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  • Public defence: 2019-08-26 09:00 Sal VIII, Uppsala
    Alves, Ricardo
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computer Systems. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Architecture and Computer Communication.
    Leveraging Existing Microarchitectural Structures to Improve First-Level Caching Efficiency2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Low-latency data access is essential for performance. To achieve this, processors use fast first-level caches combined with out-of-order execution, to decrease and hide memory access latency respectively. While these approaches are effective for performance, they cost significant energy, leading to the development of many techniques that require designers to trade-off performance and efficiency.

    Way-prediction and filter caches are two of the most common strategies for improving first-level cache energy efficiency while still minimizing latency. They both have compromises as way-prediction trades off some latency for better energy efficiency, while filter caches trade off some energy efficiency for lower latency. However, these strategies are not mutually exclusive. By borrowing elements from both, and taking into account SRAM memory layout limitations, we proposed a novel MRU-L0 cache that mitigates many of their shortcomings while preserving their benefits. Moreover, while first-level caches are tightly integrated into the cpu pipeline, existing work on these techniques largely ignores the impact they have on instruction scheduling. We show that the variable hit latency introduced by way-misspredictions causes instruction replays of load dependent instruction chains, which hurts performance and efficiency. We study this effect and propose a variable latency cache-hit instruction scheduler, that identifies potential misschedulings, reduces instruction replays, reduces negative performance impact, and further improves cache energy efficiency.

    Modern pipelines also employ sophisticated execution strategies to hide memory latency and improve performance. While their primary use is for performance and correctness, they require intermediate storage that can be used as a cache as well. In this work we demonstrate how the store-buffer, paired with the memory dependency predictor, can be used to efficiently cache dirty data; and how the physical register file, paired with a value predictor, can be used to efficiently cache clean data. These strategies not only improve both performance and energy, but do so with no additional storage and minimal additional complexity, since they recycle existing cpu structures to detect reuse, memory ordering violations, and misspeculations.

    List of papers
    1. Addressing energy challenges in filter caches
    Open this publication in new window or tab >>Addressing energy challenges in filter caches
    2017 (English)In: Proc. 29th International Symposium on Computer Architecture and High Performance Computing, IEEE Computer Society, 2017, p. 49-56Conference paper, Published paper (Refereed)
    Abstract [en]

    Filter caches and way-predictors are common approaches to improve the efficiency and/or performance of first-level caches. Filter caches use a small L0 to provide more efficient and faster access to a small subset of the data, and work well for programs with high locality. Way-predictors improve efficiency by accessing only the way predicted, which alleviates the need to read all ways in parallel without increasing latency, but hurts performance due to mispredictions.In this work we examine how SRAM layout constraints (h-trees and data mapping inside the cache) affect way-predictors and filter caches. We show that accessing the smaller L0 array can be significantly more energy efficient than attempting to read fewer ways from a larger L1 cache; and that the main source of energy inefficiency in filter caches comes from L0 and L1 misses. We propose a filter cache optimization that shares the tag array between the L0 and the L1, which incurs the overhead of reading the larger tag array on every access, but in return allows us to directly access the correct L1 way on each L0 miss. This optimization does not add any extra latency and counter-intuitively, improves the filter caches overall energy efficiency beyond that of the way-predictor.By combining the low power benefits of a physically smaller L0 with the reduction in miss energy by reading L1 tags upfront in parallel with L0 data, we show that the optimized filter cache reduces the dynamic cache energy compared to a traditional filter cache by 26% while providing the same performance advantage. Compared to a way-predictor, the optimized cache improves performance by 6% and energy by 2%.

    Place, publisher, year, edition, pages
    IEEE Computer Society, 2017
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-334221 (URN)10.1109/SBAC-PAD.2017.14 (DOI)000426895600007 ()978-1-5090-1233-6 (ISBN)
    Conference
    29th International Symposium on Computer Architecture and High Performance Computing SBAC-PAD, 2017, October 17–20, Campinas, Brazil.
    Available from: 2017-11-09 Created: 2017-11-21 Last updated: 2019-05-22Bibliographically approved
    2. Dynamically Disabling Way-prediction to Reduce Instruction Replay
    Open this publication in new window or tab >>Dynamically Disabling Way-prediction to Reduce Instruction Replay
    2018 (English)In: 2018 IEEE 36th International Conference on Computer Design (ICCD), IEEE, 2018, p. 140-143Conference paper, Published paper (Refereed)
    Abstract [en]

    Way-predictors have long been used to reduce dynamic cache energy without the performance loss of serial caches. However, they produce variable-latency hits, as incorrect predictions increase load-to-use latency. While the performance impact of these extra cycles has been well-studied, the need to replay subsequent instructions in the pipeline due to the load latency increase has been ignored. In this work we show that way-predictors pay a significant performance penalty beyond previously studied effects due to instruction replays caused by mispredictions. To address this, we propose a solution that learns the confidence of the way prediction and dynamically disables it when it is likely to mispredict and cause replays. This allows us to reduce cache latency (when we can trust the way-prediction) while still avoiding the need to replay instructions in the pipeline (by avoiding way-mispredictions). Standard way-predictors degrade IPC by 6.9% vs. a parallel cache due to 10% of the instructions being replayed (worst case 42.3%). While our solution decreases way-prediction accuracy by turning off the way-predictor in some cases when it would have been correct, it delivers higher performance than a standard way-predictor. Our confidence-based way-predictor degrades IPC by only 4.4% by replaying just 5.6% of the instructions (worse case 16.3%). This reduces the way-predictor cache energy overhead compared to serial access cache, from 8.5% to 3.7% on average and on the worst case, from 33.8% to 9.5%.

    Place, publisher, year, edition, pages
    IEEE, 2018
    Series
    Proceedings IEEE International Conference on Computer Design, ISSN 1063-6404, E-ISSN 2576-6996
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-361215 (URN)10.1109/ICCD.2018.00029 (DOI)000458293200018 ()978-1-5386-8477-1 (ISBN)
    Conference
    IEEE 36th International Conference on Computer Design (ICCD), October 7–10, 2018, Orlando, FL, USA
    Available from: 2018-09-21 Created: 2018-09-21 Last updated: 2019-05-22Bibliographically approved
    3. Minimizing Replay under Way-Prediction
    Open this publication in new window or tab >>Minimizing Replay under Way-Prediction
    2019 (English)Report (Other academic)
    Abstract [en]

    Way-predictors are effective at reducing dynamic cache energy by reducing the number of ways accessed, but introduce additional latency for incorrect way-predictions. While previous work has studied the impact of the increased latency for incorrect way-predictions, we show that the latency variability has a far greater effect as it forces replay of in-flight instructions on an incorrect way-prediction. To address the problem, we propose a solution that learns the confidence of the way-prediction and dynamically disables it when it is likely to mispredict. We further improve this approach by biasing the confidence to reduce latency variability further at the cost of reduced way-predictions. Our results show that instruction replay in a way-predictor reduces IPC by 6.9% due to 10% of the instructions being replayed. Our confidence-based way-predictor degrades IPC by only 2.9% by replaying just 3.4% of the instructions, reducing way-predictor cache energy overhead (compared to serial access cache) from 8.5% to 1.9%.

    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2019-003
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-383596 (URN)
    Available from: 2019-05-17 Created: 2019-05-17 Last updated: 2019-07-03Bibliographically approved
    4. Filter caching for free: The untapped potential of the store-buffer
    Open this publication in new window or tab >>Filter caching for free: The untapped potential of the store-buffer
    2019 (English)In: Proc. 46th International Symposium on Computer Architecture, New York: ACM Press, 2019, p. 436-448Conference paper, Published paper (Refereed)
    Abstract [en]

    Modern processors contain store-buffers to allow stores to retire under a miss, thus hiding store-miss latency. The store-buffer needs to be large (for performance) and searched on every load (for correctness), thereby making it a costly structure in both area and energy. Yet on every load, the store-buffer is probed in parallel with the L1 and TLB, with no concern for the store-buffer's intrinsic hit rate or whether a store-buffer hit can be predicted to save energy by disabling the L1 and TLB probes.

    In this work we cache data that have been written back to memory in a unified store-queue/buffer/cache, and predict hits to avoid L1/TLB probes and save energy. By dynamically adjusting the allocation of entries between the store-queue/buffer/cache, we can achieve nearly optimal reuse, without causing stalls. We are able to do this efficiently and cheaply by recognizing key properties of stores: free caching (since they must be written into the store-buffer for correctness we need no additional data movement), cheap coherence (since we only need to track state changes of the local, dirty data in the store-buffer), and free and accurate hit prediction (since the memory dependence predictor already does this for scheduling).

    As a result, we are able to increase the store-buffer hit rate and reduce store-buffer/TLB/L1 dynamic energy by 11.8% (up to 26.4%) on SPEC2006 without hurting performance (average IPC improvements of 1.5%, up to 4.7%).The cost for these improvements is a 0.2% increase in L1 cache capacity (1 bit per line) and one additional tail pointer in the store-buffer.

    Place, publisher, year, edition, pages
    New York: ACM Press, 2019
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-383473 (URN)10.1145/3307650.3322269 (DOI)978-1-4503-6669-4 (ISBN)
    Conference
    ISCA 2019, June 22–26, Phoenix, AZ
    Funder
    Knut and Alice Wallenberg FoundationEU, Horizon 2020, 715283EU, Horizon 2020, 801051Swedish Foundation for Strategic Research , SM17-0064
    Available from: 2019-06-22 Created: 2019-05-16 Last updated: 2019-07-03Bibliographically approved
    5. Efficient temporal and spatial load to load forwarding
    Open this publication in new window or tab >>Efficient temporal and spatial load to load forwarding
    2020 (English)In: Proc. 26th International Symposium on High-Performance and Computer Architecture, IEEE Computer Society, 2020Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    IEEE Computer Society, 2020
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-383477 (URN)
    Conference
    HPCA 2020, February 22–26, San Diego, CA
    Note

    to appear

    Available from: 2019-08-21 Created: 2019-05-16 Last updated: 2019-08-21Bibliographically approved
  • Public defence: 2019-08-30 09:00 Fåhraeussalen, Uppsala
    Tamsen, Fredrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Forensic Medicine.
    Homicide Injury Quantification: Measures of injury severity in homicide victims and associations with homicide characteristics2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Some previous studies have found that the amount and severity of injuries in homicide victims correlate with different homicide characteristics, such as the victim-offender relationship and drug influence of the offender. If such relationships exist, they may be used by homicide investigators as part of an offender profiling.

    Furthermore, injury severity may be helpful in understanding the nature of lethal violence. If the injuries change over time or differ between regions, this may say something about the underlying causes and thus help society to take preventive measures. However, measures of injury severity are often missing in homicide epidemiology. This may in part be due to a lack of standardized and accessible ways to quantify injuries in homicide victim.

    To address these issues, there is a need for methods to quantify injury severity in homicide victims. The aim of the current thesis was to investigate different types of injury measures and their applicability to homicide victims. The aim was also to use such measures to address research questions related to offender profiling.

    Starting off with injury scores used in trauma research and two scores developed specifically for homicide victims, these measures were applied to a general homicide population. Since there is no obvious “gold standard” for injury severity quantification on homicide victims, one had to be defined to validate the applied methods. Out of forensic experience and rational reasoning, the Sum of all AIS scores (SAIS) was proposed as a reference measure. The other scores were then evaluated through their correlations with the SAIS.

    In the following study, the injury severity in homicides from different time periods was measured. There were statistically significant increases over time with respect to excessive injuries and the number of lethal injuries per victim. These changes can reflect both a brutalization of homicidal violence, improved trauma care, or shifts in the methods by which people are killed.

    Next, the associations between injury severity and homicide characteristics were analysed. No relevant associations between injury severity and victim-offender relationship were found. Neither were there any connections between benzodiazepine influence in the offender and injury severity on the victim. Thus, the studies do not support the use of injury severity scores for offender profiling in a general homicide population.

    List of papers
    1. Homicide Injury Quantification: Correlations and Reliability of Injury Severity Scores Applied to Homicide Victims
    Open this publication in new window or tab >>Homicide Injury Quantification: Correlations and Reliability of Injury Severity Scores Applied to Homicide Victims
    2015 (English)In: Homicide Studies, ISSN 1088-7679, E-ISSN 1552-6720, Vol. 19, no 1, p. 88-100Article in journal (Refereed) Published
    Abstract [en]

    No generally accepted method exists for quantifying the degree of injury in homicide victims. This study explores six different injury severity scores with the goal to recommend a valid method that is reliable and easy to use. To investigate this issue, 103 homicides are examined regarding the correlations between these scores. This study concludes that the Homicide Injury Scale is valid, easy to use, and has a satisfactory inter-rater reliability.

    Keywords
    homicide, lethal violence, injury severity score, quantification
    National Category
    Forensic Science
    Identifiers
    urn:nbn:se:uu:diva-243424 (URN)10.1177/1088767914558142 (DOI)000346910300005 ()
    Available from: 2015-02-17 Created: 2015-02-09 Last updated: 2019-05-21Bibliographically approved
    2. Quantifying Homicide Injuries: A Swedish Time Trend Study Using the Homicide Injury Scale
    Open this publication in new window or tab >>Quantifying Homicide Injuries: A Swedish Time Trend Study Using the Homicide Injury Scale
    2017 (English)In: Scandinavian Journal of Forensic Science, ISSN 2353-0707, Vol. 23, no 2Article in journal (Refereed) Published
    National Category
    Forensic Science
    Identifiers
    urn:nbn:se:uu:diva-383632 (URN)10.1515/sjfs-2017-0005 (DOI)
    Available from: 2019-05-20 Created: 2019-05-20 Last updated: 2019-05-21
    3. Homicide injury severity in association with the victim-offender relationship
    Open this publication in new window or tab >>Homicide injury severity in association with the victim-offender relationship
    2019 (English)In: Forensic Science International, ISSN 0379-0738, E-ISSN 1872-6283, Vol. 300, p. 151-156Article in journal (Refereed) Published
    Abstract [en]

    There are previous studies that have found associations between specific injury patterns and different victim-offender relationships (VORs) in homicides. We have used quantitative injury severity scores to further investigate this issue. The amount and severity of injuries were assessed in 178 Swedish homicide victims, retrospectively included from the years 2007-2009. We analyzed whether different injury measures could be used to predict the VOR. In addition to a deeper understanding of violent behavior, such associations may be of help to homicide investigators for offender profiling. The victims' injuries were assessed with eleven different methods. The cases with known VORs were divided into four categories: partner, relative, acquaintance, and stranger. The injury seventies were then compared between these categories. No relevant differences were found. Thus, the current study does not support the claim that the VOR can be predicted from the injury severity in a general homicide population. These findings are in contrast to the results of some previous studies but confirm those of others.

