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  • 1. Abahazi, Emese
    et al.
    Satorhelyi, Peter
    Erdelyi, Balazs
    Vertessy, Beata G.
    Land, Henrik
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Paizs, Csaba
    Berglund, Per
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Poppe, Laszlo
    Covalently immobilized Trp60Cys mutant of omega‰-transaminase from Chromobacterium violaceum for kinetic resolution of racemic amines in batch and continuous-flow modes2018Ingår i: Biochemical engineering journal, ISSN 1369-703X, E-ISSN 1873-295X, Vol. 132, s. 270-278Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Covalent immobilization of an engineered omega-transaminase mutant Trp60Cys from Chromobacterium violaceum (CvTAW60C) was performed on bisepoxide-activated aminoalkyl resins. Activity of the various CvTAW60C preparations was evaluated in kinetic resolution of four racemic amines (rac-1a–d). The most active EA-G-CvTAW60C preparation (CvTAW60C attached to polymeric resin with ethylamine function activated with glycerol diglycidyl ether—EA-G) could perform the kinetic resolution of racemic 4-phenylbutan-2-amine (rac-1a) over 49% conversion up to 19 consecutive reaction cycles or in media containing up to 50% v/v DMSO as cosolvent in batch mode reactions. The immobilization process of CvTAW60C onto the EA-G resin filled in stainless steel bioreactors was also tested in flow-through mode. Kinetic resolution of three racemic amines containing aromatic moieties (rac-1a-c) was performed in continuous-flow mode resulting in easy-to-separate mixture of the corresponding ketone (2a–c) and the non-converted (R)-amine in high enantiopurity (ee(R)-1a-c ≥ 96%).

  • 2.
    Acevedo Gomez, Yasna
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik, Tillämpad elektrokemi.
    Lindbergh, Göran
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik, Tillämpad elektrokemi.
    Lagergren, Carina
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik, Tillämpad elektrokemi.
    Reformate from biogas used as fuel in a PEM fuel cell2013Ingår i: EFC 2013 - Proceedings of the 5th European Fuel Cell Piero Lunghi Conference, 2013, s. 163-164Konferensbidrag (Refereegranskat)
    Abstract [en]

    The performance of a PEM fuel cell can be easily degraded by introducing impurities in the fuel gas. Since reformate of biogas from olive mill wastes will contain at least one third of carbon dioxide, its influence was studied on a PtRu catalyst. A clean reformate gas for the anode (67% H2 and 33% CO2) without any traces of other compounds was used and electrochemical measurements showed that the performance of the fuel cell was hardly affected. However, diluting the hydrogen with higher amounts of CO2 will reduce the performance remarkably.

  • 3.
    Agaton, Charlotta
    et al.
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Falk, Ronny
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Uhlén, Mathias
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Hober, Sophia
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Selective enrichment of monospecific polyclonal antibodies for antibody-based proteomics efforts2004Ingår i: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1043, s. 33-40Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A high stringency protocol, suitable for systematic purification of polyclonal antibodies, is described. The procedure is designed to allow the generation of target protein-specific antibodies suitable for functional annotation of proteins. Antibodies were generated by immunization with recombinantly produced affinity-tagged target proteins. To obtain stringent recovery of the antibodies, a two-step affinity chromatography principle was devised to first deplete the affinity tag-specific antibodies followed by a second step for affinity capture of the target protein-specific antibodies. An analytical dot-blot array system was developed to analyze the cross-reactivity of the affinity-purified antibodies. The results suggest that the protocol can be used in a highly parallel and automated manner to generate mono-specific polyclonal antibodies for large-scale, antibody-based proteomics efforts, i.e. affinity proteomics.

  • 4.
    Agaton, Charlotta
    et al.
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Unneberg, Per
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Sievertzon, Maria
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Holmberg, Anders
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Ehn, Maria
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Larsson, Magnus
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Odeberg, Jacob
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Uhlén, Mathias
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Lundeberg, Joakim
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Gene expression analysis by signature pyrosequencing2002Ingår i: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 289, nr 1-2, s. 31-39Artikel i tidskrift (Refereegranskat)
    Abstract [en]

     We describe a novel method for transcript profiling based on high-throughput parallel sequencing of signature tags using a non-gel-based microtiter plate format. The method relies on the identification of cDNA clones by pyrosequencing of the region corresponding to the 3'-end of the mRNA preceding the poly(A) tail. Simultaneously, the method can be used for gene discovery, since tags corresponding to unknown genes can be further characterized by extended sequencing. The protocol was validated using a model system for human atherosclerosis. Two 3'-tagged cDNA libraries, representing macrophages and foam cells, which are key components in the development of atherosclerotic plaques, were constructed using a solid phase approach. The libraries were analyzed by pyrosequencing, giving on average 25 bases. As a control, conventional expressed sequence tag (EST) sequencing using slab gel electrophoresis was performed. Homology searches were used to identify the genes corresponding to each tag. Comparisons with EST sequencing showed identical, unique matches in the majority of cases when the pyrosignature was at least 18 bases. A visualization tool was developed to facilitate differential analysis using a virtual chip format. The analysis resulted in identification of genes with possible relevance for development of atherosclerosis. The use of the method for automated massive parallel signature sequencing is discussed.

  • 5.
    Agdur, Angelica
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap.
    Characterization of enzyme decomposing biological macromolecules from a fish pathogen2022Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Saprolegnia parasitica är en av de mest skadliga oomycetpatogenerna som orsakar många problem inom vattenbruket. Den påverkar vuxen fisk, fiskägg och ungfisk. För närvarande finns det ingen effektiv och miljösäker behandling mot S. parasitica, vilket understryker vikten av att utveckla ett nytt sätt att kontrollera patogenet. Toxicitetsbelastningen kan minskas genom att ha en mycket specifik behandling. Att uppnå detta skulle kräva en förståelse för de fysiologiska och molekylära vägarna som är involverade i patogenutvecklingen, infektionsprocessen och värdspecificiteten, för att hitta målproteiner. Majoriteten av Saprolegniales forskning har koncentrerats på utsöndrade proteaser och intracellulära effektorer, men rollen av kolhydrataktiva enzymer (CAZymes) i infektionen har försummats. Kitinaser är CAZymer och mer specifikt hydrolyserar glykosidhydrolasenzymer beta-1,4-bindningar i kitin. Kitin är en strukturell polysackarid som finns i exoskelettet hos kräftdjur och epitelceller hos fiskfjäll. S. parasitica kan etablera infektionen genom användning av kitinaser. Målet med projektet är att hitta fler kitinaser som för närvarande är okarakteriserade proteiner av S. parasitica. Bioinformatiska tillvägagångssätt används för att förutsäga potentiella kitinaser, och ytterligare experimentell funktionell karakterisering av förutsagt protein. 

    Åtta okarakteriserade förutsagda proteiner av S. parasitica erhölls från sekvensanalys av kitinaser från familjen GH18 med Enzyme Commission-numret: 3.2.1.14 för att vara potentiella kitinaser. Av dessa åtta proteinsekvenser är två SPRG_10284 och SPRG_09577 de mest lovande. Dessa kan testas ytterligare experimentellt och båda förutspås vara lösliga proteiner. SPRG_10284 har framgångsrikt uttryckts i Escherichia coli stammar Rosetta 2 och BL21(DE3). Protokollen för proteinuttryck, extraktion och rening måste dock standardiseras för att erhålla en stor mängd lösligt protein.

  • 6. Agerberth, B
    et al.
    Gunne, H
    Odeberg, Jacob
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Kogner, P
    Boman, H G
    Gudmundsson, G H
    FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis.1995Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 92, nr 1, s. 195-9Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    PR-39, a proline/arginine-rich peptide antibiotic, has been purified from pig intestine and later shown to originate in the bone marrow. Intending to isolate a clone for a human counterpart to PR-39, we synthesized a PCR probe derived from the PR-39 gene. However, when this probe was used to screen a human bone marrow cDNA library, eight clones were obtained with information for another putative human peptide antibiotic, designated FALL-39 after the first four residues. FALL-39 is a 39-residue peptide lacking cysteine and tryptophan. All human peptide antibiotics previously isolated (or predicted) belong to the defensin family and contain three disulfide bridges. The clone for prepro-FALL-39 encodes a cathelin-like precursor protein with 170 amino acid residues. We have postulated a dibasic processing site for the mature FALL-39 and chemically synthesized the putative peptide. In basal medium E, synthetic FALL-39 was highly active against Escherichia coli and Bacillus megaterium. Residues 13-34 in FALL-39 can be predicted to form a perfect amphiphatic helix, and CD spectra showed that medium E induced 30% helix formation in FALL-39. RNA blot analyses disclosed that the gene for FALL-39 is expressed mainly in human bone marrow and testis.

