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  • Public defence: 2020-01-20 09:15 Polhemsalen, Uppsala
    Xu, Xingxing
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Interface Studies for Gold-based Electrochemical DNA Sensors2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Gold based label-free electrochemical DNA sensors have been widely studied for biomarker diagnostics. The sensitivity and reproducibility of these sensors are determined by the sensing interface: the DNA modified gold surfaces. This thesis systematically studies the preparation processes of the DNA sensor interfaces as well as their effects on the sensor performance. First, three pretreatment methods to clean the gold electrode surface and their influence on the subsequent binding of thiolated molecules were carefully investigated. As we found that the surface pretreatment method involving cyclic voltammetry (CV) in H2SO4 may induce structural changes to the gold surface, thus greatly impacting the thiolated molecule binding, the factors influencing this pretreatment method were studied. Practical guidelines were summarized for preparing a clean and reproducible gold surface prior to functionalization. Afterwards, the effects of the surface coverage density of probe DNA and the salt concentration on the probe-target DNA hybridization on a gold sensing surface were systematically investigated using surface plasmon resonance (SPR) analysis. Based on the SPR results, the maximum potentiometric signal that could be generated by the DNA hybridization on the surface, and the detection limits, were estimated for different experimental conditions. These estimations were further compared with experimental results obtained using silicon nanowire field effect transistors (SiNW FET) with DNA modified gold on the gate oxide. Practical limitations for the potentiometric DNA sensor were analysed and discussed. Finally, the stability and reproducibility issues on the electrochemical impedance spectroscopy (EIS) analyses of DNA hybridization were also studied on the aptamer/mercaptohexanol (MCH)-modified gold surface. The root cause for the drift problems in this type of sensor and the temperature effects on the aptamer/MCH modified surface were identified. This thesis could serve as a practical reference for the preparation and understanding of the sensing interface of gold-based electrochemical DNA sensors.

    List of papers
    1. Systematic approach to the development of microfabricated biosensors: relationship between the gold surface pretreatment and thiolated molecule binding
    Open this publication in new window or tab >>Systematic approach to the development of microfabricated biosensors: relationship between the gold surface pretreatment and thiolated molecule binding
    2017 (English)In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 9, no 31, p. 26610-26621Article in journal (Refereed) Published
    Abstract [en]

    Despite the increasing popularity of microfabricated biosensors due to advances in technologic and surface functionalization strategies, their successful implementation is partially inhibited by the lack of consistency in their analytical characteristics. One of the main causes for the discrepancies is the absence of a systematic and comprehensive approach to surface functionalization. In this article microfabricated gold electrodes aimed at biosensor development have been systematically characterized in terms of surface pretreatment, thiolated molecule binding, and reproducibility by means of X-ray photoelectron scattering (XPS) and cyclic voltammetry (CV). It has been shown that after SU-8 photolithography gold surfaces were markedly contaminated, which decreased the effective surface area and surface coverage of a model molecule mercaptohexanol (MCH). Three surface pretreatment methods compatible with microfabricated devices were compared. The investigated methods were (i) cyclic voltammetry in dilute H2SO4, (ii) gentle basic piranha followed by linear sweep voltammetry in dilute KOH, and (iii) oxygen plasma treatment followed by incubation in ethanol. It was shown that all three methods significantly decreased the contamination and increased MCH surface coverage. Most importantly, it was also revealed that surface pretreatments may induce structural changes to the gold surfaces. Accordingly, these alterations influence the characteristics of MCH functionalization.

    National Category
    Other Engineering and Technologies not elsewhere specified
    Identifiers
    urn:nbn:se:uu:diva-326715 (URN)10.1021/acsami.7b08581 (DOI)000407540400106 ()28726367 (PubMedID)
    Funder
    Swedish Foundation for Strategic Research , SSF ICA 12-0047, FFL15-0174Swedish Research Council, VR 2014-5588Carl Tryggers foundation
    Available from: 2017-07-26 Created: 2017-07-26 Last updated: 2019-11-26Bibliographically approved
    2. Revisiting the factors influencing gold electrodes prepared using cyclic voltammetry
    Open this publication in new window or tab >>Revisiting the factors influencing gold electrodes prepared using cyclic voltammetry
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    2019 (English)In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 283, p. 146-153Article in journal (Refereed) Published
    Abstract [en]

    Gold is widely used as the electrode material in different chemi- and biosensing applications while cyclic voltammetry (CV) in sulfuric acid solutions is a commonly employed method for gold surface preparation and characterization. However, as shown herein, chloride leakage from the Ag/AgCl/sat. KCl reference electrode and platinum dissolution from the platinum counter electrode can severely compromise the reproducibility and hence the reliability of the prepared gold electrodes. The aim of this work is to obtain a comprehensive understanding of the separate and interdependent effects of the aforementioned factors on the voltammetric behavior of microfabricated polycrystalline gold electrodes. It is shown that the leakage of chloride gives rise to etching of both the gold working and the platinum counter electrodes and that the chloride concentration has a strong influence on the ratio between the obtained gold and platinum concentrations in the electrolyte. The dissolved gold and platinum are then re-deposited on the gold electrode on the cathodic voltammetric scan, changing the structure and properties of the electrode. It is also demonstrated that the changes in the properties of the gold electrode are determined by the ratio between the co-deposited platinum and gold rather than the absolute amount of platinum deposited on the gold electrode. In addition, the chloride and sulfate adsorption behavior on the gold electrode is carefully investigated. It is proposed that redox peaks due to the formation ofthe corresponding Au(I) complexes can be seen in the double layer region of the voltammogram. The results show that the chloride leakage from the reference electrode needs to be carefully controlled and that platinum counter electrodes should be avoided when developing gold sensing electrodes. The present comprehensive understanding of the electrochemical performance of gold electrodes prepared using CV should be of significant importance in conjunction with both fundamental investigations and practical applications.

    Keywords
    gold electrode, cyclic voltammetry, platinum, electrde etching, chloride leakage, Au(I) complexes
    National Category
    Analytical Chemistry Engineering and Technology
    Research subject
    Chemistry with specialization in Inorganic Chemistry; Engineering Science with specialization in Solid State Physics
    Identifiers
    urn:nbn:se:uu:diva-372135 (URN)10.1016/j.snb.2018.12.008 (DOI)000455854000018 ()
    Funder
    Swedish Foundation for Strategic Research , ICA 12-0047Swedish Foundation for Strategic Research , FFL15-0174Swedish Research Council, 2014-5588Wallenberg Foundations, Academy Fellow
    Available from: 2019-01-06 Created: 2019-01-06 Last updated: 2020-01-08Bibliographically approved
    3. Estimating Detection Limits of Potentiometric DNA sensors Using Surface Plasmon Resonance Analyses
    Open this publication in new window or tab >>Estimating Detection Limits of Potentiometric DNA sensors Using Surface Plasmon Resonance Analyses
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    2019 (English)In: Article in journal (Refereed) Submitted
    National Category
    Electrical Engineering, Electronic Engineering, Information Engineering
    Identifiers
    urn:nbn:se:uu:diva-397806 (URN)
    Funder
    Swedish Foundation for Strategic Research , ICA 12-0047Swedish Foundation for Strategic Research , FFL15-0174Swedish Research Council, VR 2014-5588Wallenberg Foundations
    Available from: 2019-11-25 Created: 2019-11-25 Last updated: 2019-11-26Bibliographically approved
    4. Structural Changes of Mercaptohexanol Self-assembled Monolayers on Gold and their Influence on Impedimetric Aptamer Sensors
    Open this publication in new window or tab >>Structural Changes of Mercaptohexanol Self-assembled Monolayers on Gold and their Influence on Impedimetric Aptamer Sensors
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    2019 (English)In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 91, no 22, p. 14697-14704Article in journal (Refereed) Published
    Abstract [en]

    Despite a large number of publications describing biosensors based on electrochemical impedance spectroscopy (EIS), little attention has been paid to the stability and reproducibility issues of the sensor interfaces. In this work, the stability and reproducibility of faradaic EIS analyses on the aptamer/mercaptohexanol (MCH) self-assembled monolayer (SAM) functionalized gold surfaces in ferri- and ferrocyanide solution were systematically evaluated prior to and after the aptamer-probe DNA hybridization. It is shown that the EIS data exhibited significant drift, and this significantly affected the reproducibility of the EIS signal of the hybridization. As a result, no significant difference between the charge transfer resistance (RCT) changes induced by the aptamer-target DNA hybridization and that caused by the drift could be identified. A conditioning of the electrode in the measurement solution for more than 12 hours was required to reach a stable RCT baseline prior to the aptamer-probe DNA hybridization. The monitored drift in RCT and CDL during the conditioning suggests that the MCH SAM on the gold surface reorganized to a thinner but more closely packed layer. We also observed that the hot binding buffer used in the following aptamer-probe DNA hybridization process could induce additional MCH and aptamer reorganization thus further drift in RCT. As a result, the RCT change caused by the aptamer-probe DNA hybridization was less than that caused by the hot binding buffer (blank control experiment). Therefore, it is suggested that the use of high temperature in the EIS measurement should be carefully evaluated or avoided. This work provides practical guidelines for the EIS measurements. Moreover, since SAM functionalized gold electrodes are widely used in biosensors, e.g., DNA sensors, an improved understanding of the origin of the observed drift is very important for the development of well-functioning and reproducible biosensors.

    National Category
    Analytical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-397690 (URN)10.1021/acs.analchem.9b03946 (DOI)000498280100072 ()31650834 (PubMedID)
    Funder
    Swedish Foundation for Strategic Research , ICA 12-0047Swedish Foundation for Strategic Research , FFL15-0174Swedish Research Council, VR 2014-5588Knut and Alice Wallenberg Foundation, Wallenberg Academy Fellow Program
    Available from: 2019-11-22 Created: 2019-11-22 Last updated: 2020-01-13Bibliographically approved
  • Public defence: 2020-01-24 09:00 Tripple room, Navet ground floor, Uppsala
    Atterby, Clara
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Antibiotic resistance gone wild: A One Health perspective on carriage, selection and transmission of Extended-Spectrum Cephalosporinase- and Carbapenemase-producing Enterobacteriaceae2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Antibiotics have saved millions of lives since they came into clinical use during the Second World War in the 1940s. Today, our effective use of antibiotics is under great threat due to emerging antibiotic resistance in bacteria. This thesis addresses the problems of antibiotic resistance from a ”One Health” perspective. The focus is on antibiotic resistant Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) in the environment and wildlife, and also considering the situation in healthy humans and livestock. 

    In Paper I-III, high occurrence of Extended-Spectrum Beta-Lactamase (ESBL) -producing E. coli and/or K. pneumoniae was detected in fecal samples from wild birds, and the bacteria had genetic similarities to bacteria that cause disease in humans. Proximity to humans was associated with higher occurrence of cephalosporinase (ESBL and pAmpC)-producing E. coli in wild gulls. In Paper IV, ciprofloxacin resistant E. coli was enriched in the gut of mallards exposed to low concentrations of ciprofloxacin, and plasmid conjugation between E. coli bacteria readily took place. In Paper V, carbapenem resistant and blaOXA-48 harbouring- E. coli/K. pneumoniae was rare, but present in healthy humans in rural Cambodia, while cephalosporinase-producing E. coli/K. pneumoniae was common in both humans and livestock. The same ESBL/pAmpC genes were detected in humans and livestock, and exposure to animal manure and slaughter products were risk factors for fecal carriage in humans.

    In conclusion, wild birds can function as potential resistance reservoirs and sentinels for antibiotic resistant E. coli. Environmental pollution from humans is the primary source for antibiotic resistant Enterobacteriaceae found in wildlife, but selection for antibiotic resistant bacteria may also occur in wild birds. The results indicate that transmission of cephalosporinase-producing E. coli/K. pneumoniae occur between wildlife, humans and livestock, but more in-depth molecular work is needed to determine the mechanisms of dissemination. The high community carriage of multidrug-resistant bacteria in rural Cambodia is worrying and highlights Southeast Asia as a hotspot for antibiotic resistance. Antibiotic resistance surveillance is biased towards high-income countries and research should be focused more on low- and middle-income countries, and also include the important “One Health” perspective.

    List of papers
    1. ESBL-producing Escherichia coli in Swedish gulls: A case of environmental pollution from humans?
    Open this publication in new window or tab >>ESBL-producing Escherichia coli in Swedish gulls: A case of environmental pollution from humans?
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    2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 12, article id e0190380Article in journal (Refereed) Published
    Abstract [en]

    ESBL-producing bacteria are present in wildlife and the environment might serve as a resistance reservoir. Wild gulls have been described as frequent carriers of ESBL-producing E. coli strains with genotypic characteristics similar to strains found in humans. Therefore, potential dissemination of antibiotic resistance genes and bacteria between the human population and wildlife need to be further investigated. Occurrence and characterization of ESBL-producing E. coli in Swedish wild gulls were assessed and compared to isolates from humans, livestock and surface water collected in the same country and similar time-period. Occurrence of ESBL-producing E. coli in Swedish gulls is about three times higher in gulls compared to Swedish community carriers (17% versus 5%) and the genetic characteristics of the ESBL-producing E. coli population in Swedish wild gulls and Swedish human are similar. ESBL-plasmids IncF-and IncI1-type carrying ESBL-genes blaCTX-M-15 or blaCTX-M-14 were most common in isolates from both gulls and humans, but there was limited evidence of clonal transmission. Isolates from Swedish surface water harbored similar genetic characteristics, which highlights surface waters as potential dissemination routes between wildlife and the human population. Even in a low-prevalence country such as Sweden, the occurrence of ESBL producing E. coli in wild gulls and the human population appears to be connected and the occurrence of ESBL-producing E. coli in Swedish gulls is likely a case of environmental pollution.

    Place, publisher, year, edition, pages
    PUBLIC LIBRARY SCIENCE, 2017
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-340463 (URN)10.1371/journal.pone.0190380 (DOI)000419033400056 ()29284053 (PubMedID)
    Available from: 2018-02-15 Created: 2018-02-15 Last updated: 2019-11-20Bibliographically approved
    2. High Prevalence and Temporal Variation of Extended Spectrum β-Lactamase–Producing Bacteria in Urban Swedish Mallards
    Open this publication in new window or tab >>High Prevalence and Temporal Variation of Extended Spectrum β-Lactamase–Producing Bacteria in Urban Swedish Mallards
    2018 (English)In: Microbial Drug Resistance, ISSN 1076-6294, E-ISSN 1931-8448Article in journal (Refereed) Published
    Abstract [en]

    Antibiotic resistant bacteria present a growing global healthcare challenge. Previous research demonstrates that wild birds harbor extended spectrum -lactamase (ESBL)-producing Enterobacteriaceae and may contribute to their dissemination. We aimed to assess prevalence and temporal variation in the detection rate of ESBL-producing bacteria in urban wild birds and to evaluate methods regarding sample handling. Monthly fecal sampling was performed in 2013 at an urban pond in Sweden. ESBL-producing Escherichia coli and Klebsiella pneumoniae were analyzed by polymerase chain reaction targeting bla(CTX-M). Subsets of samples were analyzed in multiple replicates and without previous freezing. Pond water samples were screened for 12 antibiotics. Out of 813 fecal samples, 47% grew ESBL-producing E. coli, a higher prevalence than in similar studies. Detection rate varied considerably between months, ranging from 4.2% in May to 84% in July, and was significantly higher during warm months. A majority of isolates harbored CTX-M-15 type ESBL. Detection rates were increased by duplicating samples and by avoiding freezing. No antibiotics were detected in pond water. This study demonstrates high prevalence and a previously undescribed temporal variation in detection rate of ESBL-producing Enterobacteriaceae in wild birds. The distribution of CTX-M genes corresponds well with Swedish human isolates, indicating communication between the genetic pools of ESBLs in humans and wild birds. Urban ponds may serve as important natural reservoirs for antimicrobial resistance.