    Keywords
    Homicide, Injury score, Injury quantification, Offender profiling
    National Category
    Forensic Science
    Identifiers
    urn:nbn:se:uu:diva-383634 (URN)10.1016/j.forsciint.2019.05.012 (DOI)000470903500030 ()
    Available from: 2019-05-20 Created: 2019-05-20 Last updated: 2019-07-05Bibliographically approved
    4. Homicide injury severity in association with benzodiazepine influence
    Open this publication in new window or tab >>Homicide injury severity in association with benzodiazepine influence
    (English)Manuscript (preprint) (Other academic)
    National Category
    Forensic Science
    Identifiers
    urn:nbn:se:uu:diva-383635 (URN)
    Note

    Submitted to Homicide Studies

    Available from: 2019-05-20 Created: 2019-05-20 Last updated: 2019-05-21
  • Public defence: 2019-08-30 09:15 Häggsalen, 10132, Uppsala
    Sterby, Mia
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Electrochemical Characterizations of Conducting Redox Polymers: Electron Transport in PEDOT/Quinone Systems2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Organic electrode materials for rechargeable batteries have caught increasing attention since they can be used in new innovative applications such as flexible electronics and smart fabrics. They can provide safer and more environmentally friendly devices than traditional batteries made from metals. Conducting polymers constitute an interesting class of organic electrode materials that have been thoroughly studied for battery applications. They have high conductivity but are heavy relative to their energy storage ability and will hence form batteries with low weight capacity. Quinones, on the other hand, are low weight molecules that participate in electron transport in both animals and plants. They could provide batteries with high capacity but are easily dissolved in the electrolyte and have low conductivity. These two constituents can be combined into a conducting redox polymer that has both high conductivity and high capacity. In the present work, the conducting polymer PEDOT and the simplest quinone, benzoquinone, are covalently attached and form the conducting redox polymer used for most studies in this thesis. The charge transport mechanism is investigated by in situ conductivity measurements and is found to mainly be governed by band transport. Other properties such as packing, kinetics, mass changes, and spectral changes are also studied. A polymerization technique is also analyzed, that allows for polymerization from a deposited layer. Lastly, two different types of batteries using conducting redox polymers are constructed. The thesis gives insight into the fundamental properties of conducting redox polymers and paves the way for the future of organic electronics.

    List of papers
    1. Characterization of PEDOT-Quinone Conducting Redox Polymers for Water Based Secondary Batteries
    Open this publication in new window or tab >>Characterization of PEDOT-Quinone Conducting Redox Polymers for Water Based Secondary Batteries
    Show others...
    2017 (English)In: Electrochimica Acta, ISSN 0013-4686, E-ISSN 1873-3859, Vol. 235, p. 356-364Article in journal (Refereed) Published
    Abstract [en]

    Lithium-ion technologies show great promise to meet the demands that the transition towards renewable energy sources and the electrification of the transport sector put forward. However, concerns regarding lithium-ion batteries, including limited material resources, high energy consumption during production, and flammable electrolytes, necessitate research on alternative technologies for electrochemical energy storage. Organic materials derived from abundant building blocks and with tunable properties, together with water based electrolytes, could provide safe, inexpensive and sustainable alternatives. In this study, two conducting redox polymers based on poly(3,4-ethylenedioxythiophene) (PEDOT) and a hydroquinone pendant group have been synthesized and characterized in an acidic aqueous electrolyte. The polymers were characterized with regards to kinetics, pH dependence, and mass changes during oxidation and reduction, as well as their conductance. Both polymers show redox matching, i.e. the quinone redox reaction occurs within the potential region where the polymer is conducting, and fast redox conversion that involves proton cycling during pendant group redox conversion. These properties make the presented materials promising candidates as electrode materials for water based all-organic batteries.

    Keywords
    Conducting Redox Polymer, Quinone, Organic Batteries, Proton Batteries, Redox Matching
    National Category
    Nano Technology
    Research subject
    Engineering Science with specialization in Nanotechnology and Functional Materials
    Identifiers
    urn:nbn:se:uu:diva-319049 (URN)10.1016/j.electacta.2017.03.068 (DOI)000398330200042 ()
    Funder
    Swedish Foundation for Strategic Research Swedish Research CouncilCarl Tryggers foundation Swedish Energy AgencyEU, Horizon 2020, 644631
    Available from: 2017-03-30 Created: 2017-03-30 Last updated: 2019-05-09Bibliographically approved
    2. An All-Organic Proton Battery
    Open this publication in new window or tab >>An All-Organic Proton Battery
    2017 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 13, p. 4828-4834Article in journal (Refereed) Published
    Abstract [en]

    Rechargeable batteries that use organic matter as. the capacity-carrying material have previously been considered a technology for the future. Earlier batteries in which both the anode and cathode consisted of organic material required significant amounts of conductive additives and were often based on metal-ion electrolytes containing Li+ or Na+. However, we have used conducting poly(3,4-ethylenedioxythiophene) (PEDOT), functionalized with anthraquinone (PEDQT-AQ) or, benzonquinone (PEDOT-BQ) pendant groups as the negative and positive electrode materials, respectively, to make an all-organic proton battery devoid of metals. The electrolyte consists of a proton donor and acceptor slurry containing substituted pyridinium triflates and the corresponding pyridine base. This slurry allows the 2e(-)/2H(+) quinone/hydroquinone redox reactions while suppressing proton reduction in the battery cell. By using strong (acidic) proton donors, the formal potential of the quinone redox reactions is tuned into the potential region in which the PEDOT backbone is conductive, thus eliminating the need for conducting additives. In this all-organic proton battery cell, PEDOT-AQ and PEDOT-BQ deliver 103 and 120 mAh g(-1), which correspond to 78% and 75%, respectively, of the theoretical specific capacity of the materials at an average cell potential of 0.5 V. We show that PEDOT-BQ determines the cycling stability of the device while PEDOT-AQ provides excellent reversibility for at least 1000 cycles. This proof-of-concept shows the feasibility of assembling all organic proton batteries which require no conductive additives and also reveals where the challenges and opportunities lie on the path to producing plastic batteries.

    Keywords
    rechargeable lithium batteries, li-ion batteries, electrode materials, energy-storage, cathode, anode, salt, electrochemistry, derivatives, polymer
    National Category
    Nano Technology
    Research subject
    Engineering Science with specialization in Nanotechnology and Functional Materials
    Identifiers
    urn:nbn:se:uu:diva-319048 (URN)10.1021/jacs.7b00159 (DOI)000398764000036 ()28293954 (PubMedID)
    Funder
    Swedish Foundation for Strategic Research Swedish Research CouncilCarl Tryggers foundation Swedish Energy AgencyEU, Horizon 2020, H2020/2014-2020 644631
    Available from: 2017-03-30 Created: 2017-03-30 Last updated: 2019-05-09Bibliographically approved
    3. Investigating electron transport in a PEDOT/Quinone conducting redox polymer with in situ methods
    Open this publication in new window or tab >>Investigating electron transport in a PEDOT/Quinone conducting redox polymer with in situ methods
    Show others...
    2019 (English)In: Electrochimica Acta, ISSN 0013-4686, E-ISSN 1873-3859, Vol. 308, p. 277-284Article in journal (Refereed) Published
    Abstract [en]

    A conducting redox polymer is investigated in acidic electrolyte using various in situ methods, including electron paramagnetic resonance (EPR), UV–vis spectroscopy, and conductance measurements. The quinone redox active pendant group has a formal potential of 0.67 V (vs. standard hydrogen electrode) where a 2e2H process occurs. By analyzing the rate constant at different temperatures, the rate-limiting step in the redox reaction was found to be a thermally activated process with an activation energy of 0.3 eV. The electron transport through the conducting polymerwas found to be non-thermally activated and, hence, not redox rate-limiting. This is also the first time a negative temperature dependence has been reported for a conducting redox polymer in the same potential region where the redox active pendant group has its formal potential. EPR and conductance data indicated that the conductivity is governed by both polarons and bipolarons but their ratio is shifting during oxidation and reduction of the polymer.

    Keywords
    Conducting Redox Polymer, PEDOT, Quinone, Temperature dependence
    National Category
    Nano Technology
    Research subject
    Engineering Science with specialization in Nanotechnology and Functional Materials
    Identifiers
    urn:nbn:se:uu:diva-383025 (URN)10.1016/j.electacta.2019.03.207 (DOI)000466713100030 ()
    Funder
    Carl Tryggers foundation Swedish Energy AgencySwedish Research CouncilStiftelsen Olle Engkvist ByggmästareSwedish Research Council Formas
    Available from: 2019-05-07 Created: 2019-05-07 Last updated: 2019-06-10Bibliographically approved
    4. Post-Deposition Polymerization: A Method for Circumventing Processing of Insoluble Conducting Polymers
    Open this publication in new window or tab >>Post-Deposition Polymerization: A Method for Circumventing Processing of Insoluble Conducting Polymers
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    (English)Manuscript (preprint) (Other (popular science, discussion, etc.))
    Abstract [en]

    A method, termed post-deposition polymerization, for the synthesis of conducting polymers is presented, which enables solid state polymerization of oligomeric layers by oxidative polymerization. The method was developed as a general tool for the preparation of conducting polymer layers that allows for industrially viable solution-processing methods to be used for substrate coating. We use trimer building blocks based on 3,4-ethylenedioxythiophene (EDOT) in the processing step, and show that the resulting trimer layer has innate conductivity when oxidized, which presumably is instrumental for successful polymerization of the solid layer. As judged by in situ conductance measurement during oxidative polymerization of the trimer layer, the layer-conductivity is greatly increased as a result of polymerization. Successful solid state polymerization was also confirmed by the irreversible spectral changes, monitored in-situ during polymerization, resulting in signature spectral transitions of conducting polymers from an initial spectrum derived solely from trimer absorption. From the in situ determined mass changes we estimate the swelling during post-deposition polymerization as well as the average polymer length. Electrochemical characterization of the resulting polymer show fast redox conversion as well as non-activated electron transport through the material indicating that the post-deposition polymerization-generated polymer indeed show promising properties. We believe that the post-deposition polymerization method will enable investigations, currently hampered by limited processability, of interesting families of conducting polymer materials.

    Keywords
    Conducting Polymer, PEDOT, polymerization
    National Category
    Nano Technology
    Research subject
    Engineering Science with specialization in Nanotechnology and Functional Materials
    Identifiers
    urn:nbn:se:uu:diva-383028 (URN)
    Available from: 2019-05-09 Created: 2019-05-09 Last updated: 2019-05-16
  • Public defence: 2019-08-30 10:15 Hörsal 2, Uppsala
    Lombardi, Stefano
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Economics. Uppsala University, Units outside the University, Office of Labour Market Policy Evaluation.
    Essays on Event History Analysis and the Effects of Social Programs on Individuals and Firms2019Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Essay I: This paper studies threat effects of unemployment insurance (UI) benefit sanctions on job exit rates. Using a difference-in-differences design, I exploit two reforms of the Swedish UI system that made monitoring and sanctions considerably stricter at different points in time for different jobseeker groups. I find that men and long-term unemployed respond to the stricter UI rules by finding jobs faster. I also estimate the effect of receiving a sanction on the job exit rates, and find significant sanction imposition effects. However, a decomposition exercise shows that these effects explain very little of the overall reform effects, which instead are driven the threat of sanction imposition.

    Essay II (with Gerard J. van den Berg and Johan Vikström): We use an Empirical Monte Carlo design and rich administrative data to generate realistic placebo treatment durations. First, we highlight important confounders to be controlled for when estimating selection models. Next, we omit some of the covariates used to simulate placebo treatments, and we estimate Timing-of-Events models. The model is generally able to adjust for a large share of the resulting unobserved heterogeneity. However, we find that specifying too many or too few support points to approximate the unobserved heterogeneity distribution leads to large bias. Information criteria that penalize parameter abundance can help selecting the appropriate number of support points.

    Essay III (with Oskar Nordström Skans and Johan Vikström): We study how targeted wage subsidies affect the performance of the recruiting firms. Using Swedish linked employer-employee data from 1998–2008, we show that the firms hiring through subsidies substantially outperform other recruiting firms, despite identical pre-treatment performance levels and trends in a wide set of key dimensions. The pattern is less clear from 2007 onwards, after a reform removed the involvement of caseworkers from the subsidy approval process. Our results suggest that targeted employment subsidies can have large positive effects on outcomes of the hiring firms, at least if the policy environment allows for pre-screening by caseworkers.

    Essay IV (with Raffaella Piccarreta and Marco Bonetti): We propose different methods for comparing the ability of competing non-nested event history models to generate trajectories that are similar to the observed ones. We first introduce alternative criteria to compare pairwise dissimilarities between observed and simulated sequences. Next, we estimate two alternative multi-state models using data on family formation and childbearing decisions from the Dutch Fertility and Family Survey. We use the estimated models to simulate event histories and to illustrate the proposed comparison criteria.

  • Public defence: 2019-08-30 13:15 Room 80101, Uppsala
    Ekstedt, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Phenomenology of new Neutral Vector Bosons and Parton Distributions from Hadronic Fluctuations2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The Higgs particle was first predicted in 1964, and was discovered in the summer of 2012 at the Large Hadron Collider (LHC). This discovery was the latest in a long list of successful Standard Model predictions spanning the last fifty years. However, some of the Standard Models predictions, such as massless neutrinos, are not in agreement with experiment. Thus, extensions of the Standard Model should be considered. Furthermore, some issues, such as how quarks are bound within the proton, are difficult to study from first principles.

    In paper I and II of this thesis, a class of models that contains a new TeV scale neutral vector boson is studied. The parameter space of this class of models is constrained using electroweak precision constraints and 13 TeV LHC data. Gauge anomalies are cancelled both by choosing appropriate fermion charges, and by adding Green-Schwarz terms.

    The Higgs mechanism is often studied at leading order, but there are also important radiative corrections. These radiative corrections, which change the ground state energy, can both be IR divergent and gauge dependent. In paper III it is shown how to solve both of these problems. In particular, IR divergences are shown to be spurious.

    In paper IV of this thesis, rapidity gaps at the LHC are explained by using a colour singlet two-gluon ladder exchange (BFKL). These exchanges, together with a soft-gluon model, are implemented in a complete Monte Carlo simulation, and reproduce observed rapidity gaps at the LHC.

    The momentum distributions of bound partons, quarks and gluons, are described by parton distribution functions (PDFs). In paper V and VI of this thesis, a physically motivated model for PDFs is presented. This model can reproduce proton structure function data, and gives a possible solution to the proton spin puzzle.