  • 7.
    Ahmadian, Afshin
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    AnderssonSvahn, Helene
    KTH, Skolan för bioteknologi (BIO), Nanobioteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Massively parallel sequencing platforms using lab on a chip technologies2011Ingår i: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 11, nr 16, s. 2653-2655Artikel i tidskrift (Refereegranskat)
  • 8.
    Ahmed, Ajaj
    et al.
    Department of Microbiology, M.G.S. University, Bikaner, India.
    Dabi, Narendra Kumar
    Department of Microbiology, M.G.S. University, Bikaner, India.
    Verma, Swati
    Department of Microbiology, M.G.S. University, Bikaner, India.
    Gehlot, Praveen
    Department of Botany, J.N.V. University, Jodhpur, India.
    Purohit, Praveen
    Department of Chemistry, Engineering College, Bikaner, 334001, India.
    Kumar, Rajender
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Glykovetenskap.
    Meghwanshi, Gautam Kumar
    Department of Microbiology, M.G.S. University, Bikaner, India.
    Evaluation of Thar Desert bacterial lipases for catalytic efficiencies and biodiesel production potentials2023Ingår i: Biologia, ISSN 0006-3088, E-ISSN 1336-9563, Vol. 78, nr 4, s. 1187-1197Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The present work describes the screening of thermotolerant bacteria isolated from Thar Desert environmental samples for lipase activity and their catalytic efficiencies, such as tolerance to extreme pHs, temperatures, and organic solvents, and efficiency to synthesize biodiesel from waste cooking oils. The selected lipases were thermos-alkaliphilic in nature showing good activity at higher temperatures and in the alkaline pH range with optimal activity at 45 °C and pH 8 or 9. The lipases efficiently converted oils to biodiesel (fatty acid methyl ester), giving up to 78% conversion under specific reaction conditions. The enzyme (lipase) mediated biodiesel production will soon offer an eco-friendly and sustainable energy source for automobiles and industrial applications. The thermos-alkaliphilic properties of these lipases along with their efficiency to produce fatty acid methyl ester from waste cooking oil and methanol as well as other prospective applications, make them potential candidates for biodiesel production and other prospective applications such as the synthesis of flavor and fragrance esters and remediation of various environmental pollutants.

  • 9.
    Aid, Graham
    et al.
    KTH, Skolan för industriell teknik och management (ITM), Industriell ekologi.
    Brandt, Nils
    KTH, Skolan för industriell teknik och management (ITM), Industriell ekologi.
    Bygg- och rivningsavfall: Action Research vid KTH2010Ingår i: Återvinnare För Industrin / [ed] Kjell-Arne Larsson, Stockholm: Rekord Media och Produktion AB , 2010Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 10.
    AI-Tamimi, Lejla
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap.
    Structural features underlying antigen presentation by the non-classical MHC class Ib molecule Qa-1b2022Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Blockering av NKG2A receptorn på NK - och CD8+ T celler med en anti-NKG2A antikropp, medför en aktivering av cytolytisk aktivitet, och är en lovande immunkontrollpunkt i immunterapi mot cancer. Nyligen har en TCR-liknande antikropp, EXX1, som binder till liganden för NKG2A receptorn, Qa-1b - en icke-klassisk MHC klass Ib molekyl i möss -studerats i tumör modeller in vitro. Resultat påvisar att den TCR-liknande antikroppen endast binder till Qa-1b om denna presenterar Qdm peptiden på sin yta, som erhålls från ledarsekvensen hos klassika MHC klass Ia H-2D. Detta väcker frågor kring strukturella faktorer som möjliggör antigenpresentation på Qa-1b och de exakta molekylära parametrarna som ger upphov till antikroppens specificitet. Syftet med denna studie var att bestämma och jämföra kristallstrukturerna för Qa-1b med Qdm (AMAPRTLLL) samt peptid 001 (AQAERTPEL). Den tunga peptidkedjan hos Qa-1b och beta-2-mikroglobulin producerades rekombinant i E.coli, återveckades med respektive peptid, renades med kromatografimetoder och slutligen kristalliserades genom ångdiffusionsmetoden med hängande droppar. Värmestabilitet hos MHC/peptid undersöktes med nano differential scanning fluorimetry, där Qa-1b /001 uppvisade bättre stabilitet. Kristaller för Qa-1b /Qdm och Qa-1b /001 kunde erhållas med 8% PEG4000, 10mM NiCl2, 0.1M natriumacetat vid pH 5.7, respektive 10% PEG4000, 10 mM NiCl2 och 0.1 M natriumacetat vid pH 6.0. Strukturen för Qa-1b /001 kunde bestämmas vid 2.43 Å med molekylär ersättning. Med anledning av negativt laddade sidogrupper i peptid 001 som har en ytlig konformation i bindningsfickan, kan avsaknaden av bindning till EXX1 förklaras av en skillnad i elektrostatiska interaktioner mellan Qdm och peptid 001. Ytterligare strukturella karakteriseringar av Qa-1b komplexen med antikroppen är av fortsatt stort intresse.

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  • 11.
    Akan, Pelin
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Alexeyenko, Andrey
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Costea, Paul Igor
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Hedberg, Lilia
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Werne Solnestam, Beata
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lundin, Sverker
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Hallman, Jimmie
    Lundberg, Emma
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Proteomik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lundeberg, Joakim
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines2012Ingår i: Genome Medicine, ISSN 1756-994X, E-ISSN 1756-994X, Vol. 4, s. 86-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We here present a comparative genome, transcriptome and functional network analysis of three human cancer cell lines (A431, U251MG and U2OS), and investigate their relation to protein expression. Gene copy numbers significantly influenced corresponding transcript levels; their effect on protein levels was less pronounced. We focused on genes with altered mRNA and/or protein levels to identify those active in tumor maintenance. We provide comprehensive information for the three genomes and demonstrate the advantage of integrative analysis for identifying tumor-related genes amidst numerous background mutations by relating genomic variation to expression/protein abundance data and use gene networks to reveal implicated pathways.

  • 12.
    Akan, Pelin
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO).
    Stranneheim, Henrik
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO).
    Lexow, Preben
    LingVitae, Oslo.
    Lundeberg, Joakim
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO).
    Design and assessment of binary DNA for nanopore sequencing2010Ingår i: Genome biology, ISSN 1474-760X, Vol. 11, s. P4-Artikel i tidskrift (Övrigt vetenskapligt)
  • 13. Akyuz, Lalehan
    et al.
    Kaya, Murat
    Ilk, Sedef
    Cakmak, Yavuz Selim
    Salaberria, Asier M.
    Labidi, Jalel
    Yılmaz, Bahar Akyuz
    Sargin, Idris
    Effect of different animal fat and plant oil additives on physicochemical, mechanical, antimicrobial and antioxidant properties of chitosan films2018Ingår i: International Journal of Biological Macromolecules, ISSN 0141-8130, E-ISSN 1879-0003, Vol. 111, s. 475-484Artikel i tidskrift (Refereegranskat)
  • 14. Aleman, Dionne M.
    et al.
    Glaser, Daniel
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Optimeringslära och systemteori.
    Romeijn, H. Edwin
    Dempsey, James F.
    Interior point algorithms: guaranteed optimality for fluence map optimization in IMRT2010Ingår i: Physics in Medicine and Biology, ISSN 0031-9155, E-ISSN 1361-6560, Vol. 55, nr 18, s. 5467-5482Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    One of the most widely studied problems of the intensity-modulated radiation therapy (IMRT) treatment planning problem is the fluence map optimization (FMO) problem, the problem of determining the amount of radiation intensity, or fluence, of each beamlet in each beam. For a given set of beams, the fluences of the beamlets can drastically affect the quality of the treatment plan, and thus it is critical to obtain good fluence maps for radiation delivery. Although several approaches have been shown to yield good solutions to the FMO problem, these solutions are not guaranteed to be optimal. This shortcoming can be attributed to either optimization model complexity or properties of the algorithms used to solve the optimization model. We present a convex FMO formulation and an interior point algorithm that yields an optimal treatment plan in seconds, making it a viable option for clinical applications.

  • 15.
    Alhamar, Sarah
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap.
    Extraction of the Coagulant Protein from Oil Waste2022Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Många utvecklingsländer har områden med undermålig vattenkvalitet. Detta beror antingen på bristande infrastruktur eller på dåliga ekonomiska förutsättningar. Ett av de första stegen av vattenrening involverar en process som kallas flockulering. 

