    Fulltekst (pdf)
    fulltext
  • 6.
    Ladhani, Laila
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Intelligenta system, Mikro- och nanosystemteknik.
    An electrostatic sampling device for point-of-care detection of bioaerosols2018Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

    Fulltekst (pdf)
    KTH_Ladhani
  • 7.
    Ladhani, Laila
    et al.
    KTH, Skolan för elektro- och systemteknik (EES), Mikro- och nanosystemteknik.
    Pardon, Gaspard
    KTH, Skolan för elektro- och systemteknik (EES), Mikro- och nanosystemteknik.
    Meeuws, Hanne
    Janssen Diagnostics.
    van Wesenbeeck, Liesbeth
    Janssen Diagnostics.
    Schmidt, Kristiane
    Janssen Diagnostics.
    Stuyver, Lieven
    Janssen Diagnostics .
    van der Wijngaart, Wouter
    KTH, Skolan för elektro- och systemteknik (EES), Mikro- och nanosystemteknik.
    Sampling and detection of airborne influenza virus towards point-of-care applications2017Inngår i: PLOS ONE, E-ISSN 1932-6203, PlosONEArtikkel i tidsskrift (Fagfellevurdert)
    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.

    Fulltekst (pdf)
    fulltext
  • 8.
    Lindmark, Manfred
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.
    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 poäng / 30 hpOppgave
    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.

    Fulltekst (pdf)
    Lindmark2015SensorDataFlow
  • 9.
    Lundstedt, Erik Torbjörn
    et al.
    AcureOmics AB.
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Gabrielsson, Jon Robert
    AcureOmics AB.
    Ekström, Gunilla
    Anamar AB.
    Metabolic profiles2012Patent (Annet (populærvitenskap, debatt, mm))
    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, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi.
    Functionalization and Evaluation of Nanoparticle Probes for the Development of a 14-Plex Diagnostic assay2021Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [sv]

    Detta projekt var ett samarbete mellan Aplex Bio AB och Scilifelab. Projektets mål var att utveckla en molekylär diagnostisk panel med förmågan att detektera och diskriminera mellan 14 olika typer av patogener. Projektet innehåller 4 kapitel med fokus på olika mål. I första kapitlet utvecklades en metod för att karakterisera emissioner av fluorescerande nanopartikel kluster. Den första utvärderade metoden utnyttjade klick-kemi för att binda nanopartiklarna till makrostrukturer uppbyggda av amplifierat DNA. Den andra utvärderade metoden skapade aggregerade komplex av nanopartiklar med amplifierat DNA för att utvärdera partiklarnas emissioner. I kapitel 2 av projektet användes azid-funktionaliserade nanopartiklar levererade av Aplex Bio AB för att tvärbinda DBCO modifierade oligonukleotider. Sedan utvecklades en hybridiserings baserad metod för att kvantifiera relativa mängden oligonukleotider på partiklarna. Denna metod användes för att reproducerbart funktionalisera partiklar och utveckla nanopartikel-sonder som kan binda till DNA genom hybridisering. I kapitel 2 utvärderades även hur effektivt och specifikt de utvecklade nanopartikel-sonderna hybridiserar till DNA. I kapitel 3 utvärderades amplifiering av syntetiska ssDNA sekvenser valda från genetiska markörer av 14 patogener, DNA amplifierades med metoden RCA. Målet var att utvärdera specificiteten av amplifieringen. Specifik amplifiering av varje DNA sekvens i panelen var en förutsättning för att möjliggöra detektion och diskriminering av alla patogener i panelen. I kapitel 4 var målet att utveckla en kostnadseffektiv metod för att funktionalisera nanopartiklar med oligonukleotid sekvenser. För att göra detta användes DBCO-NHS-ester reagens och amin-modifierade oligonukleotider. Förverkligande av detta projekt skulle skapa en diagnostisk panel med potentialen att påverka det diagnostiska fältet på en global skala. När detta projekt är fullt utvecklat kan panelen modifieras för detektion av önskade DNA/RNA sekvenser vilket möjliggör ett mångfalt av applikationer, detta skulle göra panelen konkurrerande med dagens diagnostiska metoder då den kan användas i existerande mikroskopiuppsättningar.