    List of papers
    1. Constraining minimal anomaly free U(1) extensions of the Standard Model
    Open this publication in new window or tab >>Constraining minimal anomaly free U(1) extensions of the Standard Model
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    2016 (English)In: Journal of High Energy Physics (JHEP), ISSN 1126-6708, E-ISSN 1029-8479, Vol. 1611, article id 071Article in journal (Refereed) Published
    Abstract [en]

    We consider a class of minimal anomaly free U(1) extensions of the Standard Model with three generations of right-handed neutrinos and a complex scalar. Using electroweak precision constraints, new 13 TeV LHC data, and considering theoretical limitations such as perturbativity, we show that it is possible to constrain a wide class of models. By classifying these models with a single parameter, κ, we can put a model independent upper bound on the new U(1) gauge coupling gz. We find that the new dilepton data puts strong bounds on the parameters, especially in the mass region MZ′≲3 TeV.

    Keywords
    Beyond Standard Model, Gauge Symmetry
    National Category
    Subatomic Physics
    Research subject
    Physics with specialization in Elementary Particle Physics
    Identifiers
    urn:nbn:se:uu:diva-301819 (URN)10.1007/JHEP11(2016)071 (DOI)000387691500010 ()
    Funder
    Carl Tryggers foundation , CTS-14:206Swedish Research Council, 621-2011-5107
    Available from: 2016-08-25 Created: 2016-08-25 Last updated: 2019-05-13Bibliographically approved
    2. Minimal anomalous U(1) theories and collider phenomenology
    Open this publication in new window or tab >>Minimal anomalous U(1) theories and collider phenomenology
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    2018 (English)In: Journal of High Energy Physics (JHEP), ISSN 1126-6708, E-ISSN 1029-8479, Vol. 1802, p. 152-Article in journal (Refereed) Published
    Abstract [en]

    We study the collider phenomenology of a neutral gauge boson Z′ arising in minimal but anomalous U(1) extensions of the Standard Model (SM). To retain gauge invariance of physical observables, we consider cancellation of gauge anomalies through the Green-Schwarz mechanism. We categorize a wide class of U(1) extensions in terms of the new U(1) charges of the left-handed quarks and leptons and the Higgs doublet. We derive constraints on some benchmark models using electroweak precision constraints and the latest 13 TeV LHC dilepton and dijet resonance search data. We calculate the decay rates of the exotic and rare one-loop Z′ decays to ZZ and Z-photon modes, which are the unique signatures of our framework. If observed, these decays could hint at anomaly cancellation through the Green-Schwarz mechanism. We also discuss the possible observation of such signatures at the LHC and at future ILC colliders.

    National Category
    Subatomic Physics
    Research subject
    Physics with specialization in Elementary Particle Physics
    Identifiers
    urn:nbn:se:uu:diva-336639 (URN)10.1007/JHEP02(2018)152 (DOI)000426358100007 ()
    Funder
    Carl Tryggers foundation , CTS-14:206Swedish Research Council, 621-2011-5107
    Available from: 2017-12-15 Created: 2017-12-15 Last updated: 2019-05-13Bibliographically approved
    3. On the relationship between gauge dependence and IR divergences in the -expansion of the effective potential
    Open this publication in new window or tab >>On the relationship between gauge dependence and IR divergences in the -expansion of the effective potential
    2019 (English)In: Journal of High Energy Physics (JHEP), ISSN 1126-6708, E-ISSN 1029-8479, no 1, article id 226Article in journal (Refereed) Published
    Abstract [en]

    Perturbative calculations of the effective potential evaluated at a broken minimum, Vmin, are plagued by difficulties. It is hard to get a finite and gauge invariant result for Vmin. In fact, the methods proposed to deal with gauge dependence and ir divergences are orthogonal in their approaches. Gauge dependence is dealt with through the ℏ-expansion, which establishes and maintains a strict loop-order separation of terms. On the other hand, ir divergences seem to require a resummation that mixes the different loop orders. In this paper we test these methods on Fermi gauge Abelian Higgs at two loops. We find that the resummation procedure is not capable of removing all divergences. Surprisingly, the ℏ-expansion seems to be able to deal with both the divergences and the gauge dependence. In order to isolate the physical part of Vmin, we are guided by the separation of scales that motivated the resummation procedure; the key result is that only hard momentum modes contribute to Vmin.

    Keywords
    Spontaneous Symmetry Breaking, Gauge Symmetry
    National Category
    Subatomic Physics
    Identifiers
    urn:nbn:se:uu:diva-377699 (URN)10.1007/JHEP01(2019)226 (DOI)000457501400005 ()
    Available from: 2019-02-25 Created: 2019-02-25 Last updated: 2019-05-13Bibliographically approved
    4. Hard color singlet BFKL exchange and gaps between jets at the LHC
    Open this publication in new window or tab >>Hard color singlet BFKL exchange and gaps between jets at the LHC
    2017 (English)Report (Other academic)
    Abstract [en]

    We explore the perturbative QCD dynamics of hard parton-parton scattering through the exchange of a color singlet two-gluon ladder as described by the BFKL equation, resulting in a rapidity gap between two high transverse momentum jets. Implementing this in a complete Monte Carlo event simulation that also accounts for additional QCD processes at softer scales provides dynamical modeling of gap survival probabilities, which makes possible a detailed comparison with data on such jet-gap-jet events. New data from CMS at the LHC extend the dynamic range of the previous Tevatron data, and can be reproduced reasonably well provided that the Soft Color Interaction model is modified based on the idea of reduced resolution power of softer gluon exchanges. This indicates the need for further theoretical developments in connection with other color exchange processes related to rapidity gaps in the hadronic final state.

    Keywords
    QCD, BFKL, rapidity gaps, jets, Monte Carlo
    National Category
    Subatomic Physics
    Research subject
    Physics with specialization in Elementary Particle Physics
    Identifiers
    urn:nbn:se:uu:diva-319966 (URN)
    Available from: 2017-04-11 Created: 2017-04-11 Last updated: 2019-05-13
    5. Nucleon parton distributions from hadronic quantum fluctuations
    Open this publication in new window or tab >>Nucleon parton distributions from hadronic quantum fluctuations
    (English)Manuscript (preprint) (Other academic)
    National Category
    Subatomic Physics
    Identifiers
    urn:nbn:se:uu:diva-357641 (URN)
    Available from: 2018-08-20 Created: 2018-08-20 Last updated: 2019-05-13
    6. Towards solving the proton spin puzzle
    Open this publication in new window or tab >>Towards solving the proton spin puzzle
    (English)Manuscript (preprint) (Other academic)
    National Category
    Subatomic Physics
    Identifiers
    urn:nbn:se:uu:diva-357642 (URN)
    Available from: 2018-08-20 Created: 2018-08-20 Last updated: 2019-05-13
  • Public defence: 2019-09-04 13:00 Lindahlsalen, Uppsala
    Wang, Mi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gene regulatory evolution in flycatchers: statistical approaches for the analysis of allele-specific expression2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Understanding the molecular mechanisms underlying evolutionary changes in gene expression is a major research topic in biology. While a powerful approach to study this is the analysis of allele-specific expression (ASE), most of previously published methods can only be applied to lab organisms. In this thesis, to enable the analysis of ASE in natural organisms, I developed two methods for ASE detection. The first one was Bayesian negative binomial approach, and the second one was Read-backed Phasing-based ASE approach. Both methods performed well in simulations and comparisons. By applying those methods, I found that ASE was prevalent in natural flycatcher species. Combining the analyses of differential gene expression and ASE, I found a widespread cis-trans compensation and a critical role of tissue-specific regulatory mechanism during gene expression evolution. Moreover, for cis-regulatory sequences, there was a larger proportion of slightly deleterious mutations and weaker signatures of positive selection for genes with ASE than genes without ASE. For coding sequence, no such difference was observed. These results indicated that the evolution of gene expression and coding sequences could be uncoupled and occurred independently.

    List of papers
    1. Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations
    Open this publication in new window or tab >>Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations
    2017 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 5, p. 1266-1279Article in journal (Refereed) Published
    Abstract [en]

    Polymorphism in cis-regulatory sequences can lead to different levels of expression for the two alleles of a gene, providing a starting point for the evolution of gene expression. Little is known about the genome-wide abundance of genetic variation in gene regulation in natural populations but analysis of allele-specific expression (ASE) provides a means for investigating such variation. We performed RNA-seq of multiple tissues from population samples of two closely related flycatcher species and developed a Bayesian algorithm that maximizes data usage by borrowing information from the whole data set and combines several SNPs per transcript to detect ASE. Of 2,576 transcripts analyzed in collared flycatcher, ASE was detected in 185 (7.2%) and a similar frequency was seen in the pied flycatcher. Transcripts with statistically significant ASE commonly showed the major allele in > 90% of the reads, reflecting that power was highest when expression was heavily biased toward one of the alleles. This would suggest that the observed frequencies of ASE likely are underestimates. The proportion of ASE transcripts varied among tissues, being lowest in testis and highest in muscle. Individuals often showed ASE of particular transcripts in more than one tissue (73.4%), consistent with a genetic basis for regulation of gene expression. The results suggest that genetic variation in regulatory sequences commonly affects gene expression in natural populations and that it provides a seedbed for phenotypic evolution via divergence in gene expression.

    Place, publisher, year, edition, pages
    OXFORD UNIV PRESS, 2017
    Keywords
    ASE, gene expression evolution, regulatory sequences, RNA-seq
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-333414 (URN)10.1093/gbe/evx080 (DOI)000406760400013 ()28453623 (PubMedID)
    Funder
    Swedish Research Council, 2010-5650, 2013-8271EU, European Research Council, AdG 249976Knut and Alice Wallenberg Foundation
    Available from: 2017-11-15 Created: 2017-11-15 Last updated: 2019-06-11Bibliographically approved
    2. RPASE: Individual-based allele-specific expression detection without prior knowledge of haplotype phase
    Open this publication in new window or tab >>RPASE: Individual-based allele-specific expression detection without prior knowledge of haplotype phase
    2018 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 18, no 6, p. 1247-1262Article in journal (Refereed) Published
    Abstract [en]

    Variation in gene expression is believed to make a significant contribution to phenotypic diversity and divergence. The analysis of allele-specific expression (ASE) can reveal important insights into gene expression regulation. We developed a novel method called RPASE (Read-backed Phasing-based ASE detection) to test for genes that show ASE. With mapped RNA-seq data from a single individual and a list of SNPs from the same individual as the only input, RPASE is capable of aggregating information across multiple dependent SNPs and producing individual-based gene-level tests for ASE. RPASE performs well in simulations and comparisons. We applied RPASE to multiple bird species and found a potentially rich landscape of ASE.

    Keywords
    allele-specific expression, gene expression evolution, regulatory variation, RNA-seq
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-369587 (URN)10.1111/1755-0998.12909 (DOI)000449535600007 ()29858523 (PubMedID)
    Funder
    Swedish Research CouncilKnut and Alice Wallenberg Foundation
    Available from: 2018-12-19 Created: 2018-12-19 Last updated: 2019-06-11Bibliographically approved
    3. Gene regulatory evolution in natural flycatcher populations is highly tissue-specific and shows distinctive patterns in the testis
    Open this publication in new window or tab >>Gene regulatory evolution in natural flycatcher populations is highly tissue-specific and shows distinctive patterns in the testis
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-384395 (URN)
    Available from: 2019-06-04 Created: 2019-06-04 Last updated: 2019-06-11
    4. Cis-regulatory variation and allele-specific expression in the collared flycatcher (Ficedula albicollis) genome
    Open this publication in new window or tab >>Cis-regulatory variation and allele-specific expression in the collared flycatcher (Ficedula albicollis) genome
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-384392 (URN)
    Available from: 2019-06-04 Created: 2019-06-04 Last updated: 2019-06-11
  • Public defence: 2019-09-05 09:00 C8:305, Uppsala
    Mun, Kwangchol
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Human adenovirus – host cell interplay: The role of the cellular zinc finger proteins and mitochondrial DNA2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Human adenovirus (HAdV) is an abundant DNA virus with significant clinical relevance since it cauces a variety of respiratory, ocular, and gastrointestinal diseases. It is also intensively used as a therapeutic tool to treat cancers and to boost immune responses. In order to achieve a better control over the HAdV epidemiology and improved utilization for clinical applications, it is crucial to understand the molecular interaction between the host cell and HAdV.

    The aim of the current thesis is to delineate the molecular interactions between HAdV type 5 (HAdV-C5) protein VII (pVII), two cellular zinc finger proteins (MKRN1, ZNF622)  and mitochondrial DNA (mtDNA). In paper I, we have identified MKRN1 as one of the novel pVII-interacting proteins. Surprisingly, endogenous MKRN1 protein is down-regulated in the HAdV-infected cells due to its proteasomal degradation. Further, the pVII(wt) promoted  MKRN1 self-ubiquitination, which may explain the overall instability of the MKRN1 protein in the infected cells. In addition, we show that the MKRN1 protein is also down-regulated in measles virus- and vesicular stomatitis virus-infected cells. In paper II, we report that the cellular ZNF622 protein interacts with the pVII protein. Intriguingly, ZNF622 expression was enhanced in HAdV-C5-infected cells, implying its anti-viral role. Surprisingly, lack of the ZNF622 protein significantly enhanced formation of the infectious HAdV-C5 virions. Finally, we propose a model how the ZNF622/NPM1/pVII protein complex regulates the pVII protein binding to viral DNA. In paper III, we report that HAdV-C5 infection enhanced mtDNA release into cytosol. The enhanced mtDNA release can be partially explained by accumulation of the pVII protein since its down-regulation diminished mtDNA release into cyotosol. We also report pVII-regulated gene expression profile and show that cellular cytokine IL-32 mRNA accumulates in response to the pVII protein expression.

    Collectively, in this thesis we provide molecular characterization how two cellular zinc finger proteins (MKRN1 and ZNF622) and mtDNA behave in the context of lytic HAdV-C5 infection. The ZNF622 may act as a bona fide anti-viral factor blocking infectious virion formation via targeting the essential viral core protein pVII. The MKRN1 protein is efficiently eliminated in the infected cells, highlighting the essence of HAdV-C5-controlled proteasome. Finally, dynamical change of mtDNA induced by HAdV-C5 infection, might initiate a novel signaling pathway beneficial for the cells or the viruses.