    För närvarande är aluminiumsulfat (alun) det mest populära flockningsmedlet; dock har det effekter på människors hälsa. Moringa oleifera-fröet en alternativ, icke-kemisk tillsats som historiskt har använts vid vattenrening som flockningsmedel. Moringaväxten är mångsidig och kan även användas inom kosmetika- och livsmedelsindustrin. 

    Medan Moringa oleifera-frön är en av de ursprungliga växterna som används vid vattenbehandling, visar många andra också potential. Avfallsprodukter från kallpressoljeindustrin analyserades både för att testa dess potential som alternativa flockningsmedel och för att undvika konkurrens med livsmedelsproduktion och industriella processer. Olika oljepresskakor undersöktes för att hitta ett lämpligt koaguleringsmedel. 

    Jonbyteskromatografi och antimikrobiella tester utfördes med enkla analyser. Undersökningen var fokuserade på proteinkoncentrationen och koaguleringsaktiviteten hos oljepresskakorna. Oljepresskakor av Moringa oleifera, raps, linfrö, jordnötter och sesamfrön testades, varav två visade lovande resultat och potential för användning vid vattenbehandling. 

    Oljepresskakor av Moringafrö och raps visade närvaron av koagulerande proteiner som är jämförbara med fröextrakten. Koaguleringsproteinet från oljepresskakor har en liknande molekylmassa som fröextrakten. De renade proteinerna visade antibakteriella egenskaper och deras näringsinehålla var minimala.

  • 16.
    Alm, Tove
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Interaction engineered three-helix bundle domains for protein recovery and detection2010Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    HTML clipboard The great advances in DNA technology, e.g. sequencing and recombinant DNA techniques, have given us the genetic information and the tools needed to effectively produce recombinant proteins. Recombinant proteins are valuable means in biotechnological applications and are also emerging as alternatives in therapeutic applications. Traditionally, monoclonal antibodies have been the natural choice for biotechnological and therapeutic applications due to their ability to bind a huge range of different molecules and their natural good affinity. However, the large size of antibodies (150 kDa) limits tissue penetration and the recombinant expression is complicated. Therefore, alternative binders with smaller sizes have been derived from antibodies and alternative scaffolds.

    In this thesis, two structurally similar domains, Zbasic and ABDz1, have been used as purification tags in different contexts. They are both three-helical bundles and derived from bacterial surface domains, but share no sequence homology. Furthermore, by redesign of the scaffold used for ABDz1, a molecule intended for drug targeting with extended in-vivo half-life has been engineered. In Papers I and II, the poly-cationic tag Zbasic is explored and evaluated. Paper I describes the successful investigation of Zbasic as a purification handle under denaturating conditions. Moreover, Zbasic is evaluated as an interaction domain in matrixassisted refolding. Two different proteins were successfully refolded using the same setup without individual optimization. In Paper II, Zbasic is further explored as a purification handle under non-native conditions in a multi-parallel setup. In total, 22 proteins with varying characteristics are successfully purified using a multi-parallel protein purification protocol and a robotic system. Without modifications, the system can purify up to 60 proteins without manual handling. Paper I and II clearly demonstrate that Zbasic can be used as an interaction domain in matrix-assisted refolding and that it offers a good alternative to the commonly used His6-tag under denaturating conditions. In paper III, the small bifunctional ABDz1 is selected from a phage display library. Endowed with two different binding interfaces, ABDz1 is capable of binding both the HSA-sepharose and the protein A-derived MabSelect SuRe-matrix. The bifunctionality of the domain is exploited in an orthogonal affinity setup. Three target proteins are successfully purified using the HSA-matrix and the MabSelect SuRe-matrix. Furthermore, the purity of the target proteins is effectively improved by combining the two chromatographic steps. Thus, paper III shows that the small ABDz1 can be used as an effective purification handle and dual affinity tag without target specific optimization. Paper IV describes the selection and affinity maturation of small bispecific drug-targeting molecules. First generation binders against tumor necrosis factor-α are selected using phage display. Thereafter on-cell surface display and flow cytometry is used to select second-generation binders. The binding to tumor necrosis factor-α is improved up to 30 times as compared to the best first generation binder, and a 6-fold improvement of the binding strength was possible with retained HSA affinity. Paper III and IV clearly demonstrate that dual interaction surfaces can successfully be grafted on a small proteinaceous domain, and that the strategy in paper IV can be used for dual selection of bifunctional binders.

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    FULLTEXT01
  • 17. Al-Naamani, Laila
    et al.
    Dobretsov, Sergey
    Dutta, Joydeep
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Funktionella material, FNM.
    Chitosan-zinc oxide nanoparticle composite coating for active food packaging applications2016Ingår i: Innovative Food Science & Emerging Technologies, ISSN 1466-8564, E-ISSN 1878-5522, Vol. 38, s. 231-237Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this study antimicrobial properties of chitosan and chitosan-zinc oxide (ZnO) nanocomposite coatings on PE films were studied. Oxygen plasma pretreatment of PE films led to increased adhesion by 2% of chitosan and the nanocomposite coating solutions to the packaging films. Scanning Electron Microscopy (SEM) revealed uniform coatings on PE surfaces. Incorporation of ZnO nanoparticles into the chitosan matrix resulted in 42% increase in solubility; swelling decreased by 80% while the water contact angle (WCA) increased from 60 to 95 compared to chitosan coating. PE coated with chitosan-ZnO nanocomposite films completely inactivated and prevented the growth of food pathogens, while chitosan-coated films showed only 10-fold decline in the viable cell counts of Salmonella enterica, Escherichia coli and Staphylococcus aureus after 24-h incubation compared to the control. Industrial relevance: One of the greatest challenges of food industry is microbial contamination. The present study suggests that PE coating with chitosan-ZnO nanocomposite is a promising technique to enhance antimicrobial properties of the films. Chitosan-ZnO nanocomposite coatings improved antibacterial properties of PE by inactivating about 99.9% of viable pathogenic bacteria. Hence, our results show the effectiveness of the nanocomposite coating in the development of active food packaging in order to prolong the shelf life of food products.

  • 18. Altai, M.
    et al.
    Tsourma, M.
    Mitran, B.
    Honarvar, H.
    Perols, Anna
    KTH, Skolan för bioteknologi (BIO), Proteinteknologi.
    Robillard, M.
    Rossin, R.
    ten Hoeve, W.
    Sandstrom, M.
    Orlova, A.
    Karlström, Amelie Eriksson
    KTH, Skolan för bioteknologi (BIO), Proteinteknologi.
    Tolmachev, V.
    Affibody-based bioorthogonal chemistry-mediated radionuclide pretargeting: proof-of-principle.2015Ingår i: European Journal of Nuclear Medicine and Molecular Imaging, ISSN 1619-7070, E-ISSN 1619-7089, Vol. 42, s. S246-S246Artikel i tidskrift (Refereegranskat)
  • 19. Altai, Mohamed
    et al.
    Vorobyeva, Anzhelika
    Tolmachev, Vladimir
    Eriksson Karlström, Amelie
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap, Proteinvetenskap.
    Westerlund, Kristina
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap, Proteinvetenskap.
    Preparation of Conjugates for Affibody-Based PNA-Mediated Pretargeting2020Ingår i: Methods in Molecular Biology, Humana Press Inc. , 2020, s. 283-304Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Affibody molecules are small engineered scaffold proteins suitable for in vivo tumor targeting. Radionuclide molecular imaging using directly radiolabelled affibody molecules provides excellent imaging. However, affibody molecules have a high renal reabsorption, which complicates their use for radionuclide therapy. The high renal reabsorption is a common problem for the use of engineered scaffold proteins for radionuclide therapy. Affibody-based PNA-mediated pretargeting reduces dramatically the absorbed dose to the kidneys and makes affibody-based radionuclide therapy possible. This methodology might, hopefully, solve the problem of high renal reabsorption for radionuclide therapy mediated by other engineered scaffold proteins. 