    Keywords
    Enterobacteriaceae, E.Coli, K. Pneumoniae, antibiotic resistance, wild birds, CTX-M-15
    National Category
    Microbiology Infectious Medicine
    Identifiers
    urn:nbn:se:uu:diva-341493 (URN)10.1089/mdr.2017.0263 (DOI)000419439800001 ()
    Available from: 2018-02-19 Created: 2018-02-19 Last updated: 2019-11-20Bibliographically approved
    3. Increased prevalence of antibiotic resistant E. coli in gulls sampled in Southcentral Alaska is associated with urban environments
    Open this publication in new window or tab >>Increased prevalence of antibiotic resistant E. coli in gulls sampled in Southcentral Alaska is associated with urban environments
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    2016 (English)In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 6, no 1, article id 32334Article in journal (Refereed) Published
    Abstract [en]

    Background : Antibiotic-resistant bacteria pose challenges to healthcare delivery systems globally; however, limited information is available regarding the prevalence and spread of such bacteria in the environment. The aim of this study was to compare the prevalence of antibiotic-resistant bacteria in large-bodied gulls ( Larus spp.) at urban and remote locations in Southcentral Alaska to gain inference into the association between antibiotic resistance in wildlife and anthropogenically influenced habitats. Methods : Escherichia coli was cultured ( n 115 isolates) from fecal samples of gulls (n 160) collected from a remote location, Middleton Island, and a more urban setting on the Kenai Peninsula. Results : Screening of E. coli from fecal samples collected from glaucous-winged gulls ( Larus glaucescens )at Middleton Island revealed 8% of isolates were resistant to one or more antibiotics and 2% of the isolates were resistant to three or more antibiotics. In contrast, 55% of E. coli isolates derived from fecal samples collected from large-bodied gulls (i.e. glaucous, herring [ Larus argentatus ], and potentially hybrid gulls) on the Kenai Peninsula were resistant to one or more antibiotics and 22% were resistant to three or more antibiotics. In addition, total of 16% of the gull samples from locations on the Kenai Peninsula harbored extended-spectrum cephalosporin-resistant E. coli isolates (extended-spectrum beta-lactamases [ESBL] and plasmid-encoded AmpC [pAmpC]), in contrast to Middleton Island where no ESBL- or pAmpC-producing isolates were detected. Conclusion : Our findings indicate that increased prevalence of antibiotic resistance is associated with urban environments in Southcentral Alaska and presumably influenced by anthropogenic impacts. Further investigation is warranted to assess how migratory birds may maintain and spread antimicrobial-resistant bacteria of relevance to human and animal health.

    Keywords
    ESBL, pAmpC, antimicrobial resistance, anthropogenic, gull
    National Category
    Infectious Medicine
    Identifiers
    urn:nbn:se:uu:diva-319621 (URN)10.3402/iee.v6.32334 (DOI)27649798 (PubMedID)
    Available from: 2017-04-06 Created: 2017-04-06 Last updated: 2019-11-20Bibliographically approved
    4. Spread of resistance plasmids and selection of resistant bacteria among Mallards exposed to sub-inhibitory concentrations of antibiotics in their water environment
    Open this publication in new window or tab >>Spread of resistance plasmids and selection of resistant bacteria among Mallards exposed to sub-inhibitory concentrations of antibiotics in their water environment
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Medical and Health Sciences
    Research subject
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-397213 (URN)
    Available from: 2019-11-18 Created: 2019-11-18 Last updated: 2019-11-28
    5. Carriage of carbapenemase- and extended-spectrum cephalosporinase-producing Escherichia coli and Klebsiella pneumoniae in humans and livestock in rural Cambodia: gender and age differences and detection of blaOXA-48 in humans
    Open this publication in new window or tab >>Carriage of carbapenemase- and extended-spectrum cephalosporinase-producing Escherichia coli and Klebsiella pneumoniae in humans and livestock in rural Cambodia: gender and age differences and detection of blaOXA-48 in humans
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    2019 (English)In: Zoonoses and Public Health, ISSN 1863-1959, E-ISSN 1863-2378, Vol. 66, no 6, p. 603-617Article in journal (Refereed) Published
    Abstract [en]

    Objectives: This study investigates the frequency and characteristics of carbapenemase‐producing Escherichia coli/Klebsiella pneumoniae (CPE/K) and extended‐spectrum cephalosporinase‐producing E. coli/K. pneumoniae (ESCE/K) in healthy humans and livestock in rural Cambodia. Additionally, household practices as risk factors for faecal carriage of ESCE/K are identified.

    Methods: Faecal samples were obtained from 307 humans and 285 livestock including large ruminants, pigs and poultry living in 100 households in rural Cambodia in 2011. Each household was interviewed, and multilevel logistic model determined associations between household practices/meat consumption and faecal carriage of ESCE/K. CPE and ESCE/K were detected and further screened for colistin resistance genes.

    Results: CPE/K isolates harbouring blaOXA‐48 were identified in two humans. The community carriage of ESCE/K was 20% in humans and 23% in livestock. The same ESBL genes: blaCTX‐M‐15, blaCTX‐M‐14, blaCTX‐M‐27, blaCTX‐M‐55, blaSHV‐2, blaSHV‐12, blaSHV‐28; AmpC genes: blaCMY‐2, blaCMY‐42, blaDHA‐1; and colistin resistance genes: mcr‐1‐like and mcr‐3‐like were detected in humans and livestock. ESCE/K was frequently detected in women, young children, pigs and poultry, which are groups in close contact. The practice of burning or burying meat waste and not collecting animal manure indoors and outdoors daily were identified as risk factors for faecal carriage of ESCE/K.

    Conclusions: Faecal carriage of E. coli and K. pneumoniae harbouring extended‐spectrum cephalosporinase genes are common in the Cambodian community, especially in women and young children. Exposure to animal manure and slaughter products are risk factors for intestinal colonization of ESCE/K in humans.

     

    Keywords
    AmpC, Cambodia, ESBL, carbapenemase, colistin, risk factors, rural population, zoonoses
    National Category
    Infectious Medicine
    Identifiers
    urn:nbn:se:uu:diva-388725 (URN)10.1111/zph.12612 (DOI)000473968900001 ()31264805 (PubMedID)
    Funder
    Swedish Civil Contingencies AgencySida - Swedish International Development Cooperation Agency, 2010-7876Swedish Research Council, 2016-02606
    Available from: 2019-07-03 Created: 2019-07-03 Last updated: 2019-11-20Bibliographically approved
  • Public defence: 2020-01-24 10:15 Brusewitzsalen, Uppsala
    Grech-Madin, Charlotte
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Peace and Conflict Research. Research School of the UNESCO Category II International Centre for Water Cooperation, Stockholm.
    The Water Taboo: Restraining the Weaponisation of Water in International Conflict2020Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Why do nation states in conflict with one another refrain from weaponising water? Water has long been a standard weapon of armed conflict. In the post-World War II period, however, nation states in international conflict have made concerted efforts to restrain its weaponisation. This is puzzling given the absolute vitality of water to an adversary, a long historical record of water weaponisation, and water’s heightened military utility in the face of rising scarcity. Distinct from existing scholarship, this study contends that water has become embedded in a global normative inhibition – a “water taboo” – that denounces its weaponisation as morally unacceptable. Through qualitative case research involving elite interviewing and historical analysis, this study examines the water taboo. Three focal points include its existence, how it evolved over time, and most importantly, how it influences states’ decisions on whether or not to weaponise water. The study first outlines the water taboo. Next it analyses the taboo’s historical origins, and later its strengthening from the 1950s to the present via a confluence of broader humanitarian and environmental protection movements. It then examines the taboo’s influence in a “hard” case of India in the 1999 Kargil War, and “deviant” case of the US in the 1991 Gulf War. Altogether, the study contributes that: (i) a moral aversion to weaponising water exists; (ii) it has evolved through multiple phases of norm strengthening in the past seventy years; and (iii) it influences state behaviour at an instrumental level and, in some cases, more internalised level of compliance. Where the taboo is not fully internalised, this study finds that the taboo’s influence is mediated by levels of military necessity, operational dependence of the military on politicians, and embeddedness of belligerents in the international community. These findings firmly extend IR and Peace and Conflict literature into the domain of water, and suggest future avenues for research and policy to charter long-term peace and security around water.

  • Public defence: 2020-01-24 10:15 Sal IV, Uppsala
    Wejderstam, Andreas
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Theology, Department of Theology, Church and Mission studies, Church History.
    Personlig och kyrklig förnyelse: Svenska kyrkan och Vadstenamötena 1943–19852019Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Personal and Ecclesiastic Renewal – The Church of Sweden and the Vadstena Meetings 1943–1985.

    In this study, I examine the Vadstena Meetings for Personal and Ecclesiastic Renewal in order to contribute to the understanding of the Church of Sweden during the Cold War era. The primary sources are archives: the Vadstena Meetings archive in Linköping and certain personal archives.

    After the first two chapters, Introduction and Historical background, the study is chronologically organised. In the two following chapters, three and four, I focus on the meetings first phase, 1943 and 1945-46. The fifth chapter analyses an expansive era, 1947-59, when meetings were held on several places. In chapter six I examine the last phase of the meetings, 1960-85, characterised by stagnation and withdrawal. Chapter seven concludes the study.

    The Vadstena Meetings were voluntarily organised meetings, formally detached from, but within the framework of Church of Sweden. Initiators and organisers were prominent within the Church and active contributors were bishops, directors and well-known clergy. Women constituted the majority of the attending participants.

    As a point of departure for the analysis of the meetings a comprehensive account of the meetings is given as to the organisers, contributors, participants and their programmes.  The organisation has been illustrated by applying Judith Sharken Simons model in five stages of a life cycle of non-profit organisations: Imagine and Inspire, Found and Frame, Ground and Grow, Produce and Sustain and, finally, Review and Renew.

    The Vadstena Meetings comprised both continuity and change with a continued focus on personal renewal. They provide an example of consensus aspiration and endeavour to bring together fractions within the Church of Sweden without compromising the essence of different groupings. The most prominent groupings at the time of consolidation of the Vadstena Meetings were the High Church movement and the Oxford Group Movement.

    Although the idea and aspiration for amplitude continued well into the late 1950s, the Vadstena Meetings became more and more conform. By following the historical progress of the Meetings and putting them into context, I show how they reflect the development and change within society and the Church of Sweden. Corresponding to the growing emphasis on individual participation in civil society the Vadstena Meetings illustrate the changing and expanding possibilities for individuals to influence the Church.

  • Public defence: 2020-01-24 13:00 Uppsala
    Encarnação, João Crispim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medical Radiation Science. Department of Immunology, Genetics and Pathology.
    Towards time-resolved molecular interaction assays in living bacteria2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Rare and neglected diseases such as multidrug resistant (MDR) tuberculosis, malaria and trypanosomiasis are re-emerging in Europe. New strategies are needed to accelerate drug discovery to fight these pathogens. AEGIS is a Pan-European project that combines different technologies to accelerate the discovery of molecules suitable for drug development in selected neglected diseases. This thesis is part of the AEGIS research area that considers time in a multidisciplinary approach, combining biology, physics and mathematics to provide tools to characterize biological events for improving drug development and information about the target diseases and lead compounds.

    Real-time cell binding assays (RT-CBA) of receptor-ligand interactions are fundamental in basic research and drug discovery. However, this kind of assays are still rare on living cells, especially in the microbiology field. In this project, we apply the same high-precision assay type on bacterial systems and explored the interior of the cell with a time resolved assay.

    The effect of temperature was evaluated in the RT-CBA using LigandTracer to ensure that it was possible to use the technology in a range of temperatures suitable for bacteria. A method for attaching Gram positive and negative bacteria on the surface of a normal Petri dish, showing a high reproducibly and a high cellular viability after 16 h. With these two key steps, an RT-CBA fit for microbiology is available.

    Next, to answer biological questions, intracellular interactions were explored by expression and validation of intracellular proteins with fluorescent tags suitable for RT-CBAs. First, we used the subunit B from the Shiga toxin (STxB) as a model to understand different aspects about the internalization processes. RT-CBAs allowed to discovery new features of STxB binding and mechanism to deliver small molecules or small proteins into cancer cells. Then, for exploring intracellular interactions, insect cells were bioengineered for evaluating the ability of small molecules to internalize and bind to its target. Using Carbonic anhydrase II – sulfonamides as a model system, the molecular interaction in the cytoplasm could be measured using a quencher label approach. The development of this kind of novel RT-CBA tools provide new information about drug candidates for targets that are not properly expressed in bacterial cells.

    The assays in this project can make drug design more efficient. Furthermore, the evaluation of binding activity of the new compounds developed by AEGIS, focusing on rare/neglected diseases, in a biological environment has the potential to accelerate drug discovery for the targeted emerging diseases.

    List of papers
    1. Impact of assay temperature on antibody binding characteristics in living cells: A case study
    Open this publication in new window or tab >>Impact of assay temperature on antibody binding characteristics in living cells: A case study
    2017 (English)In: BIOMEDICAL REPORTS, ISSN 2049-9434, Vol. 7, no 5, p. 400-406Article in journal (Refereed) Published
    Abstract [en]

    Kinetic and thermodynamic studies of ligand-receptor interactions are essential for increasing the understanding of receptor activation mechanisms and drug behavior. The characterization of molecular interactions on living cells in real-time goes beyond most current binding assays, and provides valuable information about the dynamics and underlying mechanism of the molecules in a living system. The effect of temperature on interactions in cell-based assays is, however, rarely discussed. In the present study, the effect of temperature on binding of monoclonal antibodies, cetuximab and pertuzumab to specific receptors on living cancer cells was evaluated, and the affinity and kinetics of the interactions were estimated at selected key temperatures. Changes in the behavior of the interactions, particularly in the on- and off-rates were observed, leading to greatly extended time to reach the equilibrium at 21 degrees C compared with at 37 degrees C. However, the observed changes in kinetic characteristics were less than a factor of 10. It was concluded that it is possible to conduct real-time measurements with living cells at different temperatures, and demonstrated that influences of the ambient temperature on the interaction behavior are likely to be less than one order of magnitude.

    Keywords
    drug kinetics, thermodynamics, real-time interactions, clinical monoclonal antibodies, growth factor receptors
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
    Identifiers
    urn:nbn:se:uu:diva-345264 (URN)10.3892/br.2017.982 (DOI)000417416000002 ()29181152 (PubMedID)
    Funder
    EU, Horizon 2020, 2014-2020
    Available from: 2018-03-09 Created: 2018-03-09 Last updated: 2019-11-22Bibliographically approved
    2. Detecting ligand interactions in real time on living bacterial cells
    Open this publication in new window or tab >>Detecting ligand interactions in real time on living bacterial cells
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    2018 (English)In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 102, no 9, p. 4193-4201Article in journal (Refereed) Published
    Abstract [en]

    Time-resolved analysis assays of receptor-ligand interactions are fundamental in basic research and drug discovery. Adequate methods are well developed for the analysis of recombinant proteins such as antibody-antigen interactions. However, assays for time-resolved ligand-binding processes on living cells are still rare, in particular within microbiology. In this report, the real-time cell-binding assay (RT-CBA) technology LigandTracerA (R), originally designed for mammalian cell culture, was extended to cover Gram-positive and Gram-negative bacteria. This required the development of new immobilization methods for bacteria, since LigandTracer depends on cells being firmly attached to a Petri dish. The evaluated Escherichia coli CJ236 and BL21 as well as Staphylococcus carnosus TM300 strains were immobilized to plastic Petri dishes using antibody capture, allowing us to depict kinetic binding traces of fluorescently labeled antibodies directed against surface-displayed bacterial proteins for as long as 10-15 h. Interaction parameters, such as the affinity and kinetic constants, could be estimated with high precision (coefficient of variation 9-44%) and the bacteria stayed viable for at least 16 h. The other tested attachment protocols were inferior to the antibody capture approach. Our attachment protocol is generic and could potentially also be applied to other assays and purposes.