    List of papers
    1. Human Adenovirus Infection Causes Cellular E3 Ubiquitin Ligase MKRN1 Degradation Involving the Viral Core Protein pVII.
    Open this publication in new window or tab >>Human Adenovirus Infection Causes Cellular E3 Ubiquitin Ligase MKRN1 Degradation Involving the Viral Core Protein pVII.
    Show others...
    2018 (English)In: Journal of Virology, ISSN 0022-538X, E-ISSN 1098-5514, Vol. 92, no 3, article id e01154-17Article in journal (Refereed) Published
    Abstract [en]

    Human adenoviruses (HAdVs) are common human pathogens encoding a highly abundant histone-like core protein, VII, which is involved in nuclear delivery and protection of viral DNA as well as in sequestering immune danger signals in infected cells. The molecular details of how protein VII acts as a multifunctional protein have remained to a large extent enigmatic. Here we report the identification of several cellular proteins interacting with the precursor pVII protein. We show that the cellular E3 ubiquitin ligase MKRN1 is a novel precursor pVII-interacting protein in HAdV-C5-infected cells. Surprisingly, the endogenous MKRN1 protein underwent proteasomal degradation during the late phase of HAdV-C5 infection in various human cell lines. MKRN1 protein degradation occurred independently of the HAdV E1B55K and E4orf6 proteins. We provide experimental evidence that the precursor pVII protein binding enhances MKRN1 self-ubiquitination, whereas the processed mature VII protein is deficient in this function. Based on these data, we propose that the pVII protein binding promotes MKRN1 self-ubiquitination, followed by proteasomal degradation of the MKRN1 protein, in HAdV-C5-infected cells. In addition, we show that measles virus and vesicular stomatitis virus infections reduce the MKRN1 protein accumulation in the recipient cells. Taken together, our results expand the functional repertoire of the HAdV-C5 precursor pVII protein in lytic virus infection and highlight MKRN1 as a potential common target during different virus infections. IMPORTANCE: Human adenoviruses (HAdVs) are common pathogens causing a wide range of diseases. To achieve pathogenicity, HAdVs have to counteract a variety of host cell antiviral defense systems, which would otherwise hamper virus replication. In this study, we show that the HAdV-C5 histone-like core protein pVII binds to and promotes self-ubiquitination of a cellular E3 ubiquitin ligase named MKRN1. This mutual interaction between the pVII and MKRN1 proteins may prime MKRN1 for proteasomal degradation, because the MKRN1 protein is efficiently degraded during the late phase of HAdV-C5 infection. Since MKRN1 protein accumulation is also reduced in measles virus- and vesicular stomatitis virus-infected cells, our results signify the general strategy of viruses to target MKRN1.

    Keywords
    adenoviruses, proteasome, ubiquitination
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-339568 (URN)10.1128/JVI.01154-17 (DOI)000423571600001 ()29142133 (PubMedID)
    Funder
    Åke Wiberg Foundation, M14-0155Swedish Cancer Society, CAN 2013/350Swedish Research Council, 2006-5038-36531-16Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
    Available from: 2018-01-20 Created: 2018-01-20 Last updated: 2019-07-29Bibliographically approved
    2. Cellular Zinc Finger Protein 622 Hinders Human Adenovirus Lytic Growth and Limits Binding of the Viral pVII Protein to Virus DNA
    Open this publication in new window or tab >>Cellular Zinc Finger Protein 622 Hinders Human Adenovirus Lytic Growth and Limits Binding of the Viral pVII Protein to Virus DNA
    2019 (English)In: Journal of Virology, ISSN 0022-538X, E-ISSN 1098-5514, Vol. 93, no 3, article id e01628-18Article in journal (Refereed) Published
    Abstract [en]

    Human adenovirus (HAdV) encodes a multifunctional DNA-binding protein pVII, which is involved in virus DNA packaging and extracellular immune signaling regulation. Although the pVII is an essential viral protein, its exact role in the virus life cycle and interplay with cellular proteins have remained to a large extent unclear. We have recently identified the cellular zinc finger protein 622 (ZNF622) as a potential pVII-interacting protein. In this study, we describe the functional consequences of the ZNF622-pVII interplay and the role of ZNF622 in the HAdV life cycle. ZNF622 protein expression increased, and it accumulated similarly to the pVII protein in the nuclei of virus-infected cells. The lack of the ZNF622 protein specifically increased pVII binding to viral DNA in the infected cells and elevated the pVII protein levels in the purified virions. In addition, ZNF622 knockout cells showed an increased cell lysis and enhanced accumulation of the infectious virus particles. Protein interaction studies revealed that ZNF622 forms a trimeric complex with the pVII protein and the cellular histone chaperon protein nucleophosmin 1 (NPM1). The integrity of this complex is important since ZNF622 mutations and NPM1 deficiency changed pVII ability to bind viral DNA. Collectively, our results implicate that ZNF622 may act as a cellular antiviral protein hindering lytic HAdV growth and limiting pVII protein binding to viral DNA.

    IMPORTANCE Human adenoviruses (HAdVs) are common human pathogens causing a wide range of acute infections. To counteract viral pathogenicity, cells encode a variety of antiviral proteins and noncoding RNAs to block virus growth. In this study, we show that the cellular zinc finger protein 622 (ZNF622) interacts with an essential HAdV protein known as pVII. This mutual interaction limits pVII binding to viral DNA. Further, ZNF622 has a role in HAdV life cycle since the lack of ZNF622 correlates with increased lysis of the infected cells and accumulation of the infectious virions. Together, our study reveals a novel cellular antiviral protein ZNF622, which may impede lytic HAdV growth.

    Keywords
    adenoviruses, chromatin remodeling
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-375801 (URN)10.1128/JVI.01628-18 (DOI)000456001300019 ()30429337 (PubMedID)
    Funder
    Swedish Research Council, 2006-5038-36531-16Åke Wiberg Foundation, M14-0155Swedish Cancer Society, CAN 2013/350
    Available from: 2019-02-13 Created: 2019-02-13 Last updated: 2019-07-29
    3. Human adenovirus core protein pVII influences mitochondrial DNA dynamics and expression of the pro-inflammatory cytokine IL-32
    Open this publication in new window or tab >>Human adenovirus core protein pVII influences mitochondrial DNA dynamics and expression of the pro-inflammatory cytokine IL-32
    (English)Manuscript (preprint) (Other academic)
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-389804 (URN)
    Available from: 2019-07-29 Created: 2019-07-29 Last updated: 2019-07-29
  • Public defence: 2019-09-06 09:00 Hambergsalen, Uppsala
    Geiger, Harri
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Mineralogy Petrology and Tectonics.
    Trans-crustal magma storage in contrasting tectonic settings2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Magmatic plumbing systems comprise magma chambers, sheet intrusions, and conduits which link the Earth’s deep interior with the Earth’s surface. As such, they are the structural framework of magma transport and storage that is governed by complex physical and chemical processes in magma reservoirs and through the interaction of magma bodies with surrounding crustal rocks over timescales from hours to millions of years. These geological processes, in turn, play a vital role in controlling eruptive behaviour and the magnitude of associated volcanic eruptions that impact the environment as well as human society. Our understanding of the nature and location of magmatic processes and plumbing system architecture remains, however, fragmentary. This lack of knowledge can partly be attributed to limits regarding the spatial resolution of geophysical methods and partly to geochemical uncertainties and errors in associated models. Ongoing advances in analytical techniques increase spatial, temporal, and chemical resolution, hence enabling us to gather more detailed knowledge on the structure and dynamics of magmatic systems, especially for individual volcanoes, but also in respect to the long-term evolution of magmatic provinces and ultimately the Earth as a whole. This process-oriented thesis examines fossil and active magmatic plumbing systems in Iceland, Indonesia, Cameroon, and the Canary Islands by applying a combination of traditional and state-of-the-art petrological and geochemical methods, mineral(-melt) thermobarometric modelling, and isotopic analytical techniques. The results add valuable insights to the growing body of evidence for multi-tiered plumbing systems in a number of volcano-tectonic settings and underline the importance of shallow-level magma storage and its influence on magma evolution and hazardous volcanic eruptions.

    List of papers
    1. Magma plumbing for the 2014–2015 Holuhraun eruption, Iceland
    Open this publication in new window or tab >>Magma plumbing for the 2014–2015 Holuhraun eruption, Iceland
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    2016 (English)In: Geochemistry Geophysics Geosystems, ISSN 1525-2027, E-ISSN 1525-2027, Vol. 17, no 8, p. 2953-2968Article in journal (Refereed) Published
    Abstract [en]

    The 2014–2015 Holuhraun eruption on Iceland was located within the Askja fissure swarm butwas accompanied by caldera subsidence in the Barðarbunga central volcano 45 km to the southwest. Geophysicalmonitoring of the eruption identified a seismic swarm that migrated from Barðarbunga to theHoluhraun eruption site over the course of two weeks. In order to better understand this lateral connectionbetween Barðarbunga and Holuhraun, we present mineral textures and compositions, mineral-meltequilibriumcalculations, whole rock and trace element data, and oxygen isotope ratios for selected Holuhraunsamples. The Holuhraun lavas are compositionally similar to recorded historical eruptions from theBarðarbunga volcanic system but are distinct from the historical eruption products of the nearby Askja system.Thermobarometry calculations indicate a polybaric magma plumbing system for the Holuhraun eruption,wherein clinopyroxene and plagioclase crystallized at average depths of 17 km and 5 km,respectively. Crystal resorption textures and oxygen isotope variations imply that this multilevel plumbingsystem facilitated magma mixing and assimilation of low-d18O Icelandic crust prior to eruption. In conjunctionwith the existing geophysical evidence for lateral migration, our results support a model of initial verticalmagma ascent within the Barðarbunga plumbing system followed by lateral transport of aggregatedmagma batches within the upper crust to the Holuhraun eruption site.

    National Category
    Geology
    Research subject
    Earth Science with specialization in Mineral Chemistry, Petrology and Tectonics
    Identifiers
    urn:nbn:se:uu:diva-304630 (URN)10.1002/2016GC006317 (DOI)000384808200001 ()
    Funder
    Swedish Research Council
    Available from: 2016-10-06 Created: 2016-10-06 Last updated: 2019-05-09Bibliographically approved
    2. Locating the depth of magma supply for volcanic eruptions, insights from Mt. Cameroon
    Open this publication in new window or tab >>Locating the depth of magma supply for volcanic eruptions, insights from Mt. Cameroon
    2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 33629Article in journal (Refereed) Published
    Abstract [en]

    Mt. Cameroon is one of the most active volcanoes in Africa and poses a possible threat to about half a million people in the area, yet knowledge of the volcano’s underlying magma supply system is sparse. To characterize Mt. Cameroon’s magma plumbing system, we employed mineral-melt equilibrium thermobarometry on the products of the volcano’s two most recent eruptions of 1999 and 2000. Our results suggest pre-eruptive magma storage between 20 and 39 km beneath Mt. Cameroon, which corresponds to the Moho level and below. Additionally, the 1999 eruption products reveal several shallow magma pockets between 3 and 12 km depth, which are not detected in the 2000 lavas. This implies that small-volume magma batches actively migrate through the plumbing system during repose intervals. Evolving and migrating magma parcels potentially cause temporary unrest and short-lived explosive outbursts, and may be remobilized during major eruptions that are fed from sub-Moho magma reservoirs.

    National Category
    Geochemistry
    Identifiers
    urn:nbn:se:uu:diva-304697 (URN)10.1038/srep33629 (DOI)000391998100001 ()27713494 (PubMedID)
    Funder
    The Royal Swedish Academy of SciencesSwedish Research Council
    Available from: 2016-10-07 Created: 2016-10-07 Last updated: 2019-05-09Bibliographically approved
    3. Pyroxene standards for SIMS oxygen isotope analysis and their application to Merapi volcano, Sunda arc, Indonesia
    Open this publication in new window or tab >>Pyroxene standards for SIMS oxygen isotope analysis and their application to Merapi volcano, Sunda arc, Indonesia
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    2016 (English)In: Chemical Geology, ISSN 0009-2541, E-ISSN 1872-6836, Vol. 447, p. 1-10Article in journal (Refereed) Published
    Abstract [en]

    Measurement of oxygen isotope ratios in common silicate minerals such as olivine, pyroxene, feldspar, garnet, and quartz is increasingly performed by Secondary Ion Mass Spectrometry (SIMS). However, certain mineral groups exhibit solid solution series, and the large compositional spectrum of these mineral phases will result in matrix effects during SIMS analysis. These matrix effects must be corrected through repeated analysis of compositionally similar standards to ensure accurate results. In order to widen the current applicability of SIMS to solid solution mineral groups in common igneous rocks, we performed SIMS homogeneity tests on new augite (NRM-AG-1) and enstatite (NRM-EN-2) reference materials sourced from Stromboli, Italy and Webster, North Carolina, respectively. Aliquots of the standard minerals were analysed by laser fluorination (LF) to establish their δ18O values. Repeated SIMS measurements were then performed on randomly oriented fragments of the same pyroxene crystals, which yielded a range in δ18O less than ± 0.42 and ± 0.58‰ (2σ) for NRM-AG-1 and NRM-EN-2, respectively. Homogeneity tests verified that NRM-AG-1 and NRM-EN-2 do not show any crystallographic orientation bias and that they are sufficiently homogeneous on the 20 μm scale to be used as routine mineral standards for SIMS δ18O analysis. We subsequently tested our new standard materials on recently erupted pyroxene crystals from Merapi volcano, Indonesia. The δ18O values for Merapi pyroxene obtained by SIMS (n = 204) agree within error with the LF-derived δ18O values for Merapi pyroxene but differ from bulk mineral and whole-rock data obtained by conventional fluorination. The bulk samples are offset to higher δ18O values as a result of incorporation of mineral and glass inclusions that in part reflects crustal contamination processes. The Merapi pyroxene SIMS data, in turn, display a frequency peak at 5.8‰, which allows us to estimate the δ18O value of the primary mafic magma at Merapi to ~ 6.1‰ when assuming closed system differentiation.

    Keywords
    Pyroxene crystals; SIMS standardisation; δ18O analysis; Merapi volcano; Sub-Java primary δ18O
    National Category
    Geochemistry
    Identifiers
    urn:nbn:se:uu:diva-309608 (URN)10.1016/j.chemgeo.2016.10.018 (DOI)000390632600001 ()
    Funder
    Swedish Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
    Available from: 2016-12-06 Created: 2016-12-06 Last updated: 2019-05-09Bibliographically approved
    4. Multi-level magma plumbing at Agung and Batur volcanoes increases risk of hazardous eruptions
    Open this publication in new window or tab >>Multi-level magma plumbing at Agung and Batur volcanoes increases risk of hazardous eruptions
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    2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 10547Article in journal (Refereed) Published
    Abstract [en]

    The island of Bali in Indonesia is home to two active stratovolcanoes, Agung and Batur, but relatively little is known of their underlying magma plumbing systems. Here we define magma storage depths and isotopic evolution of the 1963 and 1974 eruptions using mineral-melt equilibrium thermobarometry and oxygen and helium isotopes in mineral separates. Olivine crystallised from a primitive magma and has average delta O-18 values of 4.8%. Clinopyroxene records magma storage at the crust-mantle boundary, and displays mantle-like isotope values for Helium (8.62 R-A) and delta O-18 (5.0-5.8%). Plagioclase reveals crystallisation in upper crustal storage reservoirs and shows delta O-18 values of 5.5-6.4%. Our new thermobarometry and isotope data thus corroborate earlier seismic and InSAR studies that inferred upper crustal magma storage in the region. This type of multi-level plumbing architecture could drive replenishing magma to rapid volatile saturation, thus increasing the likelihood of explosive eruptions and the consequent hazard potential for the population of Bali.