  • 20.
    Alvarado Ávila, María Isabel
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    De Luca, Stefano
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Edlund, Ulrica
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Fiber- och polymerteknologi.
    Fei, Ye
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Dutta, Joydeep
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Cellulose as sacrificial agents for enhanced photoactivated hydrogen production2023Ingår i: Sustainable Energy & Fuels, E-ISSN 2398-4902, Vol. 7, nr 8, s. 1981-1991Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The search for new energy sources together with the need to control greenhouse gas emissions has led to continued interest in low-emitting renewable energy technologies. In this context, water splitting for hydrogen production is a reasonable alternative to replace fossil fuels due to its high energy density producing only water during combustion. Cellulose is abundant in nature and as residuals from human activity, and therefore a natural, ecological, and carbon-neutral source for hydrogen production. In the present work, we propose a sustainable method for hydrogen production using sunlight and cellulose as sacrificial agents during the photocatalytic water splitting process. Platinum (Pt) catalyst activates hydrogen production, and parameters such as pH of the system, cellulose concentration, and Pt loading were studied. Using different biomasses, we found that the presence of hemicellulose and xyloglucan as part of the molecular composition considerably increased the H-2 production rate from 36 mu mol L-1 in one hour for rapeseed cellulose to 167.44 mu mol L-1 for acid-treated cellulose isolated from Ulva fenestrata algae. Carboxymethylation and TEMPO-oxidation of cellulosic biomass both led to more stable suspensions with higher rates of H-2 production close to 225 mu mol L-1, which was associated with their water solubility properties. The results suggest that cellulosic biomass can be an attractive alternative as a sacrificial agent for the photocatalytic splitting of water for H-2 production.

  • 21.
    Alvfors, Per
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik, Energiprocesser.
    Arnell, Jenny
    IVL.
    Berglin, Niklas
    Innventia.
    Björnsson, Lovisa
    LU.
    Börjesson, Pål
    LU.
    Grahn, Maria
    Chalmers/SP.
    Harvey, Simon
    Chalmers.
    Hoffstedt, Christian
    Innventia.
    Holmgren, Kristina
    IVL.
    Jelse, Kristian
    IVL.
    Klintbom, Patrik
    Kusar, Henrik
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik, Kemisk teknologi.
    Lidén, Gunnar
    LU.
    Magnusson, Mimmi
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik, Energiprocesser.
    Pettersson, Karin
    Chalmers.
    Rydberg, Tomas
    IVL.
    Sjöström, Krister
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik.
    Stålbrand, Henrik
    LU.
    Wallberg, Ola
    LU.
    Wetterlund, Elisabeth
    LiU.
    Zacchi, Guido
    LU.
    Öhrman, Olof
    ETC Piteå.
    Research and development challenges for Swedish biofuel actors – three illustrative examples: Improvement potential discussed in the context of Well-to-Tank analyses2010Rapport (Övrigt vetenskapligt)
    Abstract [en]

    Currently biofuels have strong political support, both in the EU and Sweden. The EU has, for example, set a target for the use of renewable fuels in the transportation sector stating that all EU member states should use 10% renewable fuels for transport by 2020. Fulfilling this ambition will lead to an enormous market for biofuels during the coming decade. To avoid increasing production of biofuels based on agriculture crops that require considerable use of arable area, focus is now to move towards more advanced second generation (2G) biofuels that can be produced from biomass feedstocks associated with a more efficient land use. Climate benefits and greenhouse gas (GHG) balances are aspects often discussed in conjunction with sustainability and biofuels. The total GHG emissions associated with production and usage of biofuels depend on the entire fuel production chain, mainly the agriculture or forestry feedstock systems and the manufacturing process. To compare different biofuel production pathways it is essential to conduct an environmental assessment using the well-to-tank (WTT) analysis methodology. In Sweden the conditions for biomass production are favourable and we have promising second generation biofuels technologies that are currently in the demonstration phase. In this study we have chosen to focus on cellulose based ethanol, methane from gasification of solid wood as well as DME from gasification of black liquor, with the purpose of identifying research and development potentials that may result in improvements in the WTT emission values. The main objective of this study is thus to identify research and development challenges for Swedish biofuel actors based on literature studies as well as discussions with the the researchers themselves. We have also discussed improvement potentials for the agriculture and forestry part of the WTT chain. The aim of this study is to, in the context of WTT analyses, (i) increase knowledge about the complexity of biofuel production, (ii) identify and discuss improvement potentials, regarding energy efficiency and GHG emissions, for three biofuel production cases, as well as (iii) identify and discuss improvement potentials regarding biomass supply, including agriculture/forestry. The scope of the study is limited to discussing the technologies, system aspects and climate impacts associated with the production stage. Aspects such as the influence on biodiversity and other environmental and social parameters fall beyond the scope of this study. We find that improvement potentials for emissions reductions within the agriculture/forestry part of the WTT chain include changing the use of diesel to low-CO2-emitting fuels, changing to more fuel-efficient tractors, more efficient cultivation and manufacture of fertilizers (commercial nitrogen fertilizer can be produced in plants which have nitrous oxide gas cleaning) as well as improved fertilization strategies (more precise nitrogen application during the cropping season). Furthermore, the cultivation of annual feedstock crops could be avoided on land rich in carbon, such as peat soils and new agriculture systems could be introduced that lower the demand for ploughing and harrowing. Other options for improving the WTT emission values includes introducing new types of crops, such as wheat with higher content of starch or willow with a higher content of cellulose. From the case study on lignocellulosic ethanol we find that 2G ethanol, with co-production of biogas, electricity, heat and/or wood pellet, has a promising role to play in the development of sustainable biofuel production systems. Depending on available raw materials, heat sinks, demand for biogas as vehicle fuel and existing 1G ethanol plants suitable for integration, 2G ethanol production systems may be designed differently to optimize the economic conditions and maximize profitability. However, the complexity connected to the development of the most optimal production systems require improved knowledge and involvement of several actors from different competence areas, such as chemical and biochemical engineering, process design and integration and energy and environmental systems analysis, which may be a potential barrier.

  • 22.
    Amorim, Lúcia F.A.
    et al.
    FibEnTech Research Unit, Faculty of Engineering, University of Beira Interior, Covilhã, Portugal.
    Li, Lengwan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Centra, Wallenberg Wood Science Center. KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Fiber- och polymerteknologi, Biokompositer.
    Gomes, Ana P.
    FibEnTech Research Unit, Faculty of Engineering, University of Beira Interior, Covilhã, Portugal.
    Fangueiro, Raul
    Centre for Textile Science and Technology (2C2T), University of Minho, Guimarães, Portugal.
    Gouveia, Isabel C.
    FibEnTech Research Unit, Faculty of Engineering, University of Beira Interior, Covilhã, Portugal.
    Sustainable bacterial cellulose production by low cost feedstock: evaluation of apple and tea by-products as alternative sources of nutrients2023Ingår i: Cellulose, ISSN 0969-0239, E-ISSN 1572-882X, Vol. 30, nr 9, s. 5589-5606Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The high applicability of Bacterial Cellulose (BC) is often challenging due to its high production costs, which ultimately prevents its widespread use. Therefore, the present study aimed to investigate BC production using alternative feedstock to replace high-cost synthetic carbon and nitrogen sources and to evaluate the physical and structural properties of the produced BC membranes. BC was produced through a microbial consortium from kombucha, and the formulated alternative media sustained promising BC production, especially the association of apple wastes (at 10% (W/V)) with tea mixture, with a yield similar to BC produced on Hestrin–Schramm (HS) control media. Moreover, the BC samples produced in this alternative media also exhibited comparable properties to BC from HS media, with similar water-holding capacity and retention ability, thermal stability, mechanical behavior, and a crystallinity index of 87.61% and 88.08%, respectively. Thus, our findings substantiated that expensive substrates, such as glucose, peptone, and yeast extract, could be successfully replaced by apple wastes, black and green tea, for BC production while maintaining its remarkable physical and structural properties. Furthermore, besides the low-cost advantage, the bioconversion of apple waste also reduces the environmental burden caused by its disposal in landfills.

  • 23.
    Andersen, Malin
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Computational and experimental approaches to regulatory genetic variation2007Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Genetic variation is a strong risk factor for many human diseases, including diabetes, cancer, cardiovascular disease, depression, autoimmunity and asthma. Most of the disease genes identified so far alter the amino acid sequences of encoded proteins. However, a significant number of genetic variants affecting complex diseases may alter the regulation of gene transcription. The map of the regulatory elements in the human genome is still to a large extent unknown, and it remains a challenge to separate the functional regulatory genetic variations from linked neutral variations.

    The objective of this thesis was to develop methods for the identification of genetic variation with a potential to affect the transcriptional regulation of human genes, and to analyze potential regulatory polymorphisms in the CD36 glycoprotein, a candidate gene for cardiovascular disease.

    An in silico tool for the prediction of regulatory polymorphisms in human genes was implemented and is available at www.cisreg.ca/RAVEN. The tool was evaluated using experimentally verified regulatory single nucleotide polymorphisms (SNPs) collected from the scientific literature, and tested in combination with experimental detection of allele specific expression of target genes (allelic imbalance). Regulatory SNPs were shown to be located in evolutionary conserved regions more often than background SNPs, but predicted transcription factor binding sites were unable to enrich for regulatory SNPs unless additional information linking transcription factors with the target genes were available.