    Place, publisher, year, edition, pages
    SPRINGER, 2018
    Keywords
    Real-time interactions, Drug kinetics, Living bacteria, Antibodies
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-352571 (URN)10.1007/s00253-018-8919-3 (DOI)000429800600027 ()29550990 (PubMedID)
    Funder
    Swedish Research CouncilEU, European Research Council, 675555
    Available from: 2018-08-07 Created: 2018-08-07 Last updated: 2019-11-22Bibliographically approved
    3. Revealing the dynamic features of STxB-Gb3 co-internalization mechanism of molecular cargo into cancer cells
    Open this publication in new window or tab >>Revealing the dynamic features of STxB-Gb3 co-internalization mechanism of molecular cargo into cancer cells
    (English)Manuscript (preprint) (Other academic)
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
    Identifiers
    urn:nbn:se:uu:diva-397748 (URN)
    Available from: 2019-11-25 Created: 2019-11-25 Last updated: 2019-12-02
    4. Bioengineering living cells for measuring intracellular interactions of small-molecules in real-time
    Open this publication in new window or tab >>Bioengineering living cells for measuring intracellular interactions of small-molecules in real-time
    (English)Manuscript (preprint) (Other academic)
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
    Identifiers
    urn:nbn:se:uu:diva-397752 (URN)
    Available from: 2019-11-25 Created: 2019-11-25 Last updated: 2019-12-02
  • Public defence: 2020-01-25 10:00 Ihresalen, Engelska Parken, Uppsala
    Öztekin, Buket
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Linguistics and Philology.
    Typical and atypical language development in Turkish-Swedish bilingual children aged 4–72019Doctoral thesis, monograph (Other academic)
    Abstract [en]

    This thesis investigates the vocabulary and narrative macrostructure skills of 102 typically-developing (TD) 4- to 7-year-old Turkish-Swedish bilingual children (cross-sectional), the development of these skills over time from age 4 to 6 in a subgroup of 10 children (longitudinal), and six Turkish-Swedish children with a language impairment (LI) diagnosis (clinical). The children’s health, family and language backgrounds, their language use and input patterns are explored through parental questionnaires, family interviews, and interviews with teachers and speech-language pathologists. In both Turkish and Swedish, comprehension and production are assessed with comparable materials: Cross-Linguistic Lexical Tasks (CLT; Haman et al., 2015), and Multilingual Assessment Instrument for Narratives (MAIN; Gagarina et al., 2012). For vocabulary (CLT), age development, language differences (Turkish vs. Swedish), differences between comprehension and production, and effects of language use and input are explored. For narrative macrostructure (MAIN), age development, language differences and task differences (Cat/Dog vs. Baby Birds/Baby Goats) are analyzed. LI children’s scores are compared with TD children, with additional focus on the LI children’s communicative, linguistic and social behavior. 

    In both vocabulary comprehension and production, the youngest TD groups performed better in Turkish than in Swedish, but by age 6, Turkish and Swedish vocabulary scores matched due to rapid improvement in Swedish. Factors related to vocabulary scores were: daily language input, parents’ language use with each other and with the child, and child’s language with the sibling(s). For narratives, comprehension was ahead of production. There was no difference between Turkish and Swedish MAIN comprehension, but for both languages a task effect was found (higher scores on Cat/Dog than Baby Birds/Baby Goats). Narrative production scores were generally low for both languages, but increased more with age in Swedish than in Turkish. The longitudinal study largely confirmed the patterns found in the cross-sectional data.

    The majority of the LI children performed far below their TD peers in both their languages. Some LI children performed very low in only one language, despite extensive and long-term exposure to that language. In contrast, TD children with very low scores in one language usually had very limited exposure to that language. LI children were also reported to have difficulties with word learning, pragmatics, and attention, and a family history with language problems. It is suggested that bilingual children with potential language impairment should be assessed holistically in both their languages and extensive information about their family backgrounds and language input characteristics be collected.

     

  • Public defence: 2020-01-28 10:00 Axel Hambergsalen, Uppsala
    Liu, Lei
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Mineralogy Petrology and Tectonics.
    Synthesis and Tuning of Multifunctional Materials at High Pressure2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    At the present stage, human society is developing at an unprecedented speed, facing an emergence of highly pressing challenges, e.g., information explosion, energy production problems, environmental pollution, climate problems. Functional materials with tailored properties are considered as holding a key to solving these problems. In this thesis, high-pressure techniques were employed to synthesize and tune the properties of multiferroic materials relevant to spintronic and light-harvesting applications, and multifunctional high-entropy alloys.

    Melanostibite (Mn2FeSbO6, MFSO) is a very rare mineral discovered in Sweden. Previous studies indicate it is a potential multiferroic material with foreseen applications in information storage and spintronic devices. However, its multiferroic phase has not been synthesized yet. Herein, the structural evolution of MFSO was studied up to ~50 GPa, and the LiNbO3-type MFSO was synthesized at high pressure and moderate temperature. As a polar structure material, the LiNbO3-type MFSO represents a promising candidate for multiferroic materials. The double perovskite, Pb2CoTeO6, was also compressed to ~60 GPa, while no polar phase was discovered. The obtained results provide guidance to the synthesis of new multiferroic double perovskite.

    Solar energy is a promising alternative to fossil fuels and thus a viable solution to the global energy problem. Light-harvesting materials, which absorb sunlight and transform it into electricity by the photovoltaic effect, represent the core part of solar cells. Currently, the dominant commercial light-harvesting material is silicon. However, silicon and recently emerged organic-inorganic perovskites have several drawbacks. Multiferroic oxides are considered as stable and nontoxic light-harvesting materials. But, their bandgap energies are generally too large for photovoltaic applications. Herein, high-pressure technique was applied to treat Mn3TeO6, and a quenchable phase of Mn3TeO6 displaying a greatly narrowed bandgap was synthesized. The measured absorption spectrum of the quenched phase reveals that it may be suitable for photovoltaic applications. The present research opens a green way to tune the bandgap energy of multiferroic.

    High-entropy alloys (HEAs) were first synthesized in 2004. However, knowledge of this new class of promising alloys is still very limited, even in very fundamental aspects. The present results reveal that lattice distortion plays important roles in the phase transition of HEAs, and demonstrate the future possibility of designing the Invar high-entropy alloy, a promising structural material. The results show that it is possible to combine several practical properties in a single alloy, which will widen the range of applications of HEAs. 

    The presented research demonstrates that high-pressure represents an effective way to tune various properties of materials, as well as can be applied for the synthesis of materials with exotic properties which are usually not stable or attainable at ambient conditions.

    List of papers
    1. Pressure-induced polymorphism and piezochromism in Mn2FeSbO6
    Open this publication in new window or tab >>Pressure-induced polymorphism and piezochromism in Mn2FeSbO6
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    2019 (English)In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 114, no 16, article id 162903Article in journal (Refereed) Published
    Abstract [en]

    In the last decade, major efforts have been devoted to searching for polar magnets due to their vast potential applications in spintronic devices. However, the polar magnets are rare because of conflicting electronic configuration requirements of ferromagnetism and electric polarization. Double-perovskite oxides with a polar structure containing transition metal elements represent excellent candidates for the polar magnet design. Herein, the crystal structure evolution of Mn2FeSbO6 (MFSO) was investigated at pressures reaching similar to 50 GPa by in situ synchrotron X-ray diffraction (XRD), Raman scattering, and ab initio calculation techniques. The XRD results reveal ilmenite-to perovskite-type phase transition at around 35 GPa. An additional intermediate phase, observed in the range of 31-36 GPa by Raman spectroscopy, but not the XRD technique, is proposed to represent the polar LiNbO3 phase. It is argued that this phase emerged due to the heating effect of the Raman-excitation laser. The LiNbO3-type MFSO compounds, displaying an intrinsic dipole ordering, represent a promising candidate for multiferroic materials. The detected phase transitions were found to be reversible although a significant hysteresis was noticeable between compression and decompression runs. Moreover, a pressure-induced piezochromism, signifying a bandgap change, was discovered by the direct visual observations and corroborated by ab initio calculations. The present study benefits an efficient high-pressure synthesis of polar magnetic double-perovskite oxides in the future.

    Place, publisher, year, edition, pages
    AMER INST PHYSICS, 2019
    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-383857 (URN)10.1063/1.5090649 (DOI)000466264600024 ()
    Available from: 2019-05-24 Created: 2019-05-24 Last updated: 2019-11-25Bibliographically approved
    2. Pressure tuning of octahedral tilt in the ordered double perovskite Pb2CoTeO6
    Open this publication in new window or tab >>Pressure tuning of octahedral tilt in the ordered double perovskite Pb2CoTeO6
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    2019 (English)In: Journal of Alloys and Compounds, ISSN 0925-8388, E-ISSN 1873-4669, Vol. 801, p. 310-317Article in journal (Refereed) Published
    Abstract [en]

    Double perovskites represent a family of materials with promising fundamental properties (e.g. multiferroicity) and vast potential applications. However, the knowledge of pressure effects on the crystal structure of double perovskite is limited, which hinders their efficient synthesis using high-pressure techniques. Pb2CoTeO6 (PCTO) is considered as a good candidate for multiferroic materials, although a polymorph with a polar structure has not been synthesized yet. In the present study, the pressure effect on the crystal structure of PCTO was systematically studied by employing in situ synchrotron X-ray powder diffraction and Raman scattering techniques up to 60 GPa. A structural phase transition from R-3 to I2/m structure was observed at around 20 GPa, indicating that increasing the pressure has a similar effect on PCTO as decreasing the temperature, i.e., promoting the distortion of the structure. No polar structure of PCTO has been observed in the applied pressure range. The present study provides a valuable information about the crystal structure evolution of double perovskites upon compression, and will benefit high-pressure syntheses of novel double perovskites in the future. 

    Place, publisher, year, edition, pages
    ELSEVIER SCIENCE SA, 2019
    Keywords
    Double perovskite, Phase transition, High pressure, Raman spectroscopy, X-ray powder diffraction
    National Category
    Materials Chemistry
    Identifiers
    urn:nbn:se:uu:diva-390373 (URN)10.1016/j.jallcom.2019.06.096 (DOI)000474352000039 ()
    Funder
    Swedish Research Council
    Available from: 2019-08-12 Created: 2019-08-12 Last updated: 2019-11-25Bibliographically approved
    3. Bandgap engineering in Mn3TeO6: giant irreversible bandgap reduction triggered by pressure
    Open this publication in new window or tab >>Bandgap engineering in Mn3TeO6: giant irreversible bandgap reduction triggered by pressure
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    2019 (English)In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 55, p. 12000-Article in journal (Refereed) Published
    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-395737 (URN)
    Available from: 2019-10-23 Created: 2019-10-23 Last updated: 2019-11-25
    4. Lattice distortion-induced sluggish phasetransition in CoCrFeNixAl1-x (x = 0.5, 0.75) highentropyalloys at high pressures
    Open this publication in new window or tab >>Lattice distortion-induced sluggish phasetransition in CoCrFeNixAl1-x (x = 0.5, 0.75) highentropyalloys at high pressures
    2019 (English)In: High Pressure Research, ISSN 0895-7959, E-ISSN 1477-2299Article in journal (Refereed) Published
    National Category
    Metallurgy and Metallic Materials
    Identifiers
    urn:nbn:se:uu:diva-395736 (URN)10.1080/08957959.2019.1653865 (DOI)
    Available from: 2019-10-23 Created: 2019-10-23 Last updated: 2019-11-25
    5. Pressure-induced magnetovolume effect in CoCrFeAl high-entropy alloy
    Open this publication in new window or tab >>Pressure-induced magnetovolume effect in CoCrFeAl high-entropy alloy
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    2019 (English)In: Communications Physics, E-ISSN 2399-3650, Vol. 2, article id 42Article in journal (Refereed) Published
    Abstract [en]

    High-entropy alloys (HEAs) composed of multiple-principal elements with (nearly) equimolar ratio establish a new conceptual framework for alloy design and hold a promise for extensive applications in industry, akin to the controlled expansion alloys (CEAs), such as Invar alloys. Spontaneously, one question emerges - would it be possible to synthesize a novel class of alloys combining the virtues of both CEAs and HEAs? Here, we report the pressure-induced magnetovolume effect in the body-centered-cubic CoCrFeAl HEA coupled with magnetic phase transitions from ferromagnetic to paramagnetic, and to non-magnetic states, originating from the successive collapses of local magnetic moments of Co and Fe. The observed magnetovolume anomalies, occurring in a progressive way, tailor appreciably the coefficient of thermal expansion of CoCrFeAl. These results further strengthen HEAs’ anticipated potential for designing multifunctional materials in virtue of their multiple outstanding properties, and reveal possible routes for their future synthesis.

    National Category
    Condensed Matter Physics Earth and Related Environmental Sciences
    Identifiers
    urn:nbn:se:uu:diva-382796 (URN)10.1038/s42005-019-0141-9 (DOI)000467220700001 ()
    Available from: 2019-05-03 Created: 2019-05-03 Last updated: 2019-11-25Bibliographically approved
  • Public defence: 2020-01-31 13:30 Å80101, Uppsala
    Damas, Giane B.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Atomic Scale Modelling in Photoelectrocatalysis: Towards the Development of Efficient Materials for Solar Fuel Production2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Using sunlight to produce valuable chemicals has been pointed out as an interesting alternative to deal with the well-known environmental problem related to the use of fossil fuels for energy generation. Thus, it is crucial for this field the development of novel photocatalysts that could drive the uphill reactions with high efficiency while presenting low price and toxicity. In this context, conjugated polymers with a donor-acceptor architecture have shown good photoactivity for the hydrogen evolution reaction (HER) due to their advantageous properties, including a broad UV-Vis absorption spectrum and thermodynamic driving force to carry out the charge transfer processes. In this thesis, a series of fluorene- and benzothiadiazole-based polymers are evaluated by means of ab initio methods as potential candidates for photocatalytic HER. A set of small-molecules with well-defined molecular weight have also been considered for this application. In general, tailoring a chemical unit has enabled an improvement of the absorption capacity in benzo(triazole-thiadiazole)-based polymers and cyclopentadithiophene-based polymers, with a higher impact exhibited upon acceptor tailoring. On the other hand, all systems under investigation present favorable thermodynamics for proton reduction or hole removal by an appropriate sacrificial agent. In particular, it is demonstrated the active role played by nitrogen atoms from the acceptor units in the hydrogenation process, whose binding strength is significantly decreased in benzo(triazole-thiadiazole)-based polymers. Furthermore, the extension of the electron-hole separation has been assessed through the calculation of the exciton binding energies, which are diminished with an improvement in the donating ability on cyclopentadithiophene-based materials.