    Place, publisher, year, edition, pages
    NATURE PUBLISHING GROUP, 2018
    National Category
    Geochemistry Geology
    Identifiers
    urn:nbn:se:uu:diva-361269 (URN)10.1038/s41598-018-28125-2 (DOI)000438343600057 ()30002471 (PubMedID)
    Funder
    Swedish Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT), SA2015-6212
    Available from: 2018-10-05 Created: 2018-10-05 Last updated: 2019-05-09Bibliographically approved
    5. Forensic Probe of Bali’s Great Volcano
    Open this publication in new window or tab >>Forensic Probe of Bali’s Great Volcano
    2019 (English)In: EOS: Transactions, ISSN 0096-3941, E-ISSN 2324-9250, Vol. 100, no 4, p. 26-30Article in journal (Refereed) Published
    Place, publisher, year, edition, pages
    American Geophysical Union (AGU), 2019
    National Category
    Geochemistry
    Identifiers
    urn:nbn:se:uu:diva-383075 (URN)10.1029/2019EO115211 (DOI)
    Available from: 2019-05-09 Created: 2019-05-09 Last updated: 2019-05-09
    6. Felsic magma storage in the core of an ocean island (Gran Canaria, Canary Islands)
    Open this publication in new window or tab >>Felsic magma storage in the core of an ocean island (Gran Canaria, Canary Islands)
    (English)Manuscript (preprint) (Other academic)
    National Category
    Geochemistry
    Identifiers
    urn:nbn:se:uu:diva-383076 (URN)
    Available from: 2019-05-09 Created: 2019-05-09 Last updated: 2019-05-09
    7. Explosive ocean island volcanism explained by high magmatic water content in OIB magmas
    Open this publication in new window or tab >>Explosive ocean island volcanism explained by high magmatic water content in OIB magmas
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Geochemistry
    Identifiers
    urn:nbn:se:uu:diva-383077 (URN)
    Available from: 2019-05-09 Created: 2019-05-09 Last updated: 2019-05-09
    8. Mechanical weakening due to hydrothermal alteration leads to failure at andesitic volcanoes
    Open this publication in new window or tab >>Mechanical weakening due to hydrothermal alteration leads to failure at andesitic volcanoes
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Geosciences, Multidisciplinary
    Identifiers
    urn:nbn:se:uu:diva-383078 (URN)
    Available from: 2019-05-09 Created: 2019-05-09 Last updated: 2019-05-16
    9. The stiff upper LIP: investigating the High Arctic Large Igneous Province
    Open this publication in new window or tab >>The stiff upper LIP: investigating the High Arctic Large Igneous Province
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    2016 (English)In: Geology Today, ISSN 0266-6979, E-ISSN 1365-2451, Vol. 32, no 3, p. 92-98Article in journal (Other (popular science, discussion, etc.)) Published
    Abstract [en]

    The Canadian Arctic Islands expose a complex network of dykes and sills that belong to the High Arctic Large Igneous Province (HALIP), which intruded volatile-rich sedimentary rocks of the Sverdrup Basin (shale, limestone, sandstone and evaporite) some 130 to 120 million years ago. There is thus great potential in studying the HALIP to learn how volatile-rich sedimentary rocks respond to magmatic heating events during LIP emplacement. The HALIP remains, however, one of the least well known LIPs on the planet due to its remote location, short field season, and harsh climate. A Canadian–Swedish team of geologists set out in summer 2015 to further explore HALIP sills and their sedimentary host rocks, including the sampling of igneous and meta-sedimentary rocks for subsequent geochemical analysis, and high pressure-temperature petrological experiments to help define the actual processes and time-scales of magma–sediment interaction. The research results will advance our understanding of how climate-active volatiles such as CO2, SO2 and CH4 are mobilised during the magma–sediment interaction related to LIP events, a process which is hypothesised to have drastically affected Earth's carbon and sulphur cycles. In addition, assimilation of sulphate evaporites, for example, is anticipated to trigger sulphide immiscibility in the magma bodies and in so doing could promote the formation of Ni-PGE ore bodies. Here we document the joys and challenges of ‘frontier arctic fieldwork’ and discuss some of our initial observations from the High Arctic Large Igneous Province.

    National Category
    Geosciences, Multidisciplinary
    Identifiers
    urn:nbn:se:uu:diva-293548 (URN)10.1111/gto.12138 (DOI)
    Funder
    Swedish Polar Research SecretariatSwedish Research Council
    Available from: 2016-05-13 Created: 2016-05-13 Last updated: 2019-05-09Bibliographically approved
    10. Volcanic particles in agriculture and gardening
    Open this publication in new window or tab >>Volcanic particles in agriculture and gardening
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    2017 (English)In: Geology Today, Vol. 33, no 4, p. 148-154Article in journal (Refereed) Published
    Abstract [en]

    Volcanic pyroclasts of small size, such as lapilli and small pumice stones, are widely used in agriculture, gardening, and for pot plants as natural inorganic mulch. The technique of using pyroclasts to enhance topsoil stems from the eighteenth century, and specifically from the ad 1730–1736 eruption on Lanzarote. Critical observations on plant development during and after the eruption showed that the vegetation died when buried under a thick layer of lapilli, but grew vigorously when covered thinly. While the agriculture of Lanzarote was restricted to cereals before the eruption, it diversified to many kinds of fruit and vegetables afterwards, including the production of the famous Malvasía wines in the Canaries. The population of Lanzarote doubled in the years after the eruption, from about 5000 in 1730 to near 10 000 in 1768, predominantly as a result of the higher agricultural productivity. This outcome led to widespread use of lapilli and pumice fragments throughout the islands and eventually the rest of the globe. Lapilli and pumice provide vesicle space for moisture to be retained longer within the planting soil, which can create an environment for micro-bacteria to thrive in. Through this route, nutrients from volcanic matter are transported into the surrounding soil where they become available to plant life. The detailed processes that operate within the pyroclasts are less well understood, such as the breakdown of nutrients from the rock matrix and transport into the soil by biological action. Further studies promise significant potential to optimize future agricultural efforts, particularly in otherwise arid areas of the globe.

    National Category
    Geosciences, Multidisciplinary
    Identifiers
    urn:nbn:se:uu:diva-383079 (URN)10.1111/gto.12193 (DOI)
    Available from: 2019-05-09 Created: 2019-05-09 Last updated: 2019-05-09
    11. Sacred ground; the Maipés necropolis of north-west Gran Canaria
    Open this publication in new window or tab >>Sacred ground; the Maipés necropolis of north-west Gran Canaria
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    2019 (English)In: Geology Today, Vol. 35, no 2, p. 55-62Article in journal (Refereed) Published
    Abstract [en]

    Gran Canaria, like most of the Canary Islands, shows evidence for young basaltic volcanism in the form of cinder cones and valley-hugging lava flows. These landforms were of no particular use to the aboriginal population, nor to the subsequent Spanish settlers, and young lava flows and lava fields are still referred to as ‘malpaís’ (badlands) in the Canary Islands. In north-west Gran Canaria, one such lava flow fills the bottom of a steep-sided valley, which reaches the sea at the present day village of Agaete. The lava flow erupted c. 3030 ± 90 yr bp and displays a total length of ∌ 11 km. At its distal end, just outside Agaete, it hosts one of Europe’s largest and most important pre-historic burial sites constructed of volcanic rock: the Maipés necropolis. Over 700 pre-historic tombs (or tumuli) constructed from the aa-type clinker materials have been identified on top of the valley-filling lava flow. The up to soccer-ball sized vesicular clinker fragments are sufficiently low in density to provide abundant, workable basalt blocks for the construction of the tumuli, allowing the pre-hispanic aboriginal population to create a large and magnificent ‘sacred ground’ in an otherwise barren landscape.

    National Category
    Geosciences, Multidisciplinary
    Identifiers
    urn:nbn:se:uu:diva-383080 (URN)10.1111/gto.12262 (DOI)
    Available from: 2019-05-09 Created: 2019-05-09 Last updated: 2019-05-09
  • Public defence: 2019-09-06 09:15 C2:305, Uppsala
    Carvalho, Carla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology, Integrative Physiology.
    The Role of Kidney Oxygen Homeostasis for the Development of Kidney Disease2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The relation between oxygen supply and demand determines tissue oxygen tension (PO2). When intrarenal tissue PO2 decreases, any compensatory increase in oxygen supply via increased renal blood flow is likely to increase glomerular filtration rate. The resulting increased tubular load of electrolytes destined for active transport increases oxygen consumption, thus affecting intrarenal tissue PO2. Consequently, the kidney is particularly sensitive to alterations in oxygen homeostasis and kidney hypoxia is acknowledged as a common pathway to end stage renal disease. Different factors that can affect intrarenal oxygen homeostasis, including alterations in blood pressure and sodium intake dietary or pathologies such as diabetes mellitus, anemia or atherosclerosis. This thesis focuses on understanding how these factors influence kidney oxygen homeostasis.

    Pronounced reduction in sodium intake caused tissue hypoxia in kidney cortex via activation of the renin-angiotensin-aldosterone leading to increased tubular sodium reabsorption. Angiotensin II and aldosterone affect kidney oxygen handling differently. Whereas angiotensin II mainly affects kidney oxygen delivery, aldosterone mainly affects oxygen consumption.

    The hypoxia-inducible factor (HIF) system is a cellular defense mechanism against prolonged hypoxia. Although diabetes causes intrarenal hypoxia, hyperglycemia per se also prevents HIF-activation. Therefore, the effects of type 1 diabetes were evaluated in genetically modified mice with chronic HIF-activation. Diabetic mice with globally increased HIF activity, due to heterozygote prolyl hydroxylase-2 deficiency, displayed reduced mitochondria leak respiration and preserved cortical PO2. Diabetic mice with kidney-specific HIF activation, due to homozygous deficiency of von Hippel-Lindau, developed reduced mitochondria leak respiration and reduced urinary albumin excretion.

    The normal age-related decline in kidney function has been proposed to be due to, at least in part, increased oxidative stress, which can induce mitochondrial leak respiration via activation of uncoupling proteins. Indeed, two-year old mice deficient of uncoupling protein-2 presented with improved mitochondria efficiency and reduced urinary protein excretion.

    Summarizing, the data presented in this thesis provide clear support for potent influence of the renin-angiotensin-aldosterone system, HIF activation and mitochondria function on intrarenal oxygen availability. Maintaining kidney oxygen homeostasis may be a unifying strategy to protect kidney function.

    List of papers
    1. Determinants of renal oxygen metabolism during low Na+ diet: effect of angiotensin AT1 and aldosterone receptor blockade
    Open this publication in new window or tab >>Determinants of renal oxygen metabolism during low Na+ diet: effect of angiotensin AT1 and aldosterone receptor blockade
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-387381 (URN)
    Available from: 2019-06-23 Created: 2019-06-23 Last updated: 2019-06-23
    2. Activation of hypoxia inducible factor due to reduced prolyl hydroxylase 2 activity prevents renal mitochondria dysfunction and improves cortical oxygenation in type 1 diabetic mice
    Open this publication in new window or tab >>Activation of hypoxia inducible factor due to reduced prolyl hydroxylase 2 activity prevents renal mitochondria dysfunction and improves cortical oxygenation in type 1 diabetic mice
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-387385 (URN)
    Available from: 2019-06-23 Created: 2019-06-23 Last updated: 2019-06-23
    3. Hypoxia-inducible factors activation protects mitochondria function and prevents albuminuria in kidney-specific diabetic von Hippel-Lindau deficient mice
    Open this publication in new window or tab >>Hypoxia-inducible factors activation protects mitochondria function and prevents albuminuria in kidney-specific diabetic von Hippel-Lindau deficient mice
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-387387 (URN)
    Available from: 2019-06-23 Created: 2019-06-23 Last updated: 2019-06-23
    4. Uncoupling protein 2 mediates age-related mitochondria inefficiency and urinary protein excretion
    Open this publication in new window or tab >>Uncoupling protein 2 mediates age-related mitochondria inefficiency and urinary protein excretion
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-387388 (URN)
    Available from: 2019-06-23 Created: 2019-06-23 Last updated: 2019-06-23
  • Public defence: 2019-09-06 10:00 Lindahlsalen, Uppsala
    van der Valk, Tom
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Genomics of population decline2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    With human populations forecasted to grow in the next decades, many mammals face increasing anthropogenic threats. The consequential population declines are a precursor to extinctions, as small populations are not only more sensitive to stochastic events, but reduction in population size is generally also followed by a decrease in genetic diversity, which in turn reduces adaptive potential and fitness of the population. By using molecular methods I aimed to estimate the magnitude of the genomic consequences as a result of rapid population declines with a focus on the endangered eastern gorillas. First, I genotyped Grauer’s gorilla (Gorilla beringei graueri) faecal samples, which revealed lower genetic diversity and high differentiation in the peripheral compared to the central populations, indicating a strong effect of genetic drift and limited gene flow among the small, isolated forest fragments (Chapter 1). Next, by using a target capture approach I obtained complete mitochondrial genomes from degraded Grauer’s and mountain (Gorilla beringei beringei) gorilla faecal and museum samples (Chapter 2) which showed a loss of mitochondrial diversity within the last century in Grauer’s gorillas, mainly driven by the extinction of peripheral populations (Chapter 3). Genome-wide sequence data from historical samples suggests that this loss has also affected the nuclear genome, as modern Grauer’s gorillas carry on average more genetic variants with putatively negative fitness consequences than historically. No significant temporal changes were observed in the closely related mountain gorillas, which might be due to their contrasting demographic history (Chapter 4). I then switched study species to the endangered Dryas monkey and find that, despite its possible small population size, the current Dryas monkey population is genetically diverse with low levels of inbreeding and as such likely viable in the long-term if appropriate conservation measures are taken (Chapter 5). Finally, I aimed to estimate the strength of genetic purging across a range of mammalian species. This revealed that although genetic purging might be common among endangered species, it mainly acts on long evolutionary time scales with limited strength during the rapid population declines as experienced by many species today (Chapter 6).

    List of papers
    1. Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas
    Open this publication in new window or tab >>Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas
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    2018 (English)In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 165, no 3, p. 565-575Article in journal (Refereed) Published
    Abstract [en]

    Objectives: The critically endangered Grauer's gorilla (Gorilla beringei graueri) has experienced an estimated 77% population decline within a single generation. Although crucial for informed conservation decisions, there is no clear understanding about population structure and distribution of genetic diversity across the species' highly fragmented range. We fill this gap by studying several core and peripheral Grauer's gorilla populations throughout their distribution range.