    The in silico tool was applied to the CD36 glycoprotein, a candidate gene for cardiovascular disease. Potential regulatory SNPs in the alternative promoters of this gene were identified and evaluated in vitro and in vivo using a clinical study for coronary artery disease. We observed association to the plasma concentrations of inflammation markers (serum amyloid A protein and C-reactive protein) in myocardial infarction patients, which highlights the need for further analyses of potential regulatory polymorphisms in this gene.

    Taken together, this thesis describes an in silico approach to identify putative regulatory polymorphisms which can be useful for directing limited laboratory resources to the polymorphisms most likely to have a phenotypic effect.

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  • 24.
    Anderson, Mattias
    et al.
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Afewerki, Samson
    Berglund, Per
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Cõrdova, Armando
    Total Synthesis of Capsaicin Analogues from Lignin-Derived Compounds by Combined Heterogeneous Metal, Organocatalytic and Enzymatic Cascades in One Pot2014Ingår i: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 356, nr 9, s. 2113-2118Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The total synthesis of capsaicin analogues was performed in one pot, starting from compounds that can be derived from lignin. Heterogeneous palladium nanoparticles were used to oxidise alcohols to aldehydes, which were further converted to amines by an enzyme cascade system, including an amine transaminase. It was shown that the palladium catalyst and the enzyme cascade system could be successfully combined in the same pot for conversion of alcohols to amines without any purification of intermediates. The intermediate vanillyl-amine, prepared with the enzyme cascade system, could be further converted to capsaicin analogues without any purification using either fatty acids and a lipase, or Schotten-Baumann conditions, in the same pot. An aldol compound (a simple lignin model) could also be used as starting material for the synthesis of capsaicin analogues. Using l-alanine as organocatalyst, vanillin could be obtained by a retro-aldol reaction. This could be combined with the enzyme cascade system to convert the aldol compound to vanillylamine in a one-step one-pot reaction.

  • 25.
    Andersson, Anders
    KTH, Skolan för bioteknologi (BIO).
    Microarray-based investigation of genome and transcriptome organisation in the archaeon sulfolobus2005Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
  • 26.
    Andersson, Anders
    et al.
    KTH, Skolan för bioteknologi (BIO).
    Bernander, R.
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Nilsson, Peter
    KTH, Skolan för bioteknologi (BIO).
    Dual-genome primer design for construction of DNA microarrays2005Ingår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 21, nr 3, s. 325-332Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Motivation: Microarray experiments using probes covering a whole transcriptome are expensive to initiate, and a major part of the costs derives from synthesizing gene-specific PCR primers or hybridization probes. The high costs may force researchers to limit their studies to a single organism, although comparing gene expression in different species would yield valuable information. Results: We have developed a method, implemented in the software DualPrime, that reduces the number of primers required to amplify the genes of two different genomes. The software identifies regions of high sequence similarity, and from these regions selects PCR primers shared between the genomes, such that either one or, preferentially, both primers in a given PCR can be used for amplification from both genomes. To assure high microarray probe specificity, the software selects primer pairs that generate products of low sequence similarity to other genes within the same genome. We used the software to design PCR primers for 2182 and 1960 genes from the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. Primer pairs were shared among 705 pairs of genes, and single primers were shared among 1184 pairs of genes, resulting in a saving of 31% compared to using only unique primers. We also present an alternative primer design method, in which each gene shares primers with two different genes of the other genome, enabling further savings.

  • 27.
    Andersson, Anders
    et al.
    KTH, Skolan för bioteknologi (BIO).
    Eriksson, S.
    Nilsson, P.
    Bernander, R.
    Early replicating ridge-like domains in archaeal chromosomesManuskript (preprint) (Övrigt vetenskapligt)
  • 28.
    Andersson, Anders
    et al.
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Keskitalo, J.
    Sjödin, A.
    Bhalerao, Rupali
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Sterky, Fredrik
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Wissel, K.
    Tandre, K.
    Aspeborg, Henrik
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Moyle, R.
    Ohmiya, Y.
    Brunner, A.
    Gustafsson, P.
    Karlsson, J.
    Lundeberg, Joakim
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Nilsson, O.
    Sandberg, G.
    Strauss, S.
    Sundberg, B.
    Uhlén, Mathias
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    Jansson, S.
    Nilsson, Peter
    KTH, Tidigare Institutioner (före 2005), Bioteknologi.
    A transcriptional timetable of autumn senescence2004Ingår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 5, nr 4, s. R24-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

  • 29.
    Andersson, Anders
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Lundgren, Magnus
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Eriksson, Stefan
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Rosenlund, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.).
    Bernander, Rolf
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Nilsson, Peter
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Global analysis of mRNA stability in the archaeon Sulfolobus2006Ingår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 7, nr 10, s. R99-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Transcript half-lives differ between organisms, and between groups of genes within the same organism. The mechanisms underlying these differences are not clear, nor are the biochemical properties that determine the stability of a transcript. To address these issues, genome-wide mRNA decay studies have been conducted in eukaryotes and bacteria. In contrast, relatively little is known about RNA stability in the third domain of life, Archaea. Here, we present a microarray-based analysis of mRNA half-lives in the hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, constituting the first genome-wide study of RNA decay in archaea. Results: The two transcriptomes displayed similar half-life distributions, with medians of about five minutes. Growth-related genes, such as those involved in transcription, translation and energy production, were over-represented among unstable transcripts, whereas uncharacterized genes were over-represented among the most stable. Half-life was negatively correlated with transcript abundance and, unlike the situation in other organisms, also negatively correlated with transcript length. Conclusion: The mRNA half-life distribution of Sulfolobus species is similar to those of much faster growing bacteria, contrasting with the earlier observation that median mRNA half-life is proportional to the minimal length of the cell cycle. Instead, short half-lives may be a general feature of prokaryotic transcriptomes, possibly related to the absence of a nucleus and/or more limited post-transcriptional regulatory mechanisms. The pattern of growth-related transcripts being among the least stable in Sulfolobus may also indicate that the short half-lives reflect a necessity to rapidly reprogram gene expression upon sudden changes in environmental conditions.

  • 30.
    Andersson, Anders
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Pelve, Erik A.
    Lindeberg, Stefan
    Lundgren, Magnus
    Nilsson, Peter
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Bernander, Rolf
    Replication-biased genome organisation in the crenarchaeon Sulfolobus2010Ingår i: BMC Genomics, E-ISSN 1471-2164, Vol. 11, s. 454-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. Results: We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more highly expressed at all three origins. The bias by far exceeds what would be anticipated by gene dosage effects alone. In addition, early replicating regions are denser in archaeal core genes (enriched in essential functions), display lower intergenic distances, and are devoid of mobile genetic elements. Conclusion: The strong replication-biased structuring of the Sulfolobus chromosome implies that the multiple replication origins serve purposes other than simply shortening the time required for replication. The higher-level chromosomal organisation could be of importance for minimizing the impact of DNA damage, and may also be linked to transcriptional regulation.

  • 31. Andersson, K
    et al.
    Gülich, S
    KTH, Tidigare Institutioner (före 2005), Biokemi och biokemisk teknologi.
    Hämäläinen, M
    Nygren, P A
    KTH, Tidigare Institutioner (före 2005), Biokemi och biokemisk teknologi.
    Hober, Sophia
    KTH, Tidigare Institutioner (före 2005), Biokemi och biokemisk teknologi.
    Malmqvist, M
    Kinetic characterization of the interaction of the Z-fragment of protein A with mouse-IgG3 in a volume in chemical space.1999Ingår i: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 37, nr 3Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The kinetic rate parameters for the interaction between a single domain analogue of staphylococcal protein A (Z) and a mouse-IgG3 monoclonal antibody (MAb) were measured in Hepes buffer with different chemical additives. Five buffer ingredients (pH, NaCl, DMSO, EDTA, and KSCN) were varied simultaneously in 16 experiments following a statistical experimental plan. The 16 buffers thus spanned a volume in chemical space. A mathematical model, using data from the buffer composition, was developed and used to predict apparent kinetic parameters in five new buffers within the spanned volume. Association and dissociation parameters were measured in the new buffers, and these agreed with the predicted values, indicating that the model was valid within the spanned volume. The pattern of variation of the kinetic parameters in relation to buffer composition was different for association and dissociation, such that pH influenced both association and dissociation and NaCl influenced only dissociation. This indicated that the recognition mechanism (association) and the stability of the formed complex (dissociation) involve different binding forces, which can be further investigated by kinetic studies in systematically varied buffers.