    Fulltekst (pdf)
    fulltext
  • 11.
    Nordesjö, Olle
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Pontén, Victor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Herman, Stephanie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ås, Joel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Jamal, Sabri
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nyberg, Alona
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ett sannolikhetsbaserat kvalitetsmått förbättrar klassificeringen av oförväntade sekvenser i in situ sekvensering2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    In situ sekvensering är en metod som kan användas för att lokalisera differentiellt uttryck av mRNA direkt i vävnadssnitt, vilket kan ge viktiga ledtrådar om många sjukdomstillstånd. Idag förloras många av sekvenserna från in situ sekvensering på grund av det kvalitetsmått man använder för att säkerställa att sekvenser är korrekta. Det finns troligtvis möjlighet att förbättra prestandan av den nuvarande base calling-metoden eftersom att metoden är i ett tidigt utvecklingsskede. Vi har genomfört explorativ dataanalys för att undersöka förekomst av systematiska fel och korrigerat för dessa med hjälp av statistiska metoder. Vi har framförallt undersökt tre metoder för att korrigera för systematiska fel:

    I) Korrektion av överblödning som sker på grund avöverlappande emissionsspektra mellan fluorescenta prober.

    II) En sannolikhetsbaserad tolkningav intensitetsdata som resulterar i ett nytt kvalitetsmått och en alternativ klassificerare baseradpå övervakad inlärning.

    III) En utredning om förekomst av cykelberoende effekter, exempelvisofullständig dehybridisering av fluorescenta prober.

    Vi föreslår att man gör följande saker:

    • Implementerar och utvärderar det sannolikhetsbaserade kvalitetsmåttet
    • Utvecklar och implementerar den föreslagna klassificeraren
    • Genomför ytterligare experiment för att påvisa eller bestrida förekomst av ofullständigdehybridisering
    Fulltekst (pdf)
    Ett_sannolikhetsbaserat_kvalitetsmått_förbättrar_klassificeringen_av_oförväntade_sekvenser_i_in_situ_sekvensering
  • 12.
    Oresic, Matej
    Örebro universitet, Institutionen för medicinska vetenskaper. Systems Biology and Bioinformatics, VTT Technical Research Centre of Finland, Espoo, Finland.
    Obesity and psychotic disorders: uncovering common mechanisms through metabolomics2012Inngår i: Disease Models and Mechanisms, ISSN 1754-8403, E-ISSN 1754-8411, Vol. 5, nr 5, s. 614-620Artikkel i tidsskrift (Fagfellevurdert)
    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, Skolan för arkitektur och samhällsbyggnad (ABE), Hållbar utveckling, miljövetenskap och teknik, Vatten- och miljöteknik.
    Thomas, Jean-Baptiste
    KTH, Skolan för arkitektur och samhällsbyggnad (ABE), Hållbar utveckling, miljövetenskap och teknik, Vatten- och miljöteknik.
    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, Skolan för arkitektur och samhällsbyggnad (ABE), Hållbar utveckling, miljövetenskap och teknik, Vatten- och miljöteknik.
    Comparative life cycle assessment of conventional and novel microalgae production systems and environmental impact mitigation in urban-industrial symbiosis2023Inngår i: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 854, artikkel-id 158445Artikkel i tidsskrift (Fagfellevurdert)
    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, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Soderberg, Lovisa M
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Andersson Svahn, Helene
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Jönsson, Håkan
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Color-coded bead based readout from droplet PCR for the detection of pathogen biomarkersManuskript (preprint) (Annet vitenskapelig)
    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, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Reuterswärd, Philippa
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Rasti, Reza
    Herrmann, Björn
    Mårtensson, Andreas
    Alfvén, Tobias
    Gantelius, Jesper
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Svahn Andersson, Helene
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    A vertical flow paper-microarray assay with isothermal DNA amplification for detection of Neisseria meningitidis2018Inngår i: Talanta: The International Journal of Pure and Applied Analytical Chemistry, ISSN 0039-9140, E-ISSN 1873-3573, Vol. 183, s. 192-200Artikkel i tidsskrift (Fagfellevurdert)
    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
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Bestämning och jämförelse av helblodspåsars leukocyt-innehåll: vid tre olika vilotider efter blodgivning, analyserat med flödescytometri2021Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Vid blodgivning donerar blodgivare blod frivilligt. Blodet kan sedan användas inom sjukvården för exempelvis blodtransfusion, vilket kräver blodprodukter kompatibla med patienten. Förekomst av leukocyter i blodprodukter medför en ökad risk för febrila transfusionsreaktioner hos transfunderade patienter. Därför krävs det att vid framställning leukocytreducera blodprodukter och utföra kvalitetskontroll.