    In another approach to deal with the aforementioned problem, it has been considered the direct conversion of carbon dioxide into formic acid, an important chemical that finds applications in fuel cells, medicine and food industries. In this thesis, such electrocatalytic process has been investigated by using Sn-based electrodes and Ru-complexes. In the former case, a solid-state modelling approach based on slab geometries to model surface states has been employed to explore the reaction thermochemistry. The outcomes support the reaction mechanism where the carbon dioxide insertion into the Sn-OH bond is a thermodynamically favorable step prior to reduction, which has a redox potential in fair agreement with the measurements carried out by our collaborators. In a Ru-complex, the reaction mechanism is likely to follow the route with natural production of CO due to ligand release after the first reduction process, which is further protonated to originate the active species. In this case, the insertion occurs at the Ru-H bond to generate a carbon-bound species that is the intermediate in the formic acid production after the second protonation step. Finally, it has been studied the physical adsorption of carbon dioxide in metal-organic frameworks with a varying metallic center in a theoretical point of view.

    List of papers
    1. An experimental and theoretical study of an efficient polymer nano-photocatalyst for hydrogen evolution
    Open this publication in new window or tab >>An experimental and theoretical study of an efficient polymer nano-photocatalyst for hydrogen evolution
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    2017 (English)In: Energy & Environmental Science, ISSN 1754-5692, E-ISSN 1754-5706, Vol. 10, no 6, p. 1372-1376Article in journal (Refereed) Published
    Abstract [en]

    In this work, we report a highly efficient organic polymer nano-photocatalyst for light driven proton reduction. The system renders an initial rate of hydrogen evolution up to 50 +/- 0.5 mmol g(-1) h(-1), which is the fastest rate among all other reported organic photocatalysts. We also experimentally and theoretically prove that the nitrogen centre of the benzothiadiazole unit plays a crucial role in the photocatalysis and that the Pdots structure holds a close to ideal geometry to enhance the photocatalysis.

    Keywords
    CATALYSTS; H-2; SYSTEM; ENVIRONMENTAL SCIENCES; CELLS; CONJUGATED POLYMERS; ENERGY & FUELS; ARTIFICIAL PHOTOSYNTHESIS; WATER; ENGINEERING, CHEMICAL; GENERATION; CHEMISTRY, MULTIDISCIPLINARY; VISIBLE-LIGHT
    National Category
    Polymer Chemistry Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-332949 (URN)10.1039/c7ee00751e (DOI)000403320300009 ()
    Funder
    Knut and Alice Wallenberg FoundationSwedish Energy AgencyÅForsk (Ångpanneföreningen's Foundation for Research and Development)Stiftelsen Olle Engkvist ByggmästareStandUp
    Available from: 2017-11-02 Created: 2017-11-02 Last updated: 2019-12-03Bibliographically approved
    2. On the Design of Donor Acceptor Conjugated Polymers for Photocatalytic Hydrogen Evolution Reaction: First-Principles Theory-Based Assessment
    Open this publication in new window or tab >>On the Design of Donor Acceptor Conjugated Polymers for Photocatalytic Hydrogen Evolution Reaction: First-Principles Theory-Based Assessment
    2018 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 47, p. 26876-26888Article in journal (Refereed) Published
    Abstract [en]

    A set of fluorene-based polymers with a donor acceptor architecture has been investigated as a potential candidate for photocatalytic hydrogen evolution reaction. A design protocol has been employed based on first -principles theory and focusing on the following properties: (i) broad absorption spectrum to promote a higher number of photogenerated electron hole pairs, (ii) suitable redox potentials, and (iii) appropriate reaction thermodynamics using the hydrogen -binding energy as a descriptor. We have found that the polymers containing a fused -ring acceptor formed by benzo(triazole-thiadiazole) or benzo(triazole-selenodiazole) units display a suitable combination of such properties and stand out as potential candidates. In particular, PFO-DSeBTrT (poly (9,9'-dioctylfluorene)-2,7-diyl-alt-(4,7-bis(thien-2y1)-2-dodecyl-benzo-(1,2c:4,5c')-1,2,3-triazole-2,1,3-selenodiazole)) has an absorption maximum at around 950 nm for the highest occupied molecular orbital lowest unoccupied molecular orbital transition, covering a wider range of solar emission spectrum, and a reduction catalytic power of 0.78 eV. It also displays a calculated hydrogen -binding free energy of Delta G(H) = 0.02 eV, which is lower in absolute value than Furthermore, the results and trends analysis provide guidance for the rational design of novel photo-electrocatalysts. that of Pt (Delta G(H) approximate to -0.10 eV).

    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-372709 (URN)10.1021/acs.jpcc.8b09408 (DOI)000451933400012 ()
    Funder
    Swedish Research CouncilCarl Tryggers foundation StandUp
    Available from: 2019-01-09 Created: 2019-01-09 Last updated: 2019-12-03Bibliographically approved
    3. Tailoring the Electron-Rich Moiety in Benzothiadiazole-Based Polymers for an Efficient Photocatalytic Hydrogen Evolution Reaction
    Open this publication in new window or tab >>Tailoring the Electron-Rich Moiety in Benzothiadiazole-Based Polymers for an Efficient Photocatalytic Hydrogen Evolution Reaction
    2019 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 42, p. 25531-25542Article in journal (Refereed) Published
    Abstract [en]

    Polymeric materials containing an extended π-conjugated backbone have shown a wide range of applicability including photocatalytic activity for the hydrogen evolution reaction (HER). The latter requires highly efficient materials with optimal light absorption and thermodynamic driving force for charge transfer processes, properties that are tailored by linking chemical units with distinct electron affinity to form a donor−acceptor architecture. Here, this concept is explored by means of ab initio theory in benzothiadiazole-based polymers with varying electron-rich moieties, viz., fluorene (PFO), cyclopentadithiophene (CPT), methoxybenzodithiophene (O-BzT), thiophenebenzodithiophene (T-BzT), and thiophene (T, VT)and thienethiophene (TT, VTT)-based units. All materials exhibit a red-shifted absorption spectrum with respect to the reference polymer (PFO-DT-BT) while keeping the catalytic power for hydrogen production almost unchanged. In particular, a displacement ofΔλ = 167 nm in the first absorption maximum has been achieved upon combination of chemical units with high donating character in CPT-VTT-BT. Furthermore, the exciton binding energies (Eb) have been systematically investigated to unveil the effects of geometry relaxation, environment polarity, and finite temperature contributions to the free energy. For instance, we show a significant change in Eb when going from the gas phase (Eb = 1.43−1.85 eV) to the solvent environment (Eb = 0.29−0.54 eV in 1-bromooctane with ε = 5.02). Furthermore, we have found a linear correlation between the lowering of exciton binding energies and the increasing of the ratio between donor and acceptor contributions to the HOMO orbital. This is a consequence of increased donating ability and enhanced spatial separation of electron−hole pairs, which weakens their interaction. Finally, our findings reveal that the donor unit plays a crucial role in key properties that govern the photocatalytic activity of donor−acceptor polymers contributing to the development of a practical guideline to design more efficient photocatalysts for the HER. This goes through a proper combination of electron-rich moieties to tune the optical gap, favor thermodynamic driving force for charge transfer, and lower exciton binding energies.

    National Category
    Atom and Molecular Physics and Optics
    Research subject
    Physics with specialization in Quantum Chemistry
    Identifiers
    urn:nbn:se:uu:diva-395873 (URN)10.1021/acs.jpcc.9b06057 (DOI)000492803300001 ()
    Funder
    Swedish Research CouncilCarl Tryggers foundation
    Available from: 2019-10-24 Created: 2019-10-24 Last updated: 2019-12-03Bibliographically approved
    4. Symmetric Small-Molecules With Acceptor-Donor-Acceptor Architecture for Efficient Visible-Light Driven Hydrogen Production: Optical and Thermodynamic Aspects
    Open this publication in new window or tab >>Symmetric Small-Molecules With Acceptor-Donor-Acceptor Architecture for Efficient Visible-Light Driven Hydrogen Production: Optical and Thermodynamic Aspects
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    (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455Article in journal (Refereed) In press
    Abstract [en]

    Small-molecules (SM) have attracted a great deal of attention in the field of solar energy conversion due to their unique propertiescompared to polymers, such as well-defined molecular weight and lack of regio-isomeric impurities. Furthermore, these materials can be synthesized in a variety of configurational architectures, representing an opportunity for tailoring chemical and optical properties that could lead to a better photocatalytic efficiency for hydrogen generation. Here, we evaluate by means of density functional theory (DFT) and time-dependent DFT methods a set of small-molecules with A-D-A architecture (A-acceptor; D- donor) based on well-known building blocks like thiophene (T), cyclopentadithiophene (CPT) and benzothiadiazole (BT) as potential candidates for photocatalytic hydrogen evolution reaction (HER). We also propose i) the replacement of the thiophene unit by 3,4-ethylenedioxythiophene (EDOT) to form with CPT unit an extended donor core ii) an additional acceptor unit, the 1,3,4-thiadiazole (Tz), in the extremities and iii) insertion of the difluoromethoxy (DFM) as substituent in the BT unit. Our outcomes reveal that these materials have a broad absorption spectrum with λ= 318-719 nm, being the most intense absorption peak originated from an electronic transition with charge-transfer nature, as the spatial distribution of LUMO is concentrated on the acceptor units for all materials. Moreover, these small-molecules not only present catalytic power or thermodynamic driving force to carry out the chemical reactions involved in the process of hydrogen production, but can be coupled in cooperative photocatalytic systems to promote intramolecular charge transfer that is expected to boost the overall photocatalytic efficiency of these materials.

    Keywords
    Small Molecules, Photocatalysis, Hydrogen Production, Density Functional Theory
    National Category
    Other Chemistry Topics
    Research subject
    Chemistry
    Identifiers
    urn:nbn:se:uu:diva-398119 (URN)
    Available from: 2019-12-02 Created: 2019-12-02 Last updated: 2019-12-05
    5. On the Mechanism of Carbon Dioxide Reduction on Sn-Based Electrodes: Insights into the Role of Oxide Surfaces
    Open this publication in new window or tab >>On the Mechanism of Carbon Dioxide Reduction on Sn-Based Electrodes: Insights into the Role of Oxide Surfaces
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    2019 (English)In: Catalysts, E-ISSN 2073-4344, Vol. 9, no 8, article id 636Article in journal (Refereed) Published
    Abstract [en]

    The electrochemical reduction of carbon dioxide into carbon monoxide, hydrocarbons and formic acid has offered an interesting alternative for a sustainable energy scenario. In this context, Sn-based electrodes have attracted a great deal of attention because they present low price and toxicity, as well as high faradaic efficiency (FE) for formic acid (or formate) production at relatively low overpotentials. In this work, we investigate the role of tin oxide surfaces on Sn-based electrodes for carbon dioxide reduction into formate by means of experimental and theoretical methods. Cyclic voltammetry measurements of Sn-based electrodes, with different initial degree of oxidation, result in similar onset potentials for the CO2 reduction to formate, ca. −0.8 to −0.9 V vs. reversible hydrogen electrode (RHE), with faradaic efficiencies of about 90–92% at −1.25 V (vs. RHE). These results indicate that under in-situ conditions, the electrode surfaces might converge to very similar structures, with partially reduced or metastable Sn oxides, which serve as active sites for the CO2 reduction. The high faradaic efficiencies of the Sn electrodes brought by the etching/air exposition procedure is ascribed to the formation of a Sn oxide layer with optimized thickness, which is persistent under in situ conditions. Such oxide layer enables the CO2 “activation”, also favoring the electron transfer during the CO2 reduction reaction due to its better electric conductivity. In order to elucidate the reaction mechanism, we have performed density functional theory calculations on different slab models starting from the bulk SnO and Sn6O4(OH)4 compounds with focus on the formation of -OH groups at the water-oxide interface. We have found that the insertion of CO2 into the Sn-OH bond is thermodynamically favorable, leading to the stabilization of the tin-carbonate species, which is subsequently reduced to produce formic acid through a proton-coupled electron transfer process. The calculated potential for CO2 reduction (E = −1.09 V vs. RHE) displays good agreement with the experimental findings and, therefore, support the CO2 insertion onto Sn-oxide as a plausible mechanism for the CO2 reduction in the potential domain where metastable oxides are still present on the Sn surface. These results not only rationalize a number of literature divergent reports but also provide a guideline for the design of efficient CO2 reduction electrocatalysts.

    Keywords
    electrocatalysis, carbon dioxide conversion, formic acid, tin-based electrodes, tin oxide, tin-carbonate, reaction mechanism
    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-390068 (URN)10.3390/catal9080636 (DOI)000482799100047 ()
    Funder
    StandUpSwedish Research CouncilSwedish National Infrastructure for Computing (SNIC)
    Available from: 2019-08-05 Created: 2019-08-05 Last updated: 2019-12-03Bibliographically approved
    6. X‑ray Photoelectron Fingerprints of High-Valence Ruthenium−Oxo Complexes along the Oxidation Reaction Pathway in an Aqueous Environment
    Open this publication in new window or tab >>X‑ray Photoelectron Fingerprints of High-Valence Ruthenium−Oxo Complexes along the Oxidation Reaction Pathway in an Aqueous Environment
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    2019 (English)In: The Journal of Physical Chemistry Letters, Vol. 10, p. 7636-7643Article in journal (Refereed) Published
    Abstract [en]

    Recent advances in operando-synchrotron-based X-ray techniques are making it possible to address fundamental questions related to complex proton-coupled electron transfer reactions, for instance, the electrocatalytic water splitting process. However, it is still a grand challenge to assess the ability of the different techniques to characterize the relevant intermediates, with minimal interference on the reaction mechanism. To this end, we have developed a novel methodology employing X-ray photoelectron spectroscopy (XPS) in connection with the liquid-jet approach to probe the electrochemical properties of a model electrocatalyst, [RuII(bpy)2(py)-(OH2)]2+, in an aqueous environment. There is a unique fingerprint of the extremely important higher-valence ruthenium−oxo species in the XPS spectra along the oxidation reaction pathway. Furthermore, a sequential method combining quantum mechanics and molecular mechanics is used to illuminate the underlying physical chemistry of such systems. This study provides the basis for the future development of in-operando XPS techniques for water oxidation reactions.

    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-398067 (URN)10.1021/acs.jpclett.9b02756 (DOI)
    Available from: 2019-12-01 Created: 2019-12-01 Last updated: 2019-12-20Bibliographically approved
    7. Carbon Dioxide  Reduction Mechanism on Ru-based Electrocatalysts: Insights from First-principles Theory
    Open this publication in new window or tab >>Carbon Dioxide  Reduction Mechanism on Ru-based Electrocatalysts: Insights from First-principles Theory
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Solar fuel production through the so-called artificial photosynthesis has attracted a great deal of attention to the development of a new world energy matrix that is renewable and environmentally friendly. This process basically comprises the absorption of sunlight energy by an appropriate photocatalyst that is active for carbon dioxide conversion into organic fuels. Commonly, an electrocatalyst can be coupled to the system for later improvement of the photocatalytic efficiency and selectivity. In this work, we have undertaken a thorough investigation of the redox reaction mechanism of Ru-based electrocatalysts by means of density functional theory (DFT) methods under the experimental conditions that have been previously reported. More specifically, we have studied the electrochemistry and catalytic activity of the coordination complex [Ru(bpy)2(CO)2]2+. Our theoretical assessment support the following catalytic cycle: (i) [Ru(bpy)2(CO)2]2+ is transformed into [Ru(bpy)2(CO)]0 upon the two-electron reduction and CO release; (ii) [Ru(bpy)2(CO)]0 is protonated to form the hydride complex [Ru(bpy)2(CO)H]+; (iii) CO2 is activated by the hydride complex through an electrophilic addition to form the intermediate [Ru(bpy)2(CO)(OCHO)]+, with the formation of C-H bond; (iv) the resulting formate ligand ion is then released in solution; and, finally, (iv) CO ligand is reattached to the complex to recover the initial complex [Ru(bpy)2(CO)2]2+.  