  • 32.
    Andersson, Klara
    KTH, Skolan för bioteknologi (BIO).
    Development of a shake flask method suitable for effective screening of Escherichia coli expression constructs2011Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Screening av nya rekombinanta proteiner som ska användas till läkemedel sker oftast i batch-odling. Men själva odlingen av proteinläkemedlet sker sedan under fed-batch förhållanden. Dessa två typer av odling är olika och då cellerna växer olika kan detta leda till att fel, eller den inte mest lämpade kandidaten väljs. Därför vore det önskvärt att ta fram en fed-batch liknande metod i skakkolvar. Biosilta har tagit fram en metod där ett enzym bryter ned stärkelse till glukos som påminner om fed-batch. Denna metod har testats och undersökts i detta examensarbete. Det har visat sig att cellerna som växer under dessa förhållanden är begränsade på glukos men producerar stora mängder ättiksyra under den senare fasen av odlingen och att pH varierar mycket. Systemet bygger mycket på att en booster-tablett tillsätts, vad denna tablett innehåller är okänt. Men om tabletten inte tillsätts slutar cellerna att växa, detta tyder på att det finns någon mer begränsning än glukos. Det visade sig även att protein produktionen blev mycket lägre än vid odling i batch-fas. Det skulle av anledning av ovanstående inte vara bra att använda sig av EnBase som en screening metod.

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  • 33.
    Andersson, Olivia
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap.
    Engineering of the epidermal skin layer using recombinant spider silk2021Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Huden är det största mänskliga organet, och det tjänar en grundläggande roll i att skydda människokroppen från skadliga yttre stimuli genom att agera som en fysisk och biologisk barriär. Den mänskliga huden kan delas in i tre lager, där överhuden (epidermis) är av intresse i denna studie. Epidermis, huvudsakligen bestående av keratinocyter, kan i sin tur delas in i 5 cellskikt, som var och en kännetecknas av kertainocyternas differentieringsstadie. Lamininer är även utav intresse i denna studie. Lamininer är stora glykoproteiner som utsöndras, som heterotrimerer, bl.a. av keratinocyter. De är viktiga komponenter av basalmembranet av in vivo hud, och är involverade i olika signalvägar och reglering av keratinocyters adhesion, differentiering och apoptos.

    Mänskliga hudekvivalenter ämnar att efterlikna den mänskliga huden, så att vi kan studera dess fysiologi och relation till sjukdom. Även om olika biomaterial har använts för att konstruera dessa, brister många av dem i mekanisk integritet, elasticitet, ECM-struktur och/eller kräver funktionalisering. FN-4RepCT, ett rekombinant producerat spindelsilkesprotein, bildar ett biomaterial som saknar dessa brister. Det innehåller fyra repetitiva polyalaninblock och fyra glycinrika enheter, en C-terminal domän och ett cellbindande motiv från fibronectin, nämligen RGD. Proteinlösningar av FN-4RepCT kan användas för att producera makroskopiska 3Dstrukturer i olika format, som har visat sig vara proteinpermeabla, biologiskt nedbrytbara, elastiska, mekaniskt robusta och stöder cell proliferation. I denna studie används FN-silkes membran, med nanofibrillära strukturer, för att konstruera en epidermal motsvarighet bestående av silke, lamininer och keratinocyter. Metoden som presenteras för att konstruera dessa membran och belägga dem med lamininer är enkel och kan upprepas utan användning av komplex laboratorieutrustning.

    De resultat som presenteras häri ger ytterligare stöd för att FN-4RepCT skulle kunna vara ett användbart biomaterial inom området vävnadsteknik. Det visas också att när lamininer kombineras med silke främjas proliferation och differentiering av keratinocyter, vilket är en fördel om man vill konstruera en modell av epidermis som är fysiologisk relevant. De epidermala ekvivalenterna utvärderades med immunofluorescence där differentierings markörerna Keratin 5, Keratin 10 och involucrin färgades in. Resultaten visar att det epidermala vävnadskonstruktet består av flera cellager som kan identifieras utifrån cellernas morfologi samt vilka markörer de uttrycker. Sammantaget kan slutsaten dras att FN-4RepCT, i kombination med lamininer, är ett lovande alternativ för konstruktion av hudvävnad.

  • 34.
    Andersson, Sarah
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap.
    Profiling host proteins in the envelope of SARS-CoV-2 viral particles2022Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    SARS-CoV-2 är ett höljeförsett RNA-virus som orsakar pandemiutbrottet av sjukdomen covid-19. Tidigare forskning kring höljevirus has visat att proteiner från infekterade värdceller kan inkorporeras i nybildade virioner, och dessa inkorporerade proteiner tros även kunna påverka virusets patogenes. I tidigare studier har masspektrometri (MS) och proximity extension assays (PEA) använts för att profilera värdproteiner som befinner sig i ytan på SARS-CoV-2 viruspartiklar. Syftet med detta projekt var att utveckla en strategi för att validera närvaron av värdproteiner som har identifierats på ytan av SARS-CoV-2 viruspartiklar genom proteomikmetoder med hög multiplexitet. Genom att använda Luminex xMAP teknologi utvecklades en så kallad sandwich assay för att detektera viruspartiklar genom att använda angiotensinkonvertas-2 (ACE2) som fångstreagens, och antikroppar mot det virala spikproteinet samt mot utvalda värdproteiner som detektionsreagens. Analyser genomfördes i både ett FlexMap3D-instrument och i ett Intelliflex-instrument med dualt detektion-lasersystem. Genom användning av antikroppar mot spikproteinet demonstrerar vi att den utvecklade metoden är kapabel till att detektera virala ytproteiner i både enkelt och dualt detektionsläge, vilket möjliggör samtidig detektion av flera värdproteiner. Antikroppar mot förmodade inkorporerade värdproteiner i viruspartiklars lipidhölje har valts ut och utvärderats med avseende på selektivitet. I framtida experiment kommer den utvecklade metoden användas för att screena efter 31 olika värdproteiner på ytan av SARS-CoV-2 viruspartiklar.

  • 35.
    Andersson, Sofia
    et al.
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Dalhammar, Gunnel
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Land, Carl Johan
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Kuttuva Rajarao, Gunaratna
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Biological nutrient removal by individual and mixed strain biofilmsManuskript (Övrigt vetenskapligt)
  • 36.
    Andersson, Sofia
    et al.
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Dalhammar, Gunnel
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Land, Carl Johan
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Kuttuva Rajarao, Gunaratna
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Characterization of extracellular polymeric substances from denitrifying organism Comamonas denitrificans2009Ingår i: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 82, nr 3, s. 535-543Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Extracellular polymeric substances (EPS) play an important role in the formation and activity of biofilms in wastewater treatment (WWT). The EPS of the denitrifying biomarker Comamonas denitrificans strain 110, produced in different culture media and growth modes, were characterized. The EPS mainly contained protein (3-37%), nucleic acids (9-50%), and carbohydrates (3-21%). The extracellular DNA was found to be important for initial biofilm formation since biofilm, but not planktonic growth, was inhibited in the presence of DNase. The polysaccharide fraction appeared to consist of at least two distinct polymers, one branched fraction (A) made up of glucose and mannose with a molecular weight around 100 kDa. The other fraction (B) was larger and consisted of ribose, mannose, glucose, rhamnose, arabinose, galactose, and N-acetylglucosamine. Fraction B polysaccharides were mainly found in capsular EPS which was the dominant type in biofilms and agar-grown colonies. Fraction A was abundant in the released EPS, the dominant type in planktonic cultures. Biofilm and agar-grown EPS displayed similar overall properties while planktonic EPS showed clear compositional disparity. This study presents results on the physiology of a key WWT organism, which may be useful in the future development of improved biofilm techniques for WWT purposes.