    Materials and Methods: We generated genetic profiles for a sampling of an unstudied population of Grauer's gorillas from within the species' core range at 13 autosomal microsatellite loci and combined them with previously published and newly generated data from four other Grauer's gorilla populations, two mountain gorilla populations, and one western lowland gorilla population.

    Results: In agreement with previous studies, the genetic diversity of Grauer's gorillas is intermediate, falling between western lowland and mountain gorillas. Among Grauer's gorilla populations, we observe lower genetic diversity and high differentiation in peripheral compared with central populations, indicating a strong effect of genetic drift and limited gene flow among small, isolated forest fragments.

    Discussion: Although genetically less diverse, peripheral populations are frequently essential for the long-term persistence of a species and migration between peripheral and core populations may significantly enrich the overall species genetic diversity. Thus, in addition to central Grauer's gorilla populations from the core of the distribution range that clearly deserve conservation attention, we argue that conservation strategies aiming to ensure long-term species viability should include preserving peripheral populations and enhancing habitat connectivity.

    National Category
    Other Biological Topics
    Identifiers
    urn:nbn:se:uu:diva-348947 (URN)10.1002/ajpa.23393 (DOI)000425728300012 ()29313894 (PubMedID)
    Available from: 2018-04-19 Created: 2018-04-19 Last updated: 2019-06-04Bibliographically approved
    2. Whole mitochondrial genome capture from faecal samples and museum-preserved specimens
    Open this publication in new window or tab >>Whole mitochondrial genome capture from faecal samples and museum-preserved specimens
    2017 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e111-e121Article in journal (Refereed) Published
    Abstract [en]

    Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected faecal samples is a robust and reliable approach for population-wide studies of nonmodel organisms.

    Keywords
    great apes, mtDNA, natural history collections, noninvasive samples, target enrichment
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-342910 (URN)10.1111/1755-0998.12699 (DOI)000415921900010 ()28675688 (PubMedID)
    Funder
    Swedish Research Council Formas, 2015-676
    Available from: 2018-03-02 Created: 2018-03-02 Last updated: 2019-06-04
    3. Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas
    Open this publication in new window or tab >>Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas
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    2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 6551Article in journal (Refereed) Published
    Abstract [en]

    Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species' long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer's (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer's gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.

    National Category
    Biochemistry and Molecular Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-354951 (URN)10.1038/s41598-018-24497-7 (DOI)000430795000050 ()29695730 (PubMedID)
    Funder
    Swedish Research CouncilKnut and Alice Wallenberg FoundationSwedish Research Council Formas, 2015-676
    Available from: 2018-06-25 Created: 2018-06-25 Last updated: 2019-06-04Bibliographically approved
    4. The genome of the endangered dryas monkey provides new insights into the evolutionary history of the vervets
    Open this publication in new window or tab >>The genome of the endangered dryas monkey provides new insights into the evolutionary history of the vervets
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Genomic data can be a powerful tool for inferring ecology, behaviour and conservation needs of highly elusive species, particularly when other sources of information are hard to come by. Here we focus on the dryas monkey, an endangered primate endemic to the Congo Basin with cryptic behaviour and possibly less than 250 remaining individuals. Using whole genome data we show that the dryas monkey represents a sister lineage to the vervet monkeys and has diverged from them at least 1 million years ago with additional bi-directional gene flow 590,000 – 360,000 years ago. After bonobo-chimpanzee admixture, this is the second reported case of gene flow that most likely involved crossing the Congo River, a strong dispersal barrier. As the demographic history of bonobos and dryas monkey shows similar patterns of population increase during this time period, we hypothesise that the fluvial topology of the Congo River might have been more dynamic than previously recognised. As a result of dryas monkey - vervet admixture, genes involved in resistance to the simian immunodeficiency virus (SIV) have been exchanged, possibly indicating adaptive introgression. Despite the presence of several homozygous loss-of-function mutations in genes associated with reduced sperm mobility and immunity, we find high genetic diversity and low levels of inbreeding and genetic load in the studied dryas monkey individual. This suggests that the current population carries sufficient genetic variability for the long-term survival of this species. We thus provide an example of how genomic data can directly improve our understanding of elusive species.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-383458 (URN)10.1101/613273 (DOI)
    Available from: 2019-05-15 Created: 2019-05-15 Last updated: 2019-06-04
    5. Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas
    Open this publication in new window or tab >>Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas
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    2019 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 1, p. 165-170.e6, article id S0960-9822(18)31554-9Article in journal (Refereed) Published
    Abstract [en]

    Many endangered species have experienced severe population declines within the last centuries [1, 2]. However, despite concerns about negative fitness effects resulting from increased genetic drift and inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines [3-7]. Here, we use whole genomes recovered from century-old historical museum specimens to quantify the genomic consequences of small population size in the critically endangered Grauer's and endangered mountain gorillas. We find a reduction of genetic diversity and increase in inbreeding and genetic load in the Grauer's gorilla, which experienced severe population declines in recent decades. In contrast, the small but relatively stable mountain gorilla population has experienced little genomic change during the last century. These results suggest that species histories as well as the rate of demographic change may influence how population declines affect genome diversity.

    Keywords
    conservation genomics, critically endangered, genetic load, genome erosion, inbreeding, museum collections
    National Category
    Other Biological Topics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-374204 (URN)10.1016/j.cub.2018.11.055 (DOI)30595519 (PubMedID)
    Funder
    Swedish Research CouncilKnut and Alice Wallenberg FoundationSwedish Research Council Formas, 2016-00835; 2015-676
    Available from: 2019-01-18 Created: 2019-01-18 Last updated: 2019-06-04Bibliographically approved
    6. Genetic purging in mammalian populations
    Open this publication in new window or tab >>Genetic purging in mammalian populations
    (English)Manuscript (preprint) (Other academic)
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-383459 (URN)
    Available from: 2019-05-15 Created: 2019-05-15 Last updated: 2019-06-04
  • Public defence: 2019-09-06 13:15 sal IV, Uppsala
    Jönson Ring, Ingrid
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Nocturnal enuresis and rapid maxillary expansion: – long-term effect, prognostic variables, respiration during sleep and quality of life2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Background:The orthodontic technique rapid maxillary expansion (RME) has been reported to have a potentially curative effect on nocturnal enuresis (NE). The mechanism behind this is unknown but could possibly be due to placebo and/or effects on respiration during sleep. 

    Aim: This thesis aims to approach an answer to the following questions, with a randomized, placebo-controlled method: 1) Does rapid maxillary expansion have a curative effect on therapy-resistant NE? 2) Is the potential curative effect due to respiratory events that can be measured during sleep? 3) Do enuretic children have an impaired quality of life (QoL)?  

    Subjects & Methods: In study I we evaluated the QoL in enuretic children while assessing the test re-test reliability of a Swedish version of an established QoL questionnaire. Study II and IV assess respiration during sleep in children with NE; in study II comparisons are made with healthy control children and in study IV we evaluate the respiratory effects of RME. Study III is a randomized placebo-controlled study investigating whether RME is a useful therapy for NE and if the treatment effect is due to placebo.

    Results: Study I:The Swedish version of the questionnaire proved to be a reliable tool (Chronbach’s alpha 0.87) with excellent test-retest stability (ICC = 0.762). Enuresis affects the children’s QoL and interactions with peers.

    Study II:The hypopnea index (HI) and the oxygen desaturation index were both significantly higher in the enuretic children compared to the healthy controls, (p=0.04 and p=0.05) but all values fell within the normal range.

    Study III:RME resulted in a significant reduction in wet nights i.e. the mean number of wet nights out of 14 was 11.4 before and 9.2 after RME. (p=0.003) This was not observed in the placebo group (p=0.40).

    Study IV:There was a significant reduction of sleep efficiency during RME. (p=0.001) The mean HI was also affected. (p=0.005)

    Conclusions:

    Children with nocturnal enuresis have an impaired self-esteem and their quality of life is affected in their relationship with friends.

    There were no major differences in respiration during sleep between enuretic children and controls.

    Rapid maxillary expansion reduces the number of wet nights in children with enuresis, but the effect is of limited clinical value.

    The antienuretic effect does not seem to be due to a placebo effect of the appliance.

    The majority of the children in our study sample did not have sleep disordered breathing as a co-morbidity to their nocturnal enuresis. 

    List of papers
    1. Nocturnal enuresis impaired children's quality of life and friendships
    Open this publication in new window or tab >>Nocturnal enuresis impaired children's quality of life and friendships
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    2017 (English)In: Acta Paediatrica, ISSN 0803-5253, E-ISSN 1651-2227, Vol. 106, no 5, p. 806-811Article in journal (Refereed) Published
    Abstract [en]

    AimThere have not been any continence-specific measurement tools in Swedish that have allowed clinicians to investigate the quality of life (QoL) in children with bladder dysfunction. This study evaluated the QoL in Swedish children with nocturnal enuresis and tested the reliability of a Swedish translation of the Paediatric Incontinence Questionnaire (PinQ). MethodsThis prospective study comprised 46 children aged six to 18 years with nocturnal enuresis, who completed the PinQ after it was translated into Swedish. It was completed twice by 33 patients, and these responses were included in the test-retest evaluation. ResultsThe self-reported mean sum score for the whole group was 26.3 13.37 (range: 5-58), and the most affected domains were social relations with peers and self-esteem. The highest individual scores were four, three or two for 71.7%, 17.4% and 10.9% of the study population, respectively. Cronbach's alpha was 0.87 for the whole questionnaire, indicating good internal consistency. The test-retest stability was excellent, with an intra-class correlation coefficient of 0.76. ConclusionChildren with nocturnal enuresis had impaired self-esteem, and their impaired QoL affected their relationships with friends. The Swedish version of the PinQ proved to be a reliable tool that will be used in further studies.

    Place, publisher, year, edition, pages
    WILEY, 2017
    Keywords
    Nocturnal enuresis, Quality of life, Questionnaire, Self-esteem, Urinary incontinence
    National Category
    Pediatrics
    Identifiers
    urn:nbn:se:uu:diva-321783 (URN)10.1111/apa.13787 (DOI)000398859300021 ()28199734 (PubMedID)
    Available from: 2017-05-11 Created: 2017-05-11 Last updated: 2019-05-14Bibliographically approved
    2. Sleep disordered breathing in enuretic children and controls
    Open this publication in new window or tab >>Sleep disordered breathing in enuretic children and controls
    2017 (English)In: Journal of Pediatric Urology, ISSN 1477-5131, E-ISSN 1873-4898, Vol. 13, no 6, p. 620.e1-620.e6Article in journal (Refereed) Published
    Abstract [en]

    Introduction: Nocturnal enuresis and sleep disordered breathing are common childhood problems that are reported to be associated with each other. Sleep disordered breathing is often found in children with upper airway obstruction and, according to some studies, its presence is associated with an increased risk of nocturnal enuresis. Respiration during sleep in children with therapy-resistant enuresis, but no history of snoring or sleep apneas, has previously been investigated, and subclinical signs of disordered respiration were found in this group. However, sleep disordered breathing in enuretic children without a history of snoring or sleep apneas has not been thoroughly studied before.

    Aim: To evaluate sleep disordered breathing in enuretic children and compare them with healthy control children.

    Subjects and methods: Children aged 8-13 years with nocturnal enuresis were included. Exclusion criteria were: daytime incontinence, on-going anti-enuretic treatment, and concomitant urological, endocrinological, nephrological or psychiatric disorders. Twenty children (19 boys and 1 girl) suffering from therapy-resistant nocturnal enuresis, and 21 healthy controls (18 boys and 3 girls) underwent one night of polygraphic sleep registration focused on respiratory variables. The registration included electroencephalography as well as assessment of respiratory movements, nasal airflow and oxygen saturation; it was performed with a portable sleep device at the subjects' homes. In addition to this, OSA 18, a health-related quality of life instrument, was used to evaluate subjective issues related to sleep and breathing.

    Results: The mean apnea hypopnea index values were 0.96 +/- 0.8 for the patient group and 0.46 +/- 0.4 for the control group. The oxygen desaturation index was slightly higher for the children with nocturnal enuresis compared with the healthy controls (P = 0.05). No other differences were found in the respiratory variables. Both groups of children showed low levels of arousals (Summary Table). The enuretic children reported significantly more subjective sleep disturbances and a lower quality of life than their healthy peers.

    Discussion: This was the first controlled study of sleep disordered breathing in children with nocturnal enuresis. One limitation of the study was that some variables were known to be underestimated when scoring polygraphic data. The apnea hypopnea index was such a variable and was indeed lower than in a previous study.

    Conclusion: No major differences in respiration during sleep were found between enuretic children and controls.

    Place, publisher, year, edition, pages
    ELSEVIER SCI LTD, 2017
    Keywords
    Nocturnal enuresis, Sleep disordered breathing, Respiratory polygraphy, Children
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-340287 (URN)10.1016/j.jpurol.2017.05.012 (DOI)000418045800024 ()
    Available from: 2018-01-29 Created: 2018-01-29 Last updated: 2019-05-14Bibliographically approved
    3. Rapid maxillary expansion in children with nocturnal enuresis: A randomized placebo-controlled trial
    Open this publication in new window or tab >>Rapid maxillary expansion in children with nocturnal enuresis: A randomized placebo-controlled trial
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    2019 (English)In: Angle orthodontist, ISSN 0003-3219, E-ISSN 1945-7103Article in journal (Other academic) Published
    Keywords
    Rapid maxillary expansion, nocturnal enuresis
    National Category
    Medical and Health Sciences
    Research subject
    Medical Science
    Identifiers
    urn:nbn:se:uu:diva-383403 (URN)10.2319/031819-219.1. (DOI)
    Available from: 2019-05-14 Created: 2019-05-14 Last updated: 2019-07-28
    4. Respiratory changes during sleep in enuretic children treated with rapid maxillary expansion
    Open this publication in new window or tab >>Respiratory changes during sleep in enuretic children treated with rapid maxillary expansion
    (English)Manuscript (preprint) (Other academic)
    Keywords
    Rapid maxillary expansion, nocturnal enuresis, sleep disordered breathing
    National Category
    Medical and Health Sciences
    Research subject
    Medical Science
    Identifiers
    urn:nbn:se:uu:diva-383401 (URN)
    Available from: 2019-05-14 Created: 2019-05-14 Last updated: 2019-05-14
  • Public defence: 2019-09-06 13:15 Hörsal 2, Uppsala
    Stefánsson, Arnaldur
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Economics.
    Essays in Public Finance and Behavioral Economics2019Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Essay I: I study how individuals adjust their labor supply in response to a year with tax free income. Due to a transformation from a retroactive to a pay-as-you-earn tax system, income earned on the Icelandic labor market in 1987 was never taxed. Still, there was no cash-flow shock as taxpayers during the tax holiday (1987) paid taxes on income earned in the year before. This paper has three main results. First, I estimate a Frisch elasticity of 0.07 with a Wald difference-in-differences (DID) estimator by exploiting the progressivity of the tax scheme and the tax holiday. The Wald-DID estimator is biased if the Frisch elasticity differs between tax brackets. Second, I show how to overcome this bias by also exploiting changes in the tax scheme after 1987. This gives elasticities ranging from 0.7 (high income earners) to 4 (low income earners). However, this second approach to identify the Frisch elasticity gives biased results if there are frictions to labor supply adjustments during the tax holiday. Therefore, third and finally, I show that if there are frictions and the elasticity governing the response during the tax holiday is 0.05 (like that found by Martinez et al. (2018) who study a tax holiday in Switzerland) the frictionless elasticity is 0.2 for mid income earners, and 0.4 for high and low income earners. Overall, the paper adds to the literature on intertemporal labor supply responses and on how to deal with heterogeneity when perfect control groups are hard to find.