    Keywords
    Ru-complex, Carbon dioxide conversion, Electrocatalysis, formic acid production, Density Functional Theory
    National Category
    Other Chemistry Topics
    Identifiers
    urn:nbn:se:uu:diva-398121 (URN)
    Available from: 2019-12-02 Created: 2019-12-02 Last updated: 2019-12-19Bibliographically approved
    8. Understanding Carbon Dioxide Capture on Metal-Organic Frameworks from First-Principles Theory: The Case of MIL-53(X), with X=Fe, Al and Cu
    Open this publication in new window or tab >>Understanding Carbon Dioxide Capture on Metal-Organic Frameworks from First-Principles Theory: The Case of MIL-53(X), with X=Fe, Al and Cu
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Metal-organic frameworks (MOFs) constitute a class of three-dimensional porous materials that have shown applicability for carbon dioxide capture at low pressures, which is particularly advantageous to deal with the well-known environmental problem related to the carbon dioxide emissions into the atmosphere. In this work, the effect of changing the metallic center in the inorganic counterpart in MIL-53 (X), where X= Fe3+, Al3+, Cu3+ has been evaluated over the ability of the porous material to adsorb carbon dioxide by means of ab initio methodology. More specifically, we have employed a solid-state approach to study the thermochemistry of this process also considering the effects of spin-polarization. By using GGA+U methods with U= 7 eV on Fe 3d and Cu 3d states and GGA with Al-based MOF, it has been verified a preferential stabilization of the guest molecule at the pore center, which exhibits long-range interaction via oxygen atoms with the axial hydroxyl groups. In this sense, MIL-53 (Cu3+) shows potential absorption capacity for carbon dioxide, with a binding energy higher than that verified for the Al-based MOF within the same of level. Furthermore, applying Hubbard corrections on atoms exhibiting an open shell configuration (Cu, Fe) has been demonstrated to be essential for a proper assessment of the electronic structure and atomic magnetic moment, which affect the final binding energy values through an unequal influence on the electronic energies in the pure system and after carbon dioxide adsorption.

    Keywords
    Metal Organic Frameworks, Carbon Dioxide Capture, DFT methods
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-398174 (URN)
    Available from: 2019-12-03 Created: 2019-12-03 Last updated: 2019-12-12
  • Public defence: 2020-02-05 13:15 B21, BMC, Uppsala
    Kulkarni, Yashraj
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Computational Modeling of the Structure, Function and Dynamics of Biomolecular Systems2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Proteins are a structurally diverse and functionally versatile class of biomolecules. They perform a variety of life-sustaining biological processes with utmost efficiency. A profound understanding of protein function requires knowledge of its structure. Experimentally determined protein structures can serve as a starting point for computer simulations in order to study their dynamic behavior at a molecular level. In this thesis, computational methods have been used to understand structure-function relationships in two classes of proteins - intrinsically disordered proteins (IDP) and enzymes.

    Misfolding and subsequent aggregation of the amyloid beta (Aβ) peptide, an IDP, is associated with the progression of Alzheimer’s disease. Besides enriching our understanding of structural dynamics, computational studies on a medically relevant IDP such as Aβ can potentially guide therapeutic development. In the present work, binding interactions of the monomeric form of this peptide with biologically relevant molecular species such as divalent metal ions (Zn2+, Cu2+, Mn2+) and amphiphilic surfactants were characterized using long timescale molecular dynamics (MD) simulations. Among the metal ions, while Zn2+ and Cu2+ maintained coordination to a well-defined binding site in Aβ, Mn2+-binding was observed to be comparatively weak and transient. Surfactants with charged headgroups displayed strong binding interaction with Aβ. Complemented by biophysical experiments, these studies provided a multifaceted perspective of Aβ interactions with the partner molecules.

    Triosephosphate isomerase (TIM), a highly evolved and catalytically proficient enzyme, was studied using empirical valence bond (EVB) calculations to obtain deeper insights into the catalytic reaction mechanism. Multiple structural features of TIM such as the flexible loop and preorganized active site residues were investigated for their role in enzyme catalysis. The effect of substrate binding was also studied using truncated substrates. Finally, using enhanced sampling methods, dynamic behavior of the catalytically important loop 6 was characterized. The importance of structural stability and flexibility on protein function was illustrated by the work presented in this thesis, thus furthering our scientific understanding of proteins at a molecular level.

    List of papers
    1. Characterization of Mn(II) ion binding to the amyloid-beta peptide in Alzheimer's disease
    Open this publication in new window or tab >>Characterization of Mn(II) ion binding to the amyloid-beta peptide in Alzheimer's disease
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    2016 (English)In: Journal of Trace Elements in Medicine and Biology, ISSN 0946-672X, E-ISSN 1878-3252, Vol. 38, p. 183-193Article in journal (Refereed) Published
    Abstract [en]

    Growing evidence links neurodegenerative diseases to metal exposure. Aberrant metal ion concentrations have been noted in Alzheimer's disease (AD) brains, yet the role of metals in AD pathogenesis remains unresolved. A major factor in AD pathogenesis is considered to be aggregation of and amyloid formation by amyloid-beta (A beta) peptides. Previous studies have shown that A beta displays specific binding to Cu(II) and Zn(II) ions, and such binding has been shown to modulate A beta aggregation. Here, we use nuclear magnetic resonance (NMR) spectroscopy to show that Mn(II) ions also bind to the N-terminal part of the A beta(1-40) peptide, with a weak binding affinity in the milli- to micromolar range. Circular dichroism (CD) spectroscopy, solid state atomic force microscopy (AFM), fluorescence spectroscopy, and molecular modeling suggest that the weak binding of Mn(II) to A beta may not have a large effect on the peptide's aggregation into amyloid fibrils. However, identification of an additional metal ion displaying A beta binding reveals more complex AD metal chemistry than has been previously considered in the literature.

    Keywords
    Manganese, Neurodegeneration, Metal-protein binding, Spectroscopy, Molecular dynamics
    National Category
    Cell and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-308063 (URN)10.1016/j.jtemb.2016.03.009 (DOI)000385473600023 ()27085215 (PubMedID)
    Available from: 2016-11-30 Created: 2016-11-23 Last updated: 2019-12-04Bibliographically approved
    2. Amyloid-beta Peptide Interactions with Amphiphilic Surfactants: Electrostatic and Hydrophobic Effects
    Open this publication in new window or tab >>Amyloid-beta Peptide Interactions with Amphiphilic Surfactants: Electrostatic and Hydrophobic Effects
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    2018 (English)In: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 9, no 7, p. 1680-1692Article in journal (Refereed) Published
    Abstract [en]

    The amphiphilic nature of the amyloid-beta (A beta) peptide associated with Alzheimer's disease facilitates various interactions with biomolecules such as lipids and proteins, with effects on both structure and toxicity of the peptide. Here, we investigate these peptide-amphiphile interactions by experimental and computational studies of A beta(1-40) in the presence of surfactants with varying physicochemical properties. Our findings indicate that electrostatic peptide-surfactant interactions are required for coclustering and structure induction in the peptide and that the strength of the interaction depends on the surfactant net charge. Both aggregation-prone peptide-rich coclusters and stable surfactant-rich coclusters can form. Only A beta(1-40) monomers, but not oligomers, are inserted into surfactant micelles in this surfactant-rich state. Surfactant headgroup charge is suggested to be important as electrostatic peptide-surfactant interactions on the micellar surface seems to be an initiating step toward insertion. Thus, no peptide insertion or change in peptide secondary structure is observed using a nonionic surfactant. The hydrophobic peptide-surfactant interactions instead stabilize the A beta monomer, possibly by preventing self-interaction between the peptide core and C terminus, thereby effectively inhibiting the peptide aggregation process. These findings give increased understanding regarding the molecular driving forces for A beta aggregation and the peptide interaction with amphiphilic biomolecules.

    Place, publisher, year, edition, pages
    AMER CHEMICAL SOC, 2018
    Keywords
    Alzheimer's disease, A beta aggregation, surfactant interactions, optical and NMR spectroscopy, mass spectrometry, molecular dynamics simulations
    National Category
    Neurosciences
    Identifiers
    urn:nbn:se:uu:diva-386225 (URN)10.1021/acschemneuro.8b00065 (DOI)000439531400017 ()29683649 (PubMedID)
    Funder
    Swedish Research Council
    Available from: 2019-06-19 Created: 2019-06-19 Last updated: 2019-12-04Bibliographically approved
    3. Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase
    Open this publication in new window or tab >>Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase
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    2017 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 30, p. 10514-10525Article in journal (Refereed) Published
    Abstract [en]

    Triosephosphate isomerase (TIM) is a proficient catalyst of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde phosphate (GAP), via general base catalysis by E165. Historically, this enzyme has been an extremely important model system for understanding the fundamentals of biological catalysis. TIM is activated through an energetically demanding conformational change, which helps position the side chains of two key hydrophobic residues (1170 and L230), over the carboxylate side chain of E165. This is critical both for creating a hydrophobic pocket for the catalytic base and for maintaining correct active site architecture. Truncation of these residues to alanine causes significant falloffs in TIM's catalytic activity, but experiments have failed to provide a full description of the action of this clamp in promoting substrate deprotonation. We perform here detailed empirical valence bond calculations of the TIM-catalyzed deprotonation of DHAP and GAP by both wild type TIM and its 1170A, L230A, and 1170A/L230A mutants, obtaining exceptional quantitative agreement with experiment. Our calculations provide a linear free energy relationship, with slope 0.8, between the activation barriers and Gibbs free energies for these TIM-catalyzed reactions. We conclude that these clamping side chains minimize the Gibbs free energy for substrate deprotonation, and that the effects on reaction driving force are largely expressed at the transition state for proton transfer. Our combined analysis of previous experimental and current computational results allows us to provide an overview of the breakdown of ground-state and transition state effects in enzyme catalysis in unprecedented detail, providing a molecular description of the operation of a hydrophobic clamp in triosephosphate isomerase.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS), 2017
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-334051 (URN)10.1021/jacs.7b05576 (DOI)000407089500046 ()28683550 (PubMedID)
    Available from: 2017-11-21 Created: 2017-11-21 Last updated: 2019-12-04Bibliographically approved
    4. Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase
    Open this publication in new window or tab >>Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase
    2019 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 141, no 40, p. 16139-16150Article in journal (Refereed) Published
    Abstract [en]

    We report results of detailed empirical valence bond simulations that model the effect of several amino acid substitutions on the thermodynamic (ΔG°) and kinetic activation (ΔG) barriers to deprotonation of dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (GAP) bound to wild-type triosephosphate isomerase (TIM), as well as to the K12G, E97A, E97D, E97Q, K12G/E97A, I170A, L230A, I170A/L230A, and P166A variants of this enzyme. The EVB simulations model the observed effect of the P166A mutation on protein structure. The E97A, E97Q, and E97D mutations of the conserved E97 side chain result in ≤1.0 kcal mol–1 decreases in the activation barrier for substrate deprotonation. The agreement between experimental and computed activation barriers is within ±1 kcal mol–1, with a strong linear correlation between ΔG and Δ for all 11 variants, with slopes β = 0.73 (R2 = 0.994) and β = 0.74 (R2 = 0.995) for the deprotonation of DHAP and GAP, respectively. These Brønsted-type correlations show that the amino acid side chains examined in this study function to reduce the standard-state Gibbs free energy of reaction for deprotonation of the weak α-carbonyl carbon acid substrate to form the enediolate phosphate reaction intermediate. TIM utilizes the cationic side chain of K12 to provide direct electrostatic stabilization of the enolate oxyanion, and the nonpolar side chains of P166, I170, and L230 are utilized for the construction of an active-site cavity that provides optimal stabilization of the enediolate phosphate intermediate relative to the carbon acid substrate.

    National Category
    Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-397177 (URN)10.1021/jacs.9b08713 (DOI)000490358900049 ()31508957 (PubMedID)
    Funder
    Swedish Research Council, 2015-04298NIH (National Institute of Health), GM03597NIH (National Institute of Health), GM116921Knut and Alice Wallenberg Foundation, 2013.0124Knut and Alice Wallenberg Foundation, 2018.0140Swedish National Infrastructure for Computing (SNIC), 2017/12-11Swedish National Infrastructure for Computing (SNIC), 2018/2-3
    Available from: 2019-11-16 Created: 2019-11-16 Last updated: 2019-12-06Bibliographically approved
    5. Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase
    Open this publication in new window or tab >>Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase
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    2018 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 140, no 11, p. 3854-3857Article in journal (Refereed) Published
    Abstract [en]

    We have previously performed empirical valence bond calculations of the kinetic activation barriers, Delta G(calc) double dagger, for the deprotonation of complexes between TIM and the whole substrate glyceraldehyde-3-phosphate (GAP, Kulkarni et al. J. Am. Chem. Soc. 2017, 139, 10514-10525). We now extend this work to also study the deprotonation of the substrate pieces glycolaldehyde (GA) and GA.HPi [HPi = phosphite dianion]. Our combined calculations provide activation barriers, Delta G(calc)(double dagger) for the TIM-catalyzed deprotonation of GAP (12.9 +/- 0.8 kcal.mol(-1)), of the substrate piece GA (15.0 +/- 2.4 kcal.mol(-1)), and of the pieces GA.HP, (15.5 +/- 3.5 kcal.mol(-1)). The effect of bound dianion on Delta G(calc) double dagger is small (<= 2.6 kcal.mol(-1)), in comparison to the much larger 12.0 and 5.8 kcal.mol(-1) intrinsic phosphodianion and phosphite dianion binding energy utilized to stabilize the transition states for TIM-catalyzed deprotonation of GAP and GA. HP, respectively. This shows that the dianion binding energy is essentially fully expressed at our protein model for the Michaelis complex, where it is utilized to drive an activating change in enzyme conformation. The results represent an example of the synergistic use of results from experiments and calculations to advance our understanding of enzymatic reaction mechanisms.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS), 2018
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-354362 (URN)10.1021/jacs.8b00251 (DOI)000428356000010 ()29516737 (PubMedID)
    Funder
    Swedish Research Council, 2015-04928
    Available from: 2018-06-25 Created: 2018-06-25 Last updated: 2019-12-04Bibliographically approved
    6. Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case
    Open this publication in new window or tab >>Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case
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    2018 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 140, no 46, p. 15889-15903Article in journal (Refereed) Published
    Abstract [en]

    Conformational changes are crucial for the catalytic action of many enzymes. A prototypical and well-studied example is loop opening and closure in triosephosphate isomerase (TIM), which is thought to determine the rate of catalytic turnover in many circumstances. Specifically, TIM loop 6 “grips” the phosphodianion of the substrate and, together with a change in loop 7, sets up the TIM active site for efficient catalysis. Crystal structures of TIM typically show an open or a closed conformation of loop 6, with the tip of the loop moving ∼7 Å between conformations. Many studies have interpreted this motion as a two-state, rigid-body transition. Here, we use extensive molecular dynamics simulations, with both conventional and enhanced sampling techniques, to analyze loop motion in apo and substrate-bound TIM in detail, using five crystal structures of the dimeric TIM from Saccharomyces cerevisiae. We find that loop 6 is highly flexible and samples multiple conformational states. Empirical valence bond simulations of the first reaction step show that slight displacements away from the fully closed-loop conformation can be sufficient to abolish most of the catalytic activity; full closure is required for efficient reaction. The conformational change of the loops in TIM is thus not a simple “open and shut” case and is crucial for its catalytic action. Our detailed analysis of loop motion in a highly efficient enzyme highlights the complexity of loop conformational changes and their role in biological catalysis.