  • 37.
    Andersson, Sofia
    et al.
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Dalhammar, Gunnel
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Rajarao, Gunaratna Kuttuva
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Persistence and competition of denitrifying biofilms subjected to a natural wastewater floraManuskript (Övrigt vetenskapligt)
  • 38.
    Andersson, Sofia
    et al.
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Kuttuva Rajarao, Gunaratna
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Land, Carl Johan
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Dalhammar, Gunnel
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Biofilm formation and interactions of bacterial strains found in wastewater treatment systems2008Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 283, nr 1, s. 83-90Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Biofilm formation and adherence properties of 13 bacterial strains commonly found in wastewater treatment systems were studied in pure and mixed cultures using a crystal violet microtiter plate assay. Four different culture media were used, wastewater, acetate medium, glucose medium and diluted nutrient broth. The medium composition strongly affected biofilm formation. All strains were able to form pure culture biofilms within 24 h in at least one of the tested culture media and three strains were able to form biofilm in all four culture media, namely Acinetobacter calcoaceticus ATCC 23055, Comamonas denitrificans 123 and Pseudomonas aeruginosa MBL 0199. The adherence properties assessed were initial adherence, cell surface hydrophobicity, and production of amyloid fibers and extracellular polymeric substances. The growth of dual-strain biofilms showed that five organisms formed biofilm with all 13 strains while seven formed no or only weak biofilm when cocultured. In dual-strain cultures, strains with different properties were able to complement each other, giving synergistic effects. Strongest biofilm formation was observed when a mixture of all 13 bacteria were grown together. These results on attachment and biofilm formation can serve as a tool for the design of tailored systems for the degradation of municipal and industrial wastewater.

  • 39.
    Andersson, Sofia
    et al.
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Nilsson, Mirja
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Dalhammar, Gunnel
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Kuttuva Rajarao, Gunaratna
    KTH, Skolan för bioteknologi (BIO), Miljömikrobiologi.
    Assessment of carrier materials for biofilm formation and denitrification2008Ingår i: Vatten, ISSN 0042-2886, Vol. 64, s. 201-207Artikel i tidskrift (Refereegranskat)
  • 40.
    Andrade, Jorge
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Berglund, Lisa
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Odeberg, Jacob
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Using Grid Technology for Computationally Intensive Applied Bioinformatics Analyses2006Ingår i: In Silico Biology, ISSN 1386-6338, Vol. 6, nr 6, s. 495-504Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    For several applications and algorithms used in applied bioinformatics, a bottle neck in terms of computational time may arise when scaled up to facilitate analyses of large datasets and databases. Re-codification, algorithm modification or sacrifices in sensitivity and accuracy may be necessary to accommodate for limited computational capacity of single work stations. Grid computing offers an alternative model for solving massive computational problems by parallel execution of existing algorithms and software implementations. We present the implementation of a Grid-aware model for solving computationally intensive bioinformatic analyses exemplified by a blastp sliding window algorithm for whole proteome sequence similarity analysis, and evaluate the performance in comparison with a local cluster and a single workstation. Our strategy involves temporary installations of the BLAST executable and databases on remote nodes at submission, accommodating for dynamic Grid environments as it avoids the need of predefined runtime environments (preinstalled software and databases at specific Grid-nodes). Importantly, the implementation is generic where the BLAST executable can be replaced by other software tools to facilitate analyses suitable for parallelisation. This model should be of general interest in applied bioinformatics. Scripts and procedures are freely available from the authors.

  • 41.
    Anfelt, Josefine
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Metabolic engineering strategies to increase n-butanol production from cyanobacteria2016Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The development of sustainable replacements for fossil fuels has been spurred by concerns over global warming effects. Biofuels are typically produced through fermentation of edible crops, or forest or agricultural residues requiring cost-intensive pretreatment. An alternative is to use photosynthetic cyanobacteria to directly convert CO2 and sunlight into fuel. In this thesis, the cyanobacterium Synechocystis sp. PCC 6803 was genetically engineered to produce the biofuel n­-butanol. Several metabolic engineering strategies were explored with the aim to increase butanol titers and tolerance.

    In papers I-II, different driving forces for n-butanol production were evaluated. Expression of a phosphoketolase increased acetyl-CoA levels and subsequently butanol titers. Attempts to increase the NADH pool further improved titers to 100 mg/L in four days.

    In paper III, enzymes were co-localized onto a scaffold to aid intermediate channeling. The scaffold was tested on a farnesene and polyhydroxybutyrate (PHB) pathway in yeast and in E. coli, respectively, and could be extended to cyanobacteria. Enzyme co-localization increased farnesene titers by 120%. Additionally, fusion of scaffold-recognizing proteins to the enzymes improved farnesene and PHB production by 20% and 300%, respectively, even in the absence of scaffold.

    In paper IV, the gene repression technology CRISPRi was implemented in Synechocystis to enable parallel repression of multiple genes. CRISPRi allowed 50-95% repression of four genes simultaneously. The method will be valuable for repression of competing pathways to butanol synthesis.

    Butanol becomes toxic at high concentrations, impeding growth and thus limiting titers. In papers V-VI, butanol tolerance was increased by overexpressing a heat shock protein or a stress-related sigma factor.

    Taken together, this thesis demonstrates several strategies to improve butanol production from cyanobacteria. The strategies could ultimately be combined to increase titers further.

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    fulltext
  • 42.
    Anfelt, Josefine
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Kaczmarzyk, Danuta
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Shabestary, Kiyan
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Renberg, Björn
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Rockberg, Johan
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Nielsen, Jens
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi. Tech Univ Denmark.
    Hudson, Elton P.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Genetic and nutrient modulation of acetyl-CoA levels in Synechocystis for n-butanol production2015Ingår i: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 14, artikel-id 167Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: There is a strong interest in using photosynthetic cyanobacteria as production hosts for biofuels and chemicals. Recent work has shown the benefit of pathway engineering, enzyme tolerance, and co-factor usage for improving yields of fermentation products. Results: An n-butanol pathway was inserted into a Synechocystis mutant deficient in polyhydroxybutyrate synthesis. We found that nitrogen starvation increased specific butanol productivity up to threefold, but cessation of cell growth limited total n-butanol titers. Metabolite profiling showed that acetyl-CoA increased twofold during nitrogen starvation. Introduction of a phosphoketolase increased acetyl-CoA levels sixfold at nitrogen replete conditions and increased butanol titers from 22 to 37 mg/L at day 8. Flux balance analysis of photoautotrophic metabolism showed that a Calvin-Benson-Bassham-Phosphoketolase pathway had higher theoretical butanol productivity than CBB-Embden-Meyerhof-Parnas and a reduced butanol ATP demand. Conclusion: These results demonstrate that phosphoketolase overexpression and modulation of nitrogen levels are two attractive routes toward increased production of acetyl-CoA derived products in cyanobacteria and could be implemented with complementary metabolic engineering strategies.

  • 43.
    Anfelt, Josefine
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Shabestary, Kiyan
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Hudson, Elton P.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Complementary effects of ATP, acetyl-CoA and NADH driving forces increase butanol production in Synechocystis sp. PCC 6803Manuskript (preprint) (Övrigt vetenskapligt)
  • 44.
    Angleby, Helen
    KTH, Skolan för bioteknologi (BIO).
    Analysis of domestic dog mitochondrial DNA sequence variation for forensic investigations2005Licentiatavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The first method for DNA analysis in forensics was presented in 1985. Since then, the introduction of the polymerase chain reaction (PCR) has rendered possible the analysis of small amounts of DNA and automated sequencing and fragment analysis techniques have facilitated the analyses. In most cases short tandemly repeated regions (STRs) of nuclear DNA are analysed in forensic investigations, but all samples cannot be successfully analysed using this method. For samples containing minute amounts of DNA or degraded DNA, such as shed hairs, analysis of mitochondrial DNA (mtDNA) is generally more successful due to the presence of thousands of copies of mtDNA molecules per cell.

    In Sweden, ~40 % of all households have cats or dogs. With ~9 million humans shedding ~100 scalp hairs per day, and ~1.6 million cats and ~1 million dogs shedding hairs it is not surprising that shed hairs are one of the most common biological evidence found at crime scenes. However, the match probability for domestic dog mtDNA analysis has only been investigated in a few minor studies. Furthermore, although breed –sequence correlations of the noncoding mtDNA control region (CR) have been analysed in a few studies, showing limited correlations, no largescale studies have been performed previously. Thus, there have not been any comprehensive studies of forensic informativity of dog mtDNA. In the two papers presented in this thesis we have tried to lay a foundation for forensic use of analysis of domestic dog mtDNA. In the first paper, CR sequences were analysed and the exclusion capacity was investigated for a number of different populations. This is also the first comprehensive study of the correlation between mtDNA CR type and breed, type, and geographic origin of domestic dogs. Since the exclusion capacity for analysis of domestic dog CR sequences is relatively low, it was investigated in the second paper to what extent the discrimination power is improved by analysis of coding sequence. The exclusion capacity improved considerably when 3,000 base pairs of coding sequences where analysed in addition to CR sequences. This study will hopefully work as a basis for future development of analysis of dog mtDNA for forensic purposes.