    Med analysen B-leukocytpartikelkoncentration (LPK) kan totalantalet leukocyter i helblod beräknas. Flödescytometri är en metod som kan analysera optiska och fluorescerande egenskaper hos exempelvis celler i en suspension, vilket kan användas för att kvantifiera cellantal. BD Leucocount™-Kit (BD Biosciences) är avsett för flödescytometrisk analys av antalet kvarvarande leukocyter i leukocytreducerade blodprodukter.

    Vid framställning av blodprodukter ska helblodspåsen vila vid rumstemperatur i minst 3 timmar efter blodgivning. I Falun används antingen ett dagsprogram där produktion sker samma dag som blodgivningen, eller ett övernattningsprogram där produktion sker dagen därpå. Prover från 505 kontrollerade erytrocytenheter, samlade i Falun, har påvisat en skillnad i leukocytkoncentration beroende på vilket program som använts.

    Anledningen till att erytrocytenheternas leukocytinnehåll skiljer sig är inte känt. Syftet med denna studie är därav att undersöka om vilotiden har någon effekt på leukocytkoncentrationen i helblodspåsar.

    LPK varierade mellan helblodspåsarna. Ett ökande leukocytantal observerades över tid i majoriteten av helblodspåsar, inklusive medelvärde. Däremot kunde inte hypotesprövning påvisa statistisk signifikans.

    Hypotesen om att leukocytantalet ökar över tid går emot grundläggande hematologi. Utifrån resultaten i denna studie kan inte hypotesen bevisas. Vidare studier bör genomföras. 

    Fulltekst (pdf)
    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.Manuskript (preprint) (Annet vitenskapelig)
    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, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, 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, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Detection of single exosomes in microfluidic droplets by RT-PCR amplification of 18S RNA contentManuskript (preprint) (Annet vitenskapelig)
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för systemteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Reglerteknik.
    A simple model for algae-bacteria interaction in photo-bioreactors2016Inngår i: Algal Research, ISSN 2211-9264, Vol. 19, s. 155-161Artikkel i tidsskrift (Fagfellevurdert)
    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, Skolan för kemi, bioteknologi och hälsa (CBH), Fiber- och polymerteknologi, Fiberteknologi.
    Electroanalytical devices with fluidic control using textile materials and methods2020Licentiatavhandling, med artikler (Annet vitenskapelig)
    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.

    Fulltekst (pdf)
    Lic thesis Ingrid Öberg Månsson
  • 21.
    Öberg Månsson, Ingrid
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Fiber- och polymerteknologi, Fiberteknologi.
    Piper, Andrew
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Fiber- och polymerteknologi, Fiberteknologi.
    Hamedi, Mahiar
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Fiber- och polymerteknologi, Fiberteknologi.
    Weaving Off-The-Shelf Yarns into Textile Micro Total Analysis Systems (μTAS)2020Inngår i: Macromolecular Bioscience, ISSN 1616-5187, E-ISSN 1616-5195, artikkel-id 2000150Artikkel i tidsskrift (Fagfellevurdert)
    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.

    Fulltekst (pdf)
    mabi.202000150
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