    National Category
    Biochemistry and Molecular Biology
    Research subject
    Biochemistry
    Identifiers
    urn:nbn:se:uu:diva-367313 (URN)10.1021/jacs.8b09378 (DOI)000451496800048 ()30362343 (PubMedID)
    Funder
    Swedish Research CouncilSwedish National Infrastructure for Computing (SNIC), 2016/1-293Swedish National Infrastructure for Computing (SNIC), 2017/12-11
    Available from: 2018-11-29 Created: 2018-11-29 Last updated: 2019-12-04Bibliographically approved
  • Public defence: 2020-02-07 09:15 Room 80101, Uppsala
    Ali, Hasan
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Towards atomically resolved magnetic measurements in the transmission electron microscope: A study of structure and magnetic moments in thin films2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The magnetic properties of thin metallic films are significantly different from the bulk properties due to the presence of interfaces. The properties shown by such thin films are influenced by the atomic level structure of the films and the interfaces. Transmission electron microscope (TEM) has the potential to analyse the structure and the magnetic properties of such systems with atomic resolution. In this work, the TEM is employed to characterize the structure of the Fe/V and Fe/Ni multilayers and the technique of electron magnetic circular dichroism (EMCD) is developed to obtain the quantitative magnetic measurements with high spatial resolution.

    From TEM analysis of short period Fe/V  multilayers, a coherent superlattice structure is found. In short period Fe/Ni multilayer samples with different repeat frequency, only the TEM technique could verify the existence of the multilayer structure in the thinnest layers. The methods of scanning TEM imaging and electron energy loss spectroscopy (EELS) results were used and refined to determine interdiffusion at the interfaces. The confirmation of the multilayer structure helped to explain the saturation magnetization of these samples.

    Electron magnetic circular dichroism (EMCD) has the potential to quantitatively measure the magnetic moments of the materials with atomic resolution, but the technique presents several challenges. First, the EMCD measurements need to acquire two EELS spectra at two different scattering angles. These spectra are mostly acquired one after the other which makes it difficult to guaranty the identical experimental conditions and the spatial registration between the two acquisitions. We have developed a technique to simultaneously acquire the two angle-resolved EELS spectra in a single acquisition. This not only ensures the accuracy of the measurements but also improves the signal to noise ratio as compared to the previously used methods. The second important question is the effect of crystal orientations on the measured EMCD signals, considering the fact that the crystal orientation of a real crystal does not remain the same in the measured area. We developed the methodology to simultaneously acquire the EMCD signals and the local crystal orientations with high precision and experimentally showed that the crystal tilt significantly changes the magnetic signal. The third challenge is to obtain EMCD measurements with atomic resolution  which is hampered by the need of high beam convergence angles. We further developed the simultaneous acquisition technique to obtain the quantitative EMCD measurements with beam convergence angles corresponding to atomic size electron probes. 

    List of papers
    1. Shrinking of silicon nanocrystals embedded in an amorphous silicon oxide matrix during rapid thermal annealing in a forming gas atmosphere
    Open this publication in new window or tab >>Shrinking of silicon nanocrystals embedded in an amorphous silicon oxide matrix during rapid thermal annealing in a forming gas atmosphere
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    2016 (English)In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 27, no 36, article id 365601Article in journal (Refereed) Published
    Abstract [en]

    We report the effect of hydrogen on the crystallization process of silicon nanocrystals embedded in a silicon oxide matrix. We show that hydrogen gas during annealing leads to a lower sub-band gap absorption, indicating passivation of defects created during annealing. Samples annealed in pure nitrogen show expected trends according to crystallization theory. Samples annealed in forming gas, however, deviate from this trend. Their crystallinity decreases for increased annealing time. Furthermore, we observe a decrease in the mean nanocrystal size and the size distribution broadens, indicating that hydrogen causes a size reduction of the silicon nanocrystals.

    Keywords
    silicon nanocrystals, rapid thermal annealing, oxidation, forming gas, hydrogen, defects, passivation
    National Category
    Materials Engineering
    Identifiers
    urn:nbn:se:uu:diva-306271 (URN)10.1088/0957-4484/27/36/365601 (DOI)000384064400019 ()27478921 (PubMedID)
    Available from: 2016-10-26 Created: 2016-10-26 Last updated: 2019-12-06Bibliographically approved
    2. Crystal perfection by strain engineering: The case of Fe/V (001)
    Open this publication in new window or tab >>Crystal perfection by strain engineering: The case of Fe/V (001)
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    2017 (English)In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 636, p. 608-614Article in journal (Refereed) Published
    Abstract [en]

    We study the effect of bilayer thickness at fixed volume fraction on the structural quality of Fe/V (001)superlattices. We find that such artificial metallic superlattices can be manufactured with excellent crystalquality and layering up to at least 50 Å in repeat distance (K = LFe +LV). For an intended fixed ratio of theconstituents: LFe/LV= 1/7, out-of-plane coherence lengths comparable to the thicknesses of the sampleswere obtained. We evaluate the strain in- and out-of-plane of both layers as a function of the bilayer thicknessand comment on the growth using the framework of linear elasticity theory. We interpret the stabilityof the superlattice against crystal degradation due to the alternating compressive and tensile strain, yieldingclose to ideal lattice matching to the substrate.

    Keywords
    Superlattice; Iron/Vanadium; Sputtering; Epitaxy; Reciprocal space mapping; X-ray diffraction; X-ray reflectivity; Linear elasticity
    National Category
    Other Materials Engineering
    Identifiers
    urn:nbn:se:uu:diva-332050 (URN)10.1016/j.tsf.2017.07.005 (DOI)000408037800086 ()
    Available from: 2017-10-23 Created: 2017-10-23 Last updated: 2019-12-06Bibliographically approved
    3. Composition, structure and magnetic properties of ultra-thin Fe/Ni multilayers sputter deposited on epitaxial Cu/Si(001)
    Open this publication in new window or tab >>Composition, structure and magnetic properties of ultra-thin Fe/Ni multilayers sputter deposited on epitaxial Cu/Si(001)
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    2018 (English)In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 646, p. 117-125Article in journal (Refereed) Published
    Abstract [en]

    Sputter deposited symmetric multilayers of (n Fe)/(n Ni), with individual thicknesses from n = 4 to n = 48 monolayers (ML), were deposited on epitaxial Cu/Si(001), and their microstructural evolution and magnetic properties versus n have been studied. Elemental layering can be seen with transmission electron microscopy down to n = 4 ML layer thickness, although an intermixed region characterized by a finite interface width is found to be present. This width is composed of the interface roughness as well as the interdiffusion between layers, but the relative contributions from these two sources could not be concluded by the techniques used. The measured elemental layering and X-ray reflectivity (XRR) give an upper limit to the interface width which must be smaller than the thinnest layers, 4 ML. Electron energy loss spectroscopy (EELS), depth profiling X-ray photoelectron spectroscopy (XPS) and also XRR reveal that Fe has a higher tendency to mix with Ni than vice versa. XPS does not have the resolution to measure this thin elemental layering: composition variations for n = 8 ML which are clearly seen by EELS are barely resolved by XPS. The structure was determined by X-ray diffraction, and an epitaxial fcc (001) structure is found to be maintained throughout the multilayers up to n less than or similar to 8 ML. For larger n values, relaxation starts by Fe-fcc(001) layers changing into Fe-bcc(110), which is then followed by Ni-fcc(001) changing from (001) to (111) orientation along the growth direction. A decreased total measured magnetic moment for the fully epitaxial multilayers can be explained by the fcc Fe layers being partly anti-ferromagnetic, whereas the relaxed multilayers exhibit the expected magnetic properties of (bcc Fe) +(fcc Ni).

    National Category
    Condensed Matter Physics Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-305519 (URN)10.1016/j.tsf.2017.11.023 (DOI)000418575900017 ()
    Funder
    Swedish Research Council
    Available from: 2016-10-22 Created: 2016-10-18 Last updated: 2019-12-06Bibliographically approved
    4. Quantitative EMCD by use of a double aperture for simultaneous acquisition of EELS
    Open this publication in new window or tab >>Quantitative EMCD by use of a double aperture for simultaneous acquisition of EELS
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    2019 (English)In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 196, p. 192-196Article in journal (Refereed) Published
    Abstract [en]

    The weak signal strength in electron magnetic circular dichroism (EMCD) measurements remains one of the main challenges in the quantification of EMCD related EELS spectra. As a consequence, small variations in peak intensity caused by changes of background intervals, choice of method for extraction of signal intensity and equally differences in sample quality can cause strong changes in the EMCD signal. When aiming for high resolution quantitative EMCD, an additional difficulty consists in the fact that the two angular resolved EELS spectra needed to obtain the EMCD signal are taken at two different instances and it cannot be guaranteed that the acquisition conditions for these two spectra are identical.  Here, we present an experimental setup where we use a double hole aperture in the transmission electron microscope to obtain the EMCD signal in a single acquisition. This geometry allows for the parallel acquisition of the two electron energy loss spectra (EELS) under exactly the same conditions. We also compare the double aperture acquisition mode with the qE acquisition mode which has been previously used for parallel acquisition of EMCD. We show that the double aperture mode not only offers better signal to noise ratio as compared to qE mode but also allows for much higher acquisition times to significantly improve the signal quality which is crucial for quantitative analysis of the magnetic moments.

    National Category
    Other Materials Engineering
    Research subject
    Materials Science
    Identifiers
    urn:nbn:se:uu:diva-364715 (URN)10.1016/j.ultramic.2018.10.012 (DOI)000451180800026 ()30439606 (PubMedID)
    Funder
    Swedish Research Council, C0367901Swedish Research Council, 2016-05259Knut and Alice Wallenberg Foundation
    Available from: 2018-10-31 Created: 2018-10-31 Last updated: 2019-12-06Bibliographically approved
    5. Simultaneous mapping of EMCD signals and crystal orientations in a transmission electron microscope
    Open this publication in new window or tab >>Simultaneous mapping of EMCD signals and crystal orientations in a transmission electron microscope
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Nano Technology
    Identifiers
    urn:nbn:se:uu:diva-398559 (URN)
    Available from: 2019-12-06 Created: 2019-12-06 Last updated: 2019-12-06
    6. Atomic resolution electron probe magnetic circular dichroism measurements enabled by patterned apertures
    Open this publication in new window or tab >>Atomic resolution electron probe magnetic circular dichroism measurements enabled by patterned apertures
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Nano Technology
    Identifiers
    urn:nbn:se:uu:diva-398560 (URN)
    Available from: 2019-12-06 Created: 2019-12-06 Last updated: 2019-12-06
    7. An electron energy loss spectrometer based streak camera for time resolved TEM measurements
    Open this publication in new window or tab >>An electron energy loss spectrometer based streak camera for time resolved TEM measurements
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    2017 (English)In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 176, p. 5-10Article in journal (Refereed) Published
    Abstract [en]

    We propose an experimental setup based on a streak camera approach inside an energy filter to measure time resolved properties of materials in the transmission electron microscope (TEM). In order to put in place the streak camera, a beam sweeper was built inside an energy filter. After exciting the TEM sample, the beam is swept across the CCD camera of the filter. We describe different parts of the setup at the example of a magnetic measurement. This setup is capable to acquire time resolved diffraction patterns, electron energy loss spectra (EELS) and images with total streaking times in the range between 100 ns and 10 μs.

    Keywords
    Time resolved; TEM; Energy filter; Streak camera; Sweep
    National Category
    Physical Sciences Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-329982 (URN)10.1016/j.ultramic.2016.11.026 (DOI)000403992200003 ()
    Available from: 2017-09-25 Created: 2017-09-25 Last updated: 2019-12-06Bibliographically approved
  • Public defence: 2020-02-07 09:15 Room A1:111a, Uppsala
    Laan, Loora
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Induced pluripotent stem cell (iPSC) modelling for the identification of mechanisms behind neurodevelopmental disorders2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Human induced pluripotent stem cells (iPSCs) have opened new possibilities to recapitulate disease mechanisms and to model disorders in vitro. In the studies presented here, iPSCs were established to model neural differentiation in Down syndrome (DS), caused by trisomy for chromosome 21 (T21); Dravet syndrome (DRS), caused by variants in the SCN1A gene; and an ataxia syndrome, caused by a variant in the NFASC gene. The major aim has been to uncover molecular and cellular mechanisms behind perturbed neurogenesis in the three disorders.

    In Paper I, the analysis of transcriptomes and proteomes of the DS iPSC derived neural model revealed several perturbed gene clusters with strong temporal dynamics along neural differentiation, markedly down-regulated mitochondrial genes and a dysregulation of hub proteins. These results predict complex and genome-wide changes in T21 neural cells associated with prolonged cell cycle, reduced cell growth and a perturbed energy metabolism.

    In Paper II, it was demonstrated that the transcriptional profile of iPSC based neural model system for DS was enriched for differentially methylated genes and gene families when compared to a corresponding euploid model. The differentially methylated genes were enriched for transcriptional regulation and chromatin structure, suggesting novel mechanistic links between the genomic imbalance caused by T21 and the global transcriptional dysregulation in DS.

     In Paper III, it was shown that DRS patient iPSCs differentiated into GABAergic interneurons exhibit a dysregulated epilepsy gene network as well as an altered expression of genes involved in chromatin remodelling, accompanied by abnormal electrophysiological properties and increased stress sensitivity.

    In Paper IV, it was shown that neural iPSCs, established from a patient with an ataxia syndrome and a novel homozygous variant in the NFASC gene, lack a full-length neurofascin-186 important for cell adhesion. The patient derived neural iPSCs showed delayed neuronal differentiation, reduced sprouting, shorter neurites and altered electrophysiology.

    The Papers I-IV show that patient derived neural iPSCs enable to identify molecular and cellular mechanisms associated with neuropathogenesis. Besides specific dysregulated pathways and cellular defects in models of three developmental disorders, with shortlists of novel candidate disease biomarkers, the results are consistent with prior data and clinical presentation of patients. The knowledge gained is of paramount importance for translation into clinical settings and a step towards development of novel therapies with the ultimate goal to alleviate symptoms of affected individuals.