  • Public defence: 2019-09-06 13:15 Polhemsalen, Uppsala
    Wen, Chenyu
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Solid-State Nanopores for Sensing: From Theory to Applications2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Nanopore based sensing technology has been widely studied for a broad range of applications including DNA sequencing, protein profiling, metabolite molecules, and ions detection. The nanopore technology offers an unprecedented technological solution to meeting the demands of precision medicine on rapid, in-field, and low-cost biomolecule analysis. In general, nanopores are categorized in two families: solid-state nanopore (SSNP) and biological nanopore. The former is formed in a solid-state membrane made of SiNx, SiO2, silicon, graphene, MoS2, etc., while the latter represents natural protein ion-channels in cell membranes. Compared to biological pores, SSNPs are mechanically robust and their fabrication is compatible with traditional semiconductor processes, which may pave the way to their large-scale fabrication and high-density integration with standard control electronics. However, challenges remain for SSNPs, including poor stability, low repeatability, and relatively high background noise level. This thesis explores SSNPs from basic physical mechanisms to versatile applications, by entailing a balance between theory and experiment.

    The thesis starts with theoretical models of nanopores. First, resistance of the open pore state is studied based on the distribution of electric field. An important concept, effective transport length, is introduced to quantify the extent of the high field region. Based on this conductance model, the nanopores size of various geometrical shapes can be extracted from a simple resistance measurement. Second, the physical causality of ionic current rectification of geometrically asymmetrical nanopores is unveiled. Third, the origin of low-frequency noise is identified. The contribution of each noise component at different conditions is compared. Forth, a simple nano-disk model is used to describe the blockage of ionic current caused by DNA translocation. The signal and noise properties are analyzed at system level.

    Then, nanopore sensing experiments are implemented on cylinder SiNx nanopores and truncated-pyramid silicon nanopores (TPP). Prior to a systematic study, a low noise electrical characterization platform for nanopore devices is established. Signal acquisition guidelines and data processing flow are standardized. The effects of electroosmotic vortex in TPP on protein translocation dynamics are excavated. The autogenic translocation of DNA and proteins driven by the pW-level power generated by an electrolyte concentration gradient is demonstrated. Furthermore, by extending to a multiple pore system, the group translocation behavior of nanoparticles is studied. Various application scenarios, different analyte categories and divergent device structures accompanying with flexible configurations clearly point to the tremendous potential of SSNPs as a versatile sensor.

    List of papers
    1. Physical Model for Rapid and Accurate Determination of Nanopore Size via Conductance Measurement
    Open this publication in new window or tab >>Physical Model for Rapid and Accurate Determination of Nanopore Size via Conductance Measurement
    2017 (English)In: ACS SENSORS, ISSN 2379-3694, Vol. 2, no 10, p. 1523-1530Article in journal (Refereed) Published
    Abstract [en]

    Nanopores have been explored for various biochemical and nanoparticle analyses, primarily via characterizing the ionic current through the pores. At present, however, size determination for solid-state nanopores is experimentally tedious and theoretically unaccountable. Here, we establish a physical model by introducing an effective transport length, L (eff) that measures, for a symmetric nanopore, twice the distance from the center of the nanopore where the electric field is the highest to the point along the nanopore axis where the electric field falls to e-(1)of this maximum. By G = sigma(s0)/L-eff, a simple expression S-0=/(G, sigma, h, beta) is derived to algebraically correlate minimum nanopore cross-section area S (0)to nanopore conductance G, electrolyte conductivity a, and membrane thickness h with (3 to denote pore shape that is determined by the pore fabrication technique. The model agrees excellently with experimental results for nanopores in graphene, single-layer MoS2, and ultrathin SiNx films. The generality of the model is verified by applying it to micrometer-size pores.

    Keywords
    nanopores, physical model, effective transport length, algebraic solution, conductance measurement in electrolyte
    National Category
    Nano Technology
    Identifiers
    urn:nbn:se:uu:diva-340952 (URN)10.1021/acssensors.7b00576 (DOI)000414238600021 ()28974095 (PubMedID)
    Funder
    Swedish Research Council, 621-2014-6300
    Available from: 2018-02-13 Created: 2018-02-13 Last updated: 2019-06-19Bibliographically approved
    2. Zero-Depth Interfacial Nanopore Capillaries
    Open this publication in new window or tab >>Zero-Depth Interfacial Nanopore Capillaries
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    2018 (English)In: Advanced Materials, ISSN 0935-9648, E-ISSN 1521-4095, Vol. 30, no 9, article id 1703602Article in journal (Refereed) Published
    Abstract [en]

    High-fidelity analysis of translocating biomolecules through nanopores demands shortening the nanocapillary length to a minimal value. Existing nanopores and capillaries, however, inherit a finite length from the parent membranes. Here, nanocapillaries of zero depth are formed by dissolving two superimposed and crossing metallic nanorods, molded in polymeric slabs. In an electrolyte, the interface shared by the crossing fluidic channels is mathematically of zero thickness and defines the narrowest constriction in the stream of ions through the nanopore device. This novel architecture provides the possibility to design nanopore fluidic channels, particularly with a robust 3D architecture maintaining the ultimate zero thickness geometry independently of the thickness of the fluidic channels. With orders of magnitude reduced biomolecule translocation speed, and lowered electronic and ionic noise compared to nanopores in 2D materials, the findings establish interfacial nanopores as a scalable platform for realizing nanofluidic systems, capable of single-molecule detection.

    Place, publisher, year, edition, pages
    WILEY-V C H VERLAG GMBH, 2018
    Keywords
    2D nanopores, biomolecules, 1, f noise, mechanical stability, translocation speed
    National Category
    Condensed Matter Physics Atom and Molecular Physics and Optics Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-350489 (URN)10.1002/adma.201703602 (DOI)000426491600035 ()
    Funder
    Swedish Research Council, 621-2014-6300]EU, European Research Council, 335879
    Available from: 2018-05-09 Created: 2018-05-09 Last updated: 2019-06-19Bibliographically approved
    3. On rectification of ionic current in nanopores
    Open this publication in new window or tab >>On rectification of ionic current in nanopores
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    2019 (English)In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882Article in journal (Refereed) Submitted
    National Category
    Nano Technology
    Identifiers
    urn:nbn:se:uu:diva-384653 (URN)
    Available from: 2019-06-07 Created: 2019-06-07 Last updated: 2019-06-19
    4. Generalized Noise Study of Solid-State Nanopores at Low Frequencies
    Open this publication in new window or tab >>Generalized Noise Study of Solid-State Nanopores at Low Frequencies
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    2017 (English)In: ACS Sensors, ISSN 2379-3694, Vol. 2, no 2, p. 300-307Article in journal (Refereed) Published
    Abstract [en]

    Nanopore technology has been extensively investigated for analysis of biomolecules, and a success story in this field concerns DNA sequencing using a nanopore chip featuring an array of hundreds of biological nanopores (BioNs). Solid-state nanopores (SSNs) have been explored to attain longer lifetime and higher integration density than what BioNs can offer, but SSNs are generally considered to generate higher noise whose origin remains to be confirmed. Here, we systematically study lowfrequency (including thermal and flicker) noise characteristics of SSNs measuring 7 to 200 nm in diameter drilled through a 20-nmthick SiNx membrane by focused ion milling. Both bulk and surface ionic currents in the nanopore are found to contribute to the flicker noise, with their respective contributions determined by salt concentration and pH in electrolytes as well as bias conditions. Increasing salt concentration at constant pH and voltage bias leads to increase in the bulk ionic current and noise therefrom. Changing pH at constant salt concentration and current bias results in variation of surface charge density, and hence alteration of surface ionic current and noise. In addition, the noise from Ag/AgCl electrodes can become predominant when the pore size is large and/or the salt concentration is high. Analysis of our comprehensive experimental results leads to the establishment of a generalized nanopore noise model. The model not only gives an excellent account of the experimental observations, but can also be used for evaluation of various noise components in much smaller nanopores currently not experimentally available.

    Keywords
    flicker noise, nanopore, electrical double layer, model, power spectrum density, low frequency range, Hooge’s theory
    National Category
    Other Electrical Engineering, Electronic Engineering, Information Engineering
    Identifiers
    urn:nbn:se:uu:diva-315230 (URN)10.1021/acssensors.6b00826 (DOI)000395047000017 ()
    Funder
    Swedish Research Council, 621-2014-6300Stiftelsen Olle Engkvist Byggmästare, 2016/39Swedish Foundation for Strategic Research
    Note

    Chenyu Wen and Shuangshuang Zeng contributed equally to this work.

    Available from: 2017-02-10 Created: 2017-02-10 Last updated: 2019-06-19Bibliographically approved
    5. On nanopore DNA sequencing by signal and noise analysis of ionic current
    Open this publication in new window or tab >>On nanopore DNA sequencing by signal and noise analysis of ionic current
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    2016 (English)In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 27, article id 215502Article in journal (Refereed) Published
    Abstract [en]

    DNA sequencing, i.e., the process of determining the succession of nucleotides on a DNA strand, has become a standard aid in biomedical research and is expected to revolutionize medicine. With the capability of handling single DNA molecules, nanopore technology holds high promises to become speedier in sequencing at lower cost than what are achievable with the commercially available optics-or semiconductor-based massively parallelized technologies. Despite tremendous progress made with biological and solid-state nanopores, high error rates and large uncertainties persist with the sequencing results. Here, we employ a nano-disk model to quantitatively analyze the sequencing process by examining the variations of ionic current when a DNA strand translocates a nanopore. Our focus is placed on signal-boosting and noise-suppressing strategies in order to attain the single-nucleotide resolution. Apart from decreasing pore diameter and thickness, it is crucial to also reduce the translocation speed and facilitate a stepwise translocation. Our best-case scenario analysis points to severe challenges with employing plain nanopore technology, i.e., without recourse to any signal amplification strategy, in achieving sequencing with the desired single-nucleotide resolution. A conceptual approach based on strand synthesis in the nanopore of the translocating DNA from single-stranded to double-stranded is shown to yield a 10-fold signal amplification. Although it involves no advanced physics and is very simple in mathematics, this simple model captures the essence of nanopore sequencing and is useful in guiding the design and operation of nanopore sequencing.

    Keywords
    nanopore; DNA sequencing; ionic current; model; series resistance; noise; signal
    National Category
    Other Electrical Engineering, Electronic Engineering, Information Engineering
    Identifiers
    urn:nbn:se:uu:diva-295968 (URN)10.1088/0957-4484/27/21/215502 (DOI)000374507600013 ()27095148 (PubMedID)
    Funder
    Swedish Research Council, 621-2014-6300
    Available from: 2016-06-11 Created: 2016-06-11 Last updated: 2019-06-19Bibliographically approved
    6. Rectification of protein translocation in truncated-pyramidal nanopores caused by the formation of electroosmotic vortex
    Open this publication in new window or tab >>Rectification of protein translocation in truncated-pyramidal nanopores caused by the formation of electroosmotic vortex
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    2019 (English)In: Nature Nanotechnology, ISSN 1748-3387, E-ISSN 1748-3395Article in journal (Refereed) Submitted
    National Category
    Nano Technology
    Identifiers
    urn:nbn:se:uu:diva-384656 (URN)
    Available from: 2019-06-07 Created: 2019-06-07 Last updated: 2019-06-19
    7. Autogenic analyte translocation in nanopores
    Open this publication in new window or tab >>Autogenic analyte translocation in nanopores
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    2019 (English)In: Nano Energy, ISSN 2211-2855, E-ISSN 2211-3282, Vol. 60, p. 503-509Article in journal (Refereed) Published
    Abstract [en]

    Nanopores have been widely studied for power generation and single-molecule detection. Although the power level generated by a single nanopore based on electrolyte concentration gradient is too low to be practically useful, such a power level is found sufficient to drive analyte translocation in nanopores. Here, we explore the simultaneous action of a solid-state nanopore as a nanopower generator and a nanoscale biosensor by exploiting the extremely small power generated to drive the analyte translocation in the same nanopore device. This autogenic analyte translocation is demonstrated using protein and DNA for their distinct shape, size and charge. The simple device structure allows for easy implementation of either electrical or optical readout. The obtained nanopore translocation is characterized by typical behaviors expected for an ordinary nanopore sensor powered by an external source. Extensive numerical simulation confirms the power generation and power level generated. It also reveals the fundamentals of autogenic translocation. As it requires no external power source, the sensing can be conducted with simple readout electronics and may allow for integration of high-density nanopores. Our approach demonstrated in this work may pave the way to practical high-throughput single-molecule nanopore sensing powered by the distributed energy harvested by the nanopores themselves.