    Ladda ner fulltext (pdf)
    FULLTEXT01
  • 45.
    Angleby, Helen
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Oskarsson, Mattias
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Pang, Junfeng
    Zhang, Ya-ping
    Leitner, Thomas
    Braham, Caitlyn
    Arvestad, Lars
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lundeberg, Joakim
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Webb, Kristen M.
    Savolainen, Peter
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Forensic Informativity of similar to 3000bp of Coding Sequence of Domestic Dog mtDNA2014Ingår i: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 59, nr 4, s. 898-908Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The discriminatory power of the noncoding control region (CR) of domestic dog mitochondrial DNA alone is relatively low. The extent to which the discriminatory power could be increased by analyzing additional highly variable coding regions of the mitochondrial genome (mtGenome) was therefore investigated. Genetic variability across the mtGenome was evaluated by phylogenetic analysis, and the three most variable similar to 1kb coding regions identified. We then sampled 100 Swedish dogs to represent breeds in accordance with their frequency in the Swedish population. A previously published dataset of 59 dog mtGenomes collected in the United States was also analyzed. Inclusion of the three coding regions increased the exclusion capacity considerably for the Swedish sample, from 0.920 for the CR alone to 0.964 for all four regions. The number of mtDNA types among all 159 dogs increased from 41 to 72, the four most frequent CR haplotypes being resolved into 22 different haplotypes.

  • 46.
    Angleby, Helen
    et al.
    KTH, Skolan för bioteknologi (BIO), Molekylär Bioteknologi.
    Savolainen, Peter
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Forensic informativity of domestic dog mtDNA control region sequences2005Ingår i: Forensic Science International, ISSN 0379-0738, E-ISSN 1872-6283, Vol. 154, nr 03-feb, s. 99-110Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have analysed the genetic information to be obtained from analysis of mitochondrial DNA (mtDNA) in domestic dogs studying the exclusion capacity in different populations and the correlation between mtDNA types and breeds or types of dogs. The exclusion capacities for a 573 bp sequence of the mitochondrial control region was between 0.86 and 0.95 for dogs in Sweden, the UK, Germany, Japan and China. The direct correlation between mtDNA type and breed, type of dog, and geographical origin of breed was generally low, but in some cases certain mtDNA types were overrepresented in one breed, and for wider groupings such as morphologically similar breeds, some mtDNA types were in many cases found in a distinct group of breeds, often originating from the same geographic region. This type of information may be used as an indication of the breed and, with some degree of probability, to include or exclude certain breeds from being the source of evidence materials.

  • 47.
    Aniander, Gustav
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Proteinvetenskap.
    Investigation of localized B cell activation at stromal tumor microenvironment site by bispecific affinity proteins - AffimAbs2020Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Cancer är en samling sjukdomar där kroppens celler börjar växa och dela sig okontrollerat. Detär ett utbrett hälsoproblem, som kräver nya behandlingar för att bekämpas effektivt. En del nya strategier involverar att aktivera kroppens immunförsvar och låta det attackera cancercellerna.Detta har uppnåtts genom användandet av designade antikroppar, som normalt är en del avimmunförsvaret. Antikroppar binder till olika antigener och delarna som skapar bindningen är väl kända, vilket låter oss manipulera vad designade antikroppar binder till. För att aktiveraimmunförsvaret har man inriktat sig på receptorer på cellytan av T- och B-celler. En del lovande resultat har setts, men problem med systemiska bieffekter har påträffats. Ett förslag för att undvika dessa bieffekter är att endast lokalt aktivera immunförsvaret genom användning av bispecifika affinitetsproteiner. Resonemanget bakom detta är att ha specificitet mot ett aktiveringsmål och en annan specificitet mot en antigen på cancerceller. En sådan klass av bispecifiker är AffimAbs, monoklonala antikroppar (mAbs) med en affibody konjugerad till dem. En affibody är en affinitetsmolekyl härstammande från protein A från stafylokocker. Dess största fördel är dess storlek, 7 kDa jämfört med 150 kDa för antikroppar. Den här studien undersöker förmågan av en AffimAb med specificitet mot ytreceptorn CD40 på B-celler och ytreceptorn PDGFR-β, som överuttrycks i vissa cancertyper, att lokalt aktivera B-celler. För att undersöka detta designades en ko-kultursaktiveringsassay och delarna validerades först separat. Detta inkluderade att hitta en fungerande seed-densitet för PDGFR-β-uttryckande celler, etablera ett protokoll för isolering av primära B-celler, och validera bindning av AffimAben till antigenerna. Resultaten från kokultursaktiveringsassayen visar på potentiellt högre aktivering för AffimAb jämfört med en CD40 mAb, men den lilla skalan av denna assay gör att skillnaderna inte kan bedömas vara statistiskt signifikanta. Vidare, större assays behövs för att konfirmera dessa preliminära resultat.

    Ladda ner (pdf)
    sammanfattning
  • 48.
    Ao, Yuxiu
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Industriell bioteknologi.
    Optimization of mammalian CHO cell culture medium2022Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    CHO-celler har använts i stor utsträckning inom det farmaceutiska området för produktion av terapeutiska proteiner, så förbättring av dess produktivitet har alltid varit ett viktigt ämne inom forskning och industri. Som den huvudsakliga miljön där celler växer i, påverkar cellodlingsmedium starkt celltillväxtkarakteriseringen, varför modulering av cellodlingsmediet är ett direkt tillvägagångssätt för att förbättra CHO-cellproduktiviteten. Aminosyror är viktiga byggstenar för produktionen av terapeutiska proteiner och själva cellkroppen, det huvudsakliga syftet med denna avhandling är att undersöka inverkan av olika aminosyrors sammansättning på tillväxten av CHO-celler. Pseudoperfusionsläge och matningsbatchläge är två metoder som används i CHO-cellodling.

  • 49.
    Arnau, Laurent
    KTH, Skolan för kemivetenskap (CHE).
    Techno-Economic Feasibility Study for the Production of Microalgae Based Plant Biostimulant2016Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Microalgae are considered as a potential feedstock for many promising applications. Some active substances in microalgae have plant biostimulation effects potentially useful in agriculture. However, to produce such a microalgal biomass, specific microalgae cultivation and post-treatment processes must be designed to preserve active substances. A particular focus is provided on cultivation (tubular photobioreactor) and different plausible post-treatment scenarios for microalgae separation (flocculation and centrifugation) and preservation (sterilization and drying). For each step, yield and energy consumption are modeled using data taken from literature or lab and pilot scale experiments. Industrial equipment for scale-up process is also studied by comparing existing systems. These models enable to make an economic evaluation of the whole process and to study its profitability for each scenario. The breakeven price is calculated as a function of the production rate. Several parameters are suggested to improve system efficiency and profitability at the end of this study. However, a better microalgae characterization and more experiments on potential post-treatment systems are required to improve the accuracy of the model.

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  • 50.
    Atasoy, Merve
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemiteknik, Resursåtervinning.
    Cetecioglu, Zeynep
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemiteknik, Resursåtervinning.
    Butyric acid dominant volatile fatty acids production: Bio-Augmentation of mixed culture fermentation by Clostridium butyricum2020Ingår i: Journal of Environmental Chemical Engineering, E-ISSN 2213-3437, Vol. 8, nr 6, artikel-id 104496Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The most sustainable and environmentally friendly butyric acid production method is fermentation; however, low production yield and high substrate cost limit the competition with petrol-based production. The study is aimed to enhance butyric acid production via bioaugmentated mixed culture by Clostridium butyricum. Anaerobic sequencing batch reactors (bioaugmented and control) were operated under alkali pH (pH 10) at 35 °C and fed by dairy industry wastewater as substrate. The performance of bioaugmentation was monitored in three stages: before the application, during the application (C. butyricum was injected as %10 of active reactor volume on a daily basis for seven days), after bioaugmentation. The VFA concentration and composition (by GC-FID) with the copy gene number of C. butyricum (by Q-PCR) were monitored in the bioaugmented reactor during the operation. The bioaugmentation of C. butyricum increased butyric acid production (mgCOD L-1) from 260 ± 36 to 2889 ± 180. The total VFA production (mgCOD L-1) was increased from 1434 ± 217 to 4642 ± 1778 in control and bioaugmented reactors, respectively. There was a positive correlation between the gene copies of C. butyricum with butyric, hexanoic, n-heptanoic, valeric acids production. Furthermore, the bioaugmented mixed culture had better performance than pure culture regarding butyric acid production. The cycle analysis showed that the similar butyric acid production efficiency would be obtained in the first 6 h in the bioaugmented reactor, in the first 14 h in the control reactor of the cycle. The study provides a fundamental solution to step forward to achieve next-generation biorefineries by using both monocultures modularity and mixed culture robustness and stability regarding.

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