    List of papers
    1. Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions
    Open this publication in new window or tab >>Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions
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    2019 (English)In: Molecular Neurobiology, ISSN 0893-7648, E-ISSN 1559-1182, Vol. 56, no 10, p. 7113-7127Article in journal (Refereed) Published
    Abstract [en]

    Down syndrome (DS) or trisomy 21 (T21) is a leading genetic cause of intellectual disability. To gain insights into dynamics of molecular perturbations during neurogenesis in DS, we established a model using induced pluripotent stem cells (iPSC) with transcriptome profiles comparable to that of normal fetal brain development. When applied on iPSCs with T21, transcriptome and proteome signatures at two stages of differentiation revealed strong temporal dynamics of dysregulated genes, proteins and pathways belonging to 11 major functional clusters. DNA replication, synaptic maturation and neuroactive clusters were disturbed at the early differentiation time point accompanied by a skewed transition from the neural progenitor cell stage and reduced cellular growth. With differentiation, growth factor and extracellular matrix, oxidative phosphorylation and glycolysis emerged as major perturbed clusters. Furthermore, we identified a marked dysregulation of a set of genes encoded by chromosome 21 including an early upregulation of the hub gene APP, supporting its role for disturbed neurogenesis, and the transcription factors OLIG1, OLIG2 and RUNX1, consistent with deficient myelination and neuronal differentiation. Taken together, our findings highlight novel sequential and differentiation-dependent dynamics of disturbed functions, pathways and elements in T21 neurogenesis, providing further insights into developmental abnormalities of the DS brain.

    Keywords
    Down syndrome, Induced pluripotent stem cells (iPSC), Neural differentiation, RNA sequencing, Proteome profiling
    National Category
    Neurosciences
    Identifiers
    urn:nbn:se:uu:diva-395428 (URN)10.1007/s12035-019-1585-3 (DOI)000486010800032 ()30989628 (PubMedID)
    Funder
    Swedish Research Council, 2015-02424Swedish Research Council, 2015-4870Knut and Alice Wallenberg FoundationAstraZenecaScience for Life Laboratory - a national resource center for high-throughput molecular bioscienceThe Swedish Brain Foundation, FO2018-0100
    Available from: 2019-10-23 Created: 2019-10-23 Last updated: 2019-12-09Bibliographically approved
    2. DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors
    Open this publication in new window or tab >>DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Background: Down syndrome (DS) is characterized by neurodevelopmental abnormalities caused by partial or complete trisomy of human chromosome 21 (T21). Analysis of Down syndrome brain specimens has shown global epigenetic and transcriptional changes but their interplay during early neurogenesis remains largely unknown. We differentiated induced pluripotent stem cells (iPSCs) established from two DS patients with complete T21 and matched euploid donors into two distinct neural stages corresponding to early- and mid-gestational ages.

    Results: Using the Illumina Infinium 450K array, we assessed the DNA methylation pattern of known CpG regions and promoters across the genome in trisomic neural iPSC derivatives, and we identified a total of 500 stably and differentially methylated CpGs that were annotated to CpG islands of 151 genes. The genes were enriched within the DNA binding category, uncovering 37 factors of importance for transcriptional regulation and chromatin structure. In particular, we observed regional epigenetic changes of the transcription factor genes ZNF69, ZNF700 and ZNF763 as well as the HOXA3, HOXB3 and HOXD3 genes. A similar clustering of differential methylation was found in the CpG islands of the HIST1 genes suggesting effects on chromatin remodeling.

    Conclusions: The study shows that early established differential methylation in neural iPSC derivatives with T21 are associated with a set of genes relevant for DS brain development, providing a novel framework for further studies on epigenetic changes and transcriptional dysregulation during T21 neurogenesis.

    Keywords
    Down syndrome, induced pluripotent stem cells, DNA-methylation, neurogenesis, transcription factors, gene expression
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-398619 (URN)
    Funder
    Swedish Research Council, 2015-02424The Swedish Brain Foundation, FO2018-0100The Swedish Brain Foundation, FO2019-0210Knut and Alice Wallenberg Foundation, Bioinformatic supportAstraZeneca
    Available from: 2019-12-08 Created: 2019-12-08 Last updated: 2019-12-09
    3. Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment
    Open this publication in new window or tab >>Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment
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    2019 (English)In: Neurobiology of Disease, ISSN 0969-9961, E-ISSN 1095-953X, Vol. 132, article id 104583Article in journal (Refereed) Published
    Abstract [en]

    Dravet syndrome (DS) is an early onset refractory epilepsy typically caused by de novo heterozygous variants in SCN1A encoding the a-subunit of the neuronal sodium channel Na(v)1.1. The syndrome is characterized by age related progression of seizures, cognitive decline and movement disorders. We hypothesized that the distinct neurodevelopmental features in DS are caused by the disruption of molecular pathways in Na(v)1.1 haploinsufficient cells resulting in perturbed neural differentiation and maturation. Here, we established DS-patient and control induced pluripotent stem cell derived neural progenitor cells (iPSC NPC) and GABAergic interneuronal (iPSC GABA) cells. The DS-patient iPSC GABA cells showed a shift in sodium current activation and a perturbed response to induced oxidative stress. Transcriptome analysis revealed specific dysregulations of genes for chromatin structure, mitotic progression, neural plasticity and excitability in DS-patient iPSC NPCs and DS-patient iPSC GABA cells versus controls. The transcription factors FOXM1 and E2F1, positive regulators of the disrupted pathways for histone modification and cell cycle regulation, were markedly up-regulated in DS-iPSC GABA lines. Our study highlights transcriptional changes and disrupted pathways of chromatin remodeling in Na(v)1.1 haploinsufficient GABAergic cells, providing a molecular framework that overlaps with that of neurodevelopmental disorders and other epilepsies.

    Place, publisher, year, edition, pages
    ACADEMIC PRESS INC ELSEVIER SCIENCE, 2019
    Keywords
    Dravet syndrome, SCN1A, Na(v)1.1, iPSC, Neural differentiation, Neurodevelopment, Chromatin architecture
    National Category
    Neurosciences
    Identifiers
    urn:nbn:se:uu:diva-398427 (URN)10.1016/j.nbd.2019.104583 (DOI)000497252500015 ()31445158 (PubMedID)
    Funder
    Swedish Research Council, 2015-02424Swedish Research Council, 2015-02417Knut and Alice Wallenberg FoundationAstraZenecaThe Swedish Brain Foundation, FO2018-0100The Swedish Brain Foundation, FO2019-0210Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
    Note

    De tre första författarna delar förstaförfattarskapet.

    Available from: 2019-12-06 Created: 2019-12-06 Last updated: 2019-12-09Bibliographically approved
    4. Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186
    Open this publication in new window or tab >>Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186
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    2019 (English)In: Frontiers in Genetics, ISSN 1664-8021, E-ISSN 1664-8021, Vol. 10, article id 896Article in journal (Refereed) Published
    Abstract [en]

    The etiology of hereditary ataxia syndromes is heterogeneous, and the mechanisms underlying these disorders are often unknown. Here, we utilized exome sequencing in two siblings with progressive ataxia and muscular weakness and identified a novel homozygous splice mutation (c.3020-1G > A) in neurofascin (NFASC). In RNA extracted from fibroblasts, we showed that the mutation resulted in inframe skipping of exon 26, with a deprived expression of the full-length transcript that corresponds to NFASC isoform NF186. To further investigate the disease mechanisms, we reprogrammed fibroblasts from one affected sibling to induced pluripotent stem cells, directed them to neuroepithelial stem cells and finally differentiated to neurons. In early neurogenesis, differentiating cells with selective depletion of the NF186 isoform showed significantly reduced neurite outgrowth as well as fewer emerging neurites. Furthermore, whole-cell patch-clamp recordings of patient-derived neuronal cells revealed a lower threshold for openings, indicating altered Na+ channel kinetics, suggesting a lower threshold for openings as compared to neuronal cells without the NFASC mutation. Taken together, our results suggest that loss of the full-length NFASC isoform NF186 causes perturbed neurogenesis and impaired neuronal biophysical properties resulting in a novel early-onset autosomal recessive ataxia syndrome.

    Keywords
    neurofascin, neuronal isoform NF186, ataxia, patient-specific induced pluripotent stem cells, neuroepithelial stem cells, neurites
    National Category
    Neurosciences
    Identifiers
    urn:nbn:se:uu:diva-395798 (URN)10.3389/fgene.2019.00896 (DOI)000487628800001 ()
    Funder
    Swedish Research Council, 2015-02424Swedish Research Council, 2017-03407Swedish Research Council, 2017-02936Swedish Foundation for Strategic Research , IB13-0074The Swedish Brain FoundationSwedish Society for Medical Research (SSMF)
    Available from: 2019-10-25 Created: 2019-10-25 Last updated: 2019-12-09Bibliographically approved
  • Public defence: 2020-02-07 13:00 Friessalen, Uppsala
    Vass, Máté
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bound to the past: Historical contingency in aquatic microbial metacommunities2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The composition of ecological communities differs due to a combination of different processes, which includes selection by local environmental conditions, dispersal from the regional species pool and random events. Additionally, historical processes such as past dispersal events may leave their imprint on communities as well, resulting in historically contingent communities. However, in most ecological studies the existence and the effect of historical processes remained hidden, even though they could be important predictors of contemporary variations in ecological communities.

    This thesis focuses on how historical processes could influence aquatic microbial metacommunities by investigating when and where history matters, and which factors may regulate historical contingency.

    Using null model approaches, evidence for historical contingency was found in natural ecosystems, more specifically rock pool metacommunities, and appeared to be more likely to influence bacterial than microeukaryotic communities.

    The thesis further used an outdoor mesocosm experiment to test how ecosystem-sized induced differences in environmental fluctuations influenced community assembly processes along a disturbance gradient. This study did, however, not provide strong and clear evidence for the importance of historical contingency.

    In the face of climate change, results from a laboratory experiment showed that historical contingencies might be strengthened with warming. Specifically, warming increased the resistance of local communities against invasion by decreasing the establishment success of migrant species. Hence, temperature-dependent historical contingency was found in aquatic bacterial communities, although its persistence differed between local communities and the degree of invasion they were exposed to.

    Taken together, this thesis suggests that historical processes can leave their imprint on aquatic microbial communities, even though their importance is highly context dependent. Future studies, should therefore consider historical contingency, or in other words, the legacy of the past as a potentially important mechanism that can contribute to the spatial diversity of microbial communities.  

    List of papers
    1. The legacy of the past: effects of historical processes on microbial metacommunities
    Open this publication in new window or tab >>The legacy of the past: effects of historical processes on microbial metacommunities
    2017 (English)In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 79, p. 13-19Article, review/survey (Refereed) Published
    Abstract [en]

    Distinguishing the importance of different community assembly mechanisms is an emerging topic in microbial ecology and much focus has been placed in recent years on investigating how contemporary environmental conditions, dispersal and stochastic processes influence the spatial turnover of communities. However, historical events, such as past environmental conditions or dispersal events, can be important as well. We provide a short summary of the processes that can lead to so-called legacy effects, where past biotic or abiotic factors influence the composition of present-day communities. Priority effects, which arise if early colonizers gain advantage over later-arriving species, can lead to persistent legacy effects. In contrast, time-lags in environmental selection can lead to transient legacy effects. Dispersal rates as well as factors that influence the adaptability of species to changing environmental conditions should be important factors that determine the relative importance of contemporary selection versus historical processes and whether legacy effects are likely to be permanent or temporary. Working with microbial communities offers the advantage of feasible time series studies and multi-generation experiments, and can therefore make important contributions to a novel systematic framework on how historical processes shape complex metacommunities in nature.

    National Category
    Ecology Microbiology
    Identifiers
    urn:nbn:se:uu:diva-322248 (URN)10.3354/ame01816 (DOI)000402653700002 ()
    Funder
    Swedish Research Council
    Available from: 2017-05-17 Created: 2017-05-17 Last updated: 2019-12-09Bibliographically approved
    2. Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions
    Open this publication in new window or tab >>Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions
    (English)Manuscript (preprint) (Other academic)
    National Category
    Biological Sciences
    Research subject
    Biology with specialization in Limnology; Biology with specialization in Microbiology
    Identifiers
    urn:nbn:se:uu:diva-398607 (URN)
    Available from: 2019-12-08 Created: 2019-12-08 Last updated: 2019-12-09
    3. Effects of ecosystem size-induced environmental fluctuations on the temporal dynamics of community assembly mechanisms
    Open this publication in new window or tab >>Effects of ecosystem size-induced environmental fluctuations on the temporal dynamics of community assembly mechanisms
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-398608 (URN)
    Available from: 2019-12-09 Created: 2019-12-09 Last updated: 2019-12-09
    4. Warming-enhanced priority effects at population and community levels in aquatic bacteria
    Open this publication in new window or tab >>Warming-enhanced priority effects at population and community levels in aquatic bacteria
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-398733 (URN)
    Available from: 2019-12-09 Created: 2019-12-09 Last updated: 2019-12-09
  • Public defence: 2020-02-08 10:15 Humanistiska teatern, hus 22, Engelska Parken, Uppsala
    Ims, Gunvald Axner
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Linguistics and Philology.
    Conflicted Selves: Ironic Representations of Westernization in Three Twentieth-century Turkish Novels2020Doctoral thesis, monograph (Other academic)
    Abstract [en]

    For over a century, a dichotomous East–West debate has influenced conceptions of Turkish literature, threatening to reduce single works to products of westernization. This study critically reviews this discourse by investigating how it is addressed through irony in three novels from a period of forty years of the late 20th century: Ahmet Hamdi Tanpınar’s Saatleri Ayarlama Enstitüsü (The Time Regulation Institute, 1961), Adalet Ağaoğlu’s Ölmeye Yatmak (Lying Down To Die, 1973), and Orhan Pamuk’s Yeni Hayat (The New Life, 1994).

    This investigation examines how these novels participate in the discourse of westernization and the role of irony in them. The term “discourse” is used in its Foucauldian sense of “a limited number of statements that belong to a single system of formation,” while irony is understood according to Linda Hutcheon, as a discursive practice that signals “difference at the heart of similarity.”

    This study combines contextualization and close reading. The analysis of each novel is preceded by the presentation of, firstly, a theoretical framework concerning irony, discourse, and westernization and, secondly, background for interpreting irony, westernization, and literary periods in a Turkish context as well as overviews of the three authorships and prior reception.

    Guided by Hutcheon’s description of “the cutting edge of irony” and Wayne Booth’s caution about knowing “where to stop” the investigation illustrates how westernization is represented through irony in these novels. It shows how first-person narration plays a crucial role in subverting the discourse of westernization through the narratives of self-reflective individuals. The study concludes that these novels disrupt the discourse of westernization by undermining its dichotomous tenets; in doing so, they also reveal how the Turkish discourse of westernization, while undergoing significant transformations, is sustained at the cost of suppressing individual voices.

  • Public defence: 2020-02-12 09:15 Enghoffsalen, Uppsala
    Genberg, Margareta
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Physiology.
    Cardiopulmonary Function in Healthy Individuals and in Patients After Hematopoietic Cell Transplantation2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Background: The cardiopulmonary exercise test (CPET) is the gold standard of clinical exercise tests, combining conventional stress testing with measurement of oxygen uptake and carbon dioxide production. In order to interpret CPET findings, adequate reference values are needed. Currently, no Swedish reference values exist.

    Hematopoietic cell transplantation (HCT) is an established treatment for childhood leukemia, with a growing number of long-term survivors. This increases the importance of identifying and treating this therapy’s late cardiac and pulmonary consequences.

    Aims: The main aim of Study I was to compare the peak oxygen uptake (VO2peak) of healthy, 50-year-old Swedes with four commonly used international reference values. Secondary aims were to analyze peak workload and VO2peak in regard to achieved respiratory exchange ratio (RER), and the significance of breathing reserve (BR) at peak exercise in healthy individuals.

    The main aim of Studies II–IV was to investigate long-term cardiopulmonary effects in a group of patients, in median 18 years after HCT including preparative chemotherapy and total body irradiation.

    Methods: A group of healthy, 50-year-old Swedes (n = 181; 91 females) were investigated in Study I, using CPET. The investigated subjects in Studies II–IV were aged 17–37 years and were compared with an age- and sex-matched control group. Cardiac function and pulmonary function were studied through echocardiography, spirometry and CPET at a single occasion.

    Results: All reference values analyzed in Study I underestimated VO2peak in women. VO2peak was best predicted, for both men and women, using reference values by Jones et al. No evidence was found that RER > 1.1 would be better than RER > 1.0 as an indicator of good exercise performance in healthy individuals. In healthy individuals, lower BR is likely a response to higher workloads.

    In Studies II–IV, all echocardiographic parameters were within normal range in patients after HCT. However, systolic and diastolic left ventricular function, and right ventricular function, were reduced in comparison with healthy controls. Exercise tests and CPET showed that long-term survivors after HCT, when compared with healthy individuals, had significantly decreased exercise capacity and reduced VO2peak and other CPET parameters, reflecting effects on both the cardiac and the pulmonary functions.

    Conclusions: All investigated reference values underestimated VO2peak in 50-year-old Swedes, suggesting a need for Swedish reference values. HCT-treated leukemia patients displayed reduced exercise capacity and VO2peak. Regular follow-up of these patients with CPET could contribute to early detection of functional impairment.

    List of papers
    1. Exercise capacity in young adults after hematopoietic cell transplantation in childhood.
    Open this publication in new window or tab >>Exercise capacity in young adults after hematopoietic cell transplantation in childhood.
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    2018 (English)In: American Journal of Transplantation, ISSN 1600-6135, E-ISSN 1600-6143, Vol. 18, no 2, p. 417-423Article in journal (Refereed) Published
    Abstract [en]

    A symptom-limited incremental cycle ergometer test was performed in 17 young adult patients treated with hematopoietic cell transplantation and total body irradiation for hematologic malignancies during childhood. These 17 young adult patients were compared with 17 sex- and age-matched healthy control subjects. Assessments of pulmonary function, cardiac function, body composition, and levels of growth hormone were made. The median follow-up was 17.7 years. Patients achieved 63.2% of the predicted peak workload, whereas controls achieved 96.1% (P < .001). All patients, but only 1 control, failed to achieve a peak workload >80% (P < .001). Fat-free mass was significantly lower (43.5 vs 57.6 kg, P < .001) and fat mass percentage was significantly higher (31.8% vs 24.2%, P = .011) in the patients. The peak workload adjusted for fat-free mass was significantly lower in the patients (3.3 vs 4.3, P < .001). In the patients, peak workload correlated significantly with total lung capacity (r = .54, P = .025). In summary, long-term survivors have significantly decreased exercise capacity compared with healthy individuals. Together with their altered body composition, this may predispose them to cardiovascular disease.

    Keywords
    bone marrow/hematopoietic stem cell transplantation, cancer/malignancy/neoplasia: hematogenous/leukemia/lymphoma, cardiovascular disease, clinical research/practice, complication: medical/metabolic, hematology/oncology, lung (native) function/dysfunction, metabolic syndrome, pediatrics
    National Category
    Cancer and Oncology
    Identifiers
    urn:nbn:se:uu:diva-343519 (URN)10.1111/ajt.14456 (DOI)000423666200016 ()28787762 (PubMedID)
    Available from: 2018-02-27 Created: 2018-02-27 Last updated: 2019-12-07Bibliographically approved
    2. Long-term effects on cardiopulmonary exercise testing parameters in young adults treated with stem cell transplantation in childhood
    Open this publication in new window or tab >>Long-term effects on cardiopulmonary exercise testing parameters in young adults treated with stem cell transplantation in childhood
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Clinical Medicine
    Identifiers
    urn:nbn:se:uu:diva-398069 (URN)
    Available from: 2019-12-01 Created: 2019-12-01 Last updated: 2019-12-07
    3. Cardiac Function After Hematopoietic Cell Transplantation: An Echocardiographic Cross-Sectional Study in Young Adults Treated in Childhood
    Open this publication in new window or tab >>Cardiac Function After Hematopoietic Cell Transplantation: An Echocardiographic Cross-Sectional Study in Young Adults Treated in Childhood
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    2015 (English)In: Pediatric Blood & Cancer, ISSN 1545-5009, E-ISSN 1545-5017, Vol. 62, no 1, p. 143-147Article in journal (Refereed) Published
    Abstract [en]

    BackgroundHematopoietic cell transplantation (HCT) including preparative regimens with chemotherapy and total body irradiation (TBI) is an accepted treatment for many malignant disorders but may have side-effects for several organs, including the cardiovascular system. The aim of this study was to study very long-term consequences on cardiac function after childhood HCT. ProcedureCardiac function was evaluated using echocardiography and levels of NT-proBNP and growth hormone (GHmax) in 18 patients, at a median of 18 years after HCT including TBI, and in 18 matched controls. ResultsPatients after HCT had cardiac dimensions, volumes, and left ventricular ejection fractions within normal range after correction for body size. However, compared with the control group, patients after HCT had significantly lower E/A ratio, as a measure of left ventricular diastolic function, significantly lower fractional shortening and mitral annular plane systolic excursion, as measures of left ventricular systolic function, significantly lower tricuspid annular plane systolic excursion, as a measure of right ventricular function, and significantly higher NT-proBNP, as a measure of total cardiac function. Also, pulmonary flow acceleration time was shorter in the group after HCT, indicating possible pulmonary involvement. Heart rate was significantly higher and GHmax significantly lower in patients after HCT. ConclusionsAlmost two decades after HCT, including preparative regimens with TBI, cardiac function in patients was found to be within normal range. However, when compared with a healthy control group, patients after HCT showed lower systolic and diastolic left ventricular function as well as lower right ventricular function. Pediatr Blood Cancer 2015;62:143-147.

    Keywords
    cardiac function, children, echocardiography, hematopoietic cell transplantation, total body irradiation
    National Category
    Hematology Pediatrics
    Identifiers
    urn:nbn:se:uu:diva-240060 (URN)10.1002/pbc.25135 (DOI)000345319300026 ()25251023 (PubMedID)
    Available from: 2015-01-08 Created: 2015-01-05 Last updated: 2019-12-07Bibliographically approved
    4. Commonly used reference values underestimate oxygen uptake in healthy, 50-year-old Swedish women.
    Open this publication in new window or tab >>Commonly used reference values underestimate oxygen uptake in healthy, 50-year-old Swedish women.
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    2018 (English)In: Clinical Physiology and Functional Imaging, ISSN 1475-0961, E-ISSN 1475-097X, Vol. 38, no 1, p. 25-33Article in journal (Refereed) Published
    Abstract [en]

    Cardiopulmonary exercise testing (CPET) is the gold standard among clinical exercise tests. It combines a conventional stress test with measurement of oxygen uptake (VO2 ) and CO2 production. No validated Swedish reference values exist, and reference values in women are generally understudied. Moreover, the importance of achieved respiratory exchange ratio (RER) and the significance of breathing reserve (BR) at peak exercise in healthy individuals are poorly understood. We compared VO2 at maximal load (peakVO2 ) and anaerobic threshold (VO2@AT ) in healthy Swedish individuals with commonly used reference values, taking gender into account. Further, we analysed maximal workload and peakVO2 with regard to peak RER and BR. In all, 181 healthy, 50-year-old individuals (91 women) performed CPET. PeakVO2 was best predicted using Jones et al. (100·5%), while SHIP reference values underestimated peakVO2 most: 112·5%. Furthermore, underestimation of peakVO2 in women was found for all studied reference values (P<0·001) and was largest for SHIP: women had 128% of predicted peakVO2 , while men had 104%. PeakVO2 was similar in subjects with peak RER of 1-1·1 and RER > 1·1 (2 328·7 versus 2 176·7 ml min(-1) , P = 0·11). Lower BR (≤30%) related to significantly higher peakVO2 (P<0·001). In conclusion, peakVO2 was best predicted by Jones. All studied reference values underestimated oxygen uptake in women. No evidence for demanding RER > 1·1 in healthy individuals was found. A lowered BR is probably a normal response to higher workloads in healthy individuals.

    National Category
    Cardiac and Cardiovascular Systems Respiratory Medicine and Allergy
    Identifiers
    urn:nbn:se:uu:diva-312359 (URN)10.1111/cpf.12377 (DOI)000417877700005 ()27312352 (PubMedID)
    Available from: 2017-01-09 Created: 2017-01-09 Last updated: 2019-12-07Bibliographically approved
  • Public defence: 2020-02-28 13:15 Room C8:305, Uppsala
    Han, Fan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Genetic Adaptation and Speciation in Darwin’s Finches and Atlantic Herring2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Natural selection acts on existing genetic variation to drive genetic adaptation of organisms to various ecological niches. Interaction between closely related populations, through processes such as competition and hybridization, may either lead to their divergence or population fusion, which has consequences for adaptation and the formation of species. This thesis aims to use two natural populations, Darwin’s finches and Atlantic herring, as models to explore the genetic mechanisms underlying ecological adaptation and speciation.

    The ecological adaptation of Darwin’s finches across the Galápagos Islands is primarily reflected by variation in beak morphology. Using whole-genome re-sequencing of all Darwin’s finch species, we discover that a locus, HMGA2, is highly associated with variation in beak size. Data collected before and after a severe drought show that this locus plays a critical role for ecological character displacement in large ground finches Geospiza magnirostris and medium ground finches G. fortis.

    Genomic islands of divergence refer to genomic regions of elevated divergence when comparing the genomes of closely related taxa. Establishment of these genomic islands can reflect a role in reproductive isolation or be related to ecological adaptation or background selection. Investigating their properties can shed light on how new species evolve. We study the landscape of genomic islands in Darwin’s finches, and find that the most pronounced genomic islands are likely ancient balanced polymorphisms, which govern adaptive variation in beak morphology.

    Hybridization is increasingly recognized as an important evolutionary process which may lead to speciation. We study two cases of hybridization in Darwin’s finches. In the first case, a new lineage of Darwin’s finches was founded through hybridization between a resident medium ground finch G. fortis and an immigrant Española cactus finch G. conirostris. In the second case, female-biased introgression occurred predominantly from medium ground finches G. fortis to common cactus finches G. scandens. Our genetic analysis on the mosaic genomes of hybrid finches show that non-random mating and natural selection primarily determine the outcome of hybridization.

    We generate a chromosome-level assembly of the Atlantic herring with a total size of 726 Mb, which coincides with a high-resolution linkage map and an LD-based recombination map. This facilitates the identification of an ~8Mb inversion, which is likely to be associated with ecological adaptation in herring to differences in water temperature. The contiguity of the assembly sorts placement of loci under selection that were identified based on a previous, highly fragmented draft assembly of the herring genome.

    List of papers
    1. A beak size locus in Darwin’s finches facilitated character displacement during a drought
    Open this publication in new window or tab >>A beak size locus in Darwin’s finches facilitated character displacement during a drought
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    2016 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 352, no 6284, p. 470-474Article in journal (Refereed) Published
    Abstract [en]

    Ecological character displacement is a process of morphological divergence that reducescompetition for limited resources. We used genomic analysis to investigate the geneticbasis of a documented character displacement event in Darwin’s finches on Daphne Majorin the Galápagos Islands: The medium ground finch diverged from its competitor, the largeground finch, during a severe drought. We discovered a genomic region containing theHMGA2gene that varies systematically among Darwin’s finch species with different beaksizes. Two haplotypes that diverged early in the radiation were involved in the characterdisplacement event: Genotypes associated with large beak size were at a strong selectivedisadvantage in medium ground finches (selection coefficients= 0.59). Thus, a majorlocus has apparently facilitated a rapid ecological diversification in the adaptive radiationof Darwin’s finches.

    National Category
    Genetics and Breeding
    Identifiers
    urn:nbn:se:uu:diva-279968 (URN)10.1126/science.aad8786 (DOI)000374479700050 ()27102486 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish Research Council, 80576801Swedish Research Council, 70374401
    Available from: 2016-03-06 Created: 2016-03-06 Last updated: 2019-11-28Bibliographically approved
    2. Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
    Open this publication in new window or tab >>Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
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    2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 6, p. 1004-1015Article in journal (Refereed) Published
    Abstract [en]

    Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-340985 (URN)10.1101/gr.212522.116 (DOI)000402521400011 ()28442558 (PubMedID)
    Funder
    Knut and Alice Wallenberg Foundation
    Available from: 2018-02-05 Created: 2018-02-05 Last updated: 2019-11-28Bibliographically approved
    3. Rapid hybrid speciation in Darwin's finches
    Open this publication in new window or tab >>Rapid hybrid speciation in Darwin's finches
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    2018 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 359, no 6372, p. 224-228Article in journal (Refereed) Published
    Abstract [en]

    Homoploid hybrid speciation in animals has been inferred frequently from patterns of variation, but few examples have withstood critical scrutiny. Here we report a directly documented example, from its origin to reproductive isolation. An immigrant Darwin's finch to Daphne Major in the Galápagos archipelago initiated a new genetic lineage by breeding with a resident finch (Geospiza fortis). Genome sequencing of the immigrant identified it as a G. conirostris male that originated on Española >100 kilometers from Daphne Major. From the second generation onward, the lineage bred endogamously and, despite intense inbreeding, was ecologically successful and showed transgressive segregation of bill morphology. This example shows that reproductive isolation, which typically develops over hundreds of generations, can be established in only three.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-340986 (URN)10.1126/science.aao4593 (DOI)000419816600048 ()29170277 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
    Available from: 2018-02-05 Created: 2018-02-05 Last updated: 2019-11-28
    4. Female-biased gene flow between two species of Darwin’s finches
    Open this publication in new window or tab >>Female-biased gene flow between two species of Darwin’s finches
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    2019 (English)In: Article in journal (Refereed) Submitted
    Abstract [en]

    The mosaic nature of hybrid genomes is well recognized, but little is known of how they are shaped initially by patterns of breeding, selection, recombination and differential incompatibilities. On the small Galápagos island of Daphne Major two species of Darwin’s finches, Geospiza fortis and G. scandens, hybridize rarely and backcross bidirectionally with little or no loss of fitness under conditions of plentiful food. We used whole genome sequences to compare genomes from periods before and after successful interbreeding followed by backcrossing. We inferred extensive introgression from G. fortis to G. scandens on autosomes and mitochondria but not on the Z chromosome. The unique combination of long-term field observations and genomic data shows that the reduction of gene flow for Z-linked loci reflects female-biased gene flow, arising from hybrid male disadvantage in competition for territories and mates, rather than from genetic incompatibilities at Z-linked loci.

    Keywords
    Darwin's finches, introgression, hybridisation
    National Category
    Ecology Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-396776 (URN)
    Available from: 2019-11-09 Created: 2019-11-09 Last updated: 2019-11-28
    5. A chromosome-level assembly of the Atlantic herring: detection of a supergene and other signals of selection
    Open this publication in new window or tab >>A chromosome-level assembly of the Atlantic herring: detection of a supergene and other signals of selection
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    2019 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 29, no 11, p. 1919-1928Article in journal (Refereed) Published
    Abstract [en]

    The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.

    Place, publisher, year, edition, pages
    Cold Spring Harbor Laboratory Press (CSHL), 2019
    Keywords
    Atlantic herring, assembly, ecological adaptation, supergene
    National Category
    Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-396775 (URN)10.1101/gr.253435.119 (DOI)000493952800015 ()31649060 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Research Council of Norway, 254774Wellcome trust, WT108749/Z/15/Z
    Available from: 2019-11-09 Created: 2019-11-09 Last updated: 2019-11-28Bibliographically approved