    Place, publisher, year, edition, pages
    Elsevier, 2019
    National Category
    Nano Technology
    Identifiers
    urn:nbn:se:uu:diva-384648 (URN)10.1016/j.nanoen.2019.03.092 (DOI)000467774100056 ()
    Funder
    Swedish Research Council, 621-2014-6300Stiftelsen Olle Engkvist Byggmästare, 2016/39
    Available from: 2019-06-07 Created: 2019-06-07 Last updated: 2019-06-19Bibliographically approved
    8. Group behavior of nanoparticles translocating multiple nanopores
    Open this publication in new window or tab >>Group behavior of nanoparticles translocating multiple nanopores
    2018 (English)In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 90, no 22, p. 13483-13490Article in journal (Refereed) Published
    Abstract [en]

    Nanopores have been implemented as nanosensors for DNA sequencing, biomolecule inspection, chemical analysis, nanoparticle detection, etc. For high-throughput and parallelized measurement using nanopore arrays, individual addressability has been a crucial technological solution in order to enable scrutiny of signals generated at each and every nanopore. Here, an alternative pathway of employing arrayed nanopores to perform sensor functions is investigated by examining the group behavior of nanoparticles translocating multiple nanopores. As no individual addressability is required, fabrication of nanopore devices along with microfluidic cells and readout circuits can be greatly simplified. Experimentally, arrays of less than 10 pores are shown to be capable of analyzing translocating nanoparticles with a good signal-to-noise margin. According to theoretical predictions, more pores (than 10) per array can perform high-fidelity analysis if the noise level of the measurement system can be better controlled. More pores per array would also allow for faster measurement at lower concentration because of larger capture cross sections for target nanoparticles. By experimentally varying the number of pores, the concentration of nanoparticles, or the applied bias voltage across the nanopores, we have identified the basic characteristics of this multievent process. By characterizing average pore current and associated standard deviation during translocation and by performing physical modeling and extensive numerical simulations, we have shown the possibility of determining the size and concentration of two kinds of translocating nanoparticles over 4 orders of magnitude in concentration. Hence, we have demonstrated the potential and versatility of the multiple-nanopore approach for high-throughput nanoparticle detection.

    Place, publisher, year, edition, pages
    Washington: American Chemical Society (ACS), 2018
    National Category
    Nano Technology
    Identifiers
    urn:nbn:se:uu:diva-369418 (URN)10.1021/acs.analchem.8b03408 (DOI)000451246100048 ()30372031 (PubMedID)
    Funder
    Swedish Research Council, 621-2014-6300Stiftelsen Olle Engkvist Byggmästare, 2016/39
    Available from: 2018-12-13 Created: 2018-12-13 Last updated: 2019-06-19Bibliographically approved
  • Public defence: 2019-09-09 10:15 Hörsal 2, Uppsala
    Larsson, Ida
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Business Studies.
    Att översätta Lean till praktik i hälso- och sjukvården2019Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Lean has been widely discussed and introduced in Sweden as well as internationally. This thesis deals with the question of how Lean has been translated from idea into practice in healthcare. It contributes to Scandinavian institutional theory, more specifically translation theory. The thesis shows how Lean is translated at the micro level, i.e. at two healthcare units that deal directly with patients. Lean is quite a broad and flexible management idea. In this thesis Lean has been specified into the central concepts of value and flow. The thesis focuses on how these concepts have been translated in healthcare, investigating the role of translators and arenas in local translation processes at the micro level. The thesis is based on a comparative case study of two healthcare units, at two different hospitals, within public healthcare. In 2009 the healthcare units started to implement Lean with the aim that they would improve patient flow and increase quality. The thesis includes a vast number of internal documents, interviews and observations. It also includes a follow-up of the two cases a few years after the initial interviews were carried out. The study presents a number of contributions. Analysis shows that the local translation process in each case resulted in a mutual adaptation between Lean and practice. Furthermore, the introduction of Lean didn´t change the work of the units completely. Lean was translated in a way that supported how the units were organized already before the introduction of Lean instead of changing them. The analysis also shows that the translation of Lean was not isolated within the healthcare units, but spilled over into and was influenced by the surrounding context, both to the private sphere and to other organizations. The findings indicate that translation is something that is going on everywhere, all the time and that the connection between the public and the private sphere, through conversations and small talk about Lean, can be a way of spreading and translating ideas. The introduction of Lean at the units started as a top-down process. But Lean was also translated horizontally to and from friends and family members who had met Lean in other contexts. The translators and arenas at the micro-level filled an important function in the way in which Lean was translated into practice in the operational core where small talk and discussions seemed to be important. But in addition to this the thesis also shows that an actor in a formal position is required to add energy and drive the work with Lean forward.

  • Public defence: 2019-09-11 13:15 B42 BMC, Uppsala
    Omar-Hmeadi, Muhmmad
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Regulation of docking and priming in pancreatic α- and β-cells2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The secretion of islet hormones from endocrine cells of the pancreas plays vital roles in maintaining glucose homeostasis. Dysfunction of these cells leads to diabetes, a devastating metabolic disorder affecting millions worldwide, but underlying mechanisms remain poorly understood. In hyperglycemic conditions, β-cells secrete insulin, whereas α-cells secrete an increased amount of glucagon in hypoglycemic conditions. Both insulin and glucagon are stored in secretory granules preceding their release by regulated exocytosis. This process involves several steps, including tethering, docking, priming, and finally, a fusion of the granules with the plasma membrane. Soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) proteins and phosphoinositides (PIs) drive pancreatic hormone exocytosis and secretion, which follows a biphasic time course. Biphasic secretion is thought to reflect the vastly different release probabilities of individual granules, but direct evidence for this is still lacking.  Therefore, this thesis investigates exocytosis in the two main pancreatic cell types with a particular focus on preceding steps docking and priming, to identify rate-limiting steps in health and type-2 diabetes (T2D). Our data indicated that granule docking is critical for sustained secretion in α- and β-cells. Glucagon granule exocytosis had a U-shaped sensitivity to glucose in both healthy and T2D α-cells. However, T2D α-cells exhibited a marginal decrease in exocytosis, as well as docking, and they were markedly insensitive to somatostatin and insulin. T2D β-cells reduced exocytosis dramatically, and docking was compromised and no longer responsive to glucose, which correlated with reduced insulin secretion and elevated donor HbA1c. These results were further strengthened by the finding that expression of a group of genes that are involved explicitly in granule docking was reduced (by RNAseq of islets from over 200 human donors), and overexpression of the corresponding proteins increased granule docking in human β-cells.

    We further aimed to study the basis for the recruitment of these proteins to the docking site. Here we tested the hypothesis that highly charged lipids mainly PIs act as a hotspot to interact with SNARE proteins that initiate docking. We showed the homogenous distribution of all PIs markers in the plasma membrane, with no PIs microdomains at the exocytotic site during granule docking. However, rapid and local PI(4,5)P2 signaling at fusion sites was crucial for stabilizing fusion pore by binding to proteins related to the release site. These results suggested a role of PI(4,5)P2 in priming and fusion regulation rather than docking. Overall, this work gives new insights into the mechanisms underlying pancreatic hormone secretion in both healthy and diabetic conditions.

    List of papers
    1. Glucose-Dependent Granule Docking Limits Insulin Secretion and Is Decreased in Human Type 2 Diabetes
    Open this publication in new window or tab >>Glucose-Dependent Granule Docking Limits Insulin Secretion and Is Decreased in Human Type 2 Diabetes
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    2018 (English)In: Cell Metabolism, ISSN 1550-4131, E-ISSN 1932-7420, Vol. 27, no 2, p. 470-478Article in journal (Refereed) Published
    Abstract [en]

    Glucose-stimulated insulin secretion is biphasic, with a rapid first phase and a slowly developing sustained second phase; both are disturbed in type 2 diabetes (T2D). Biphasic secretion results from vastly different release probabilities of individual insulin granules, but the morphological and molecular basis for this is unclear. Here, we show that human insulin secretion and exocytosis critically depend on the availability of membrane-docked granules and that T2D is associated with a strong reduction in granule docking. Glucose accelerated granule docking, and this effect was absent in T2D. Newly docked granules only slowly acquired release competence; this was regulated by major signaling pathways, but not glucose. Gene expression analysis indicated that key proteins involved in granule docking are downregulated in T2D, and overexpression of these proteins increased granule docking. The findings establish granule docking as an important glucose-dependent step in human insulin secretion that is dysregulated in T2D.

    Keywords
    GLP-1, biphasic secretion, dense core vesicle, docking, exocytosis, genome-wide association, insulin secretion, priming, somatostatin, type 2 diabetes
    National Category
    Cell and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-341518 (URN)10.1016/j.cmet.2017.12.017 (DOI)000424465200021 ()29414688 (PubMedID)
    Funder
    Swedish Research CouncilSwedish Diabetes AssociationSwedish Society for Medical Research (SSMF)The Swedish Brain FoundationNovo NordiskErnfors Foundation
    Available from: 2018-02-09 Created: 2018-02-09 Last updated: 2019-08-02Bibliographically approved
    2. Paracrine control of α-cell glucagon exocytosis is compromised in human type-2 diabetes
    Open this publication in new window or tab >>Paracrine control of α-cell glucagon exocytosis is compromised in human type-2 diabetes
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Cell and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-389793 (URN)
    Available from: 2019-07-27 Created: 2019-07-27 Last updated: 2019-08-02
    3. PtdIns(4,5)P2 is not required for secretory granule docking
    Open this publication in new window or tab >>PtdIns(4,5)P2 is not required for secretory granule docking
    2018 (English)In: Traffic: the International Journal of Intracellular Transport, ISSN 1398-9219, E-ISSN 1600-0854, Vol. 19, no 6, p. 436-445Article in journal (Refereed) Published
    Abstract [en]

    Phosphoinositides (PtdIns) play important roles in exocytosis and are thought to regulate secretory granule docking by co-clustering with the SNARE protein syntaxin to form a docking receptor in the plasma membrane. Here we tested this idea by high-resolution total internal reflection imaging of EGFP-labeled PtdIns markers or syntaxin-1 at secretory granule release sites in live insulin-secreting cells. In intact cells, PtdIns markers distributed evenly across the plasma membrane with no preference for granule docking sites. In contrast, syntaxin-1 was found clustered in the plasma membrane, mostly beneath docked granules. We also observed rapid accumulation of syntaxin-1 at sites where granules arrived to dock. Acute depletion of plasma membrane phosphatidylinositol (4,5) bisphosphate (PtdIns(4,5)P-2) by recruitment of a 5-phosphatase strongly inhibited Ca2+-dependent exocytosis, but had no effect on docked granules or the distribution and clustering of syntaxin-1. Cell permeabilization by -toxin or formaldehyde-fixation caused PtdIns marker to slowly cluster, in part near docked granules. In summary, our data indicate that PtdIns(4,5)P-2 accelerates granule priming, but challenge a role of PtdIns in secretory granule docking or clustering of syntaxin-1 at the release site.

    Keywords
    exocytosis, insulin, live cell imaging, phosphoinositides, PtdIns(4, 5)P-2, syntaxin clustering, vesicle docking
    National Category
    Cell and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-356858 (URN)10.1111/tra.12562 (DOI)000432037000005 ()29542271 (PubMedID)
    Funder
    Swedish Research CouncilSwedish Child Diabetes FoundationSwedish Society for Medical Research (SSMF)Novo NordiskThe Swedish Brain FoundationErnfors Foundation
    Available from: 2018-08-15 Created: 2018-08-15 Last updated: 2019-08-02Bibliographically approved
    4. Fusion pore regulation by transient local generation of PI(4,5)P2 in pancreatic in β-cells
    Open this publication in new window or tab >>Fusion pore regulation by transient local generation of PI(4,5)P2 in pancreatic in β-cells
    (English)Manuscript (preprint) (Other academic)
    National Category
    Cell and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-389794 (URN)
    Available from: 2019-07-27 Created: 2019-07-27 Last updated: 2019-08-02
  • Public defence: 2019-09-13 09:15 B42, Uppsala
    Wegler, Christine
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Proteomics-informed analysis of drug disposition in the human liver and small intestine2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Orally administered drugs are absorbed in the intestine and generally metabolized in the liver. Therefore, understanding factors determining drug distribution and elimination in these tissues is important. This thesis aimed at using mass spectrometry (MS)-based proteomics and functional studies to better understand in vitro model systems used for drug clearance predictions. Further, it aimed at understanding the changes in drug disposition caused by obesity and gastric bypass surgery (GBP).

    The study was initiated by investigating factors influencing MS-based protein quantification by comparing results from different proteomics methods, and by studying protein distribution during subcellular fractionation. The largest variability in protein quantification was ascribed to insufficient enrichment from subcellular fractionation, most likely due to collection of the majority of the proteins in the initial fraction of the fractionation protocols.

    Proteomics and metabolic activity analyses were then used to investigate differences in intrinsic clearance from two commonly used in vitro systems, human liver microsomes and hepatocytes. For some compounds, the faster microsomal metabolism could be explained by a higher available unbound drug concentration and CYP content in the microsomes as compared to in the hepatocytes.

    Next, inter-individual protein expression variability in human liver and jejunum was explored. This showed that proteins covered a wide inter-individual variability spectrum, in which proteins with low variabilities were associated with essential cellular functions, while many proteins with high variabilities were disease-related.

    Further, the effects of obesity, GBP, and weight loss on the proteomes of human liver and jejunum were analyzed. After GBP and subsequent weight loss, patients showed lower levels of jejunal proteins involved in inflammatory response and drug metabolism.

    Finally, proteomics data from patients with and without obesity was combined with parameters from in vitro transport kinetics, and a mechanistic model to predict drug disposition was developed. The model successfully predicted rosuvastatin plasma concentrations in the patients.

    In conclusion, this thesis has provided insights into factors influencing protein quantification and function in vitro. Furthermore, this thesis demonstrates how proteomics contributes to improved understanding of inter-individual and physiological differences, and how it can be used for in vitro-in vivo scaling of drug clearance.

    List of papers
    1. Variability in Mass Spectrometry-based Quantification of Clinically Relevant Drug Transporters and Drug Metabolizing Enzymes
    Open this publication in new window or tab >>Variability in Mass Spectrometry-based Quantification of Clinically Relevant Drug Transporters and Drug Metabolizing Enzymes
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    2017 (English)In: Molecular Pharmaceutics, ISSN 1543-8384, E-ISSN 1543-8392, Vol. 14, no 9, p. 3142-3151Article in journal (Refereed) Published
    Abstract [en]

    Many different methods are used for mass-spectrometry-based protein quantification in pharmacokinetics and systems pharmacology. It has not been established to what extent the results from these various methods are comparable. Here, we compared six different mass spectrometry-based proteomics methods by measuring the expression of clinically relevant drug transporters and metabolizing enzymes in human liver. Mean protein concentrations were in general quantified to similar levels by methods using whole tissue lysates. Methods using subcellular membrane fractionation gave incomplete enrichment of the proteins. When the enriched proteins were adjusted to levels in whole tissue lysates, they were on average 4 fold lower than those quantified directly in whole tissue lysates. The differences in protein levels were propagated into differences in predictions of hepatic clearance. In conclusion, caution is needed when comparing and applying quantitative proteomics data obtained with different methods, especially since membrane fractionation is common practice for protein quantification used in drug clearance predictions.

    Place, publisher, year, edition, pages
    AMER CHEMICAL SOC, 2017
    Keywords
    drug transporters, drug metabolizing enzymes, membrane proteins, protein quantification, targeted proteomics, label-free proteomics
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-335414 (URN)10.1021/acs.molpharmaceut.7b00364 (DOI)000410005100027 ()28767254 (PubMedID)
    Funder
    Swedish Research Council, 2822, 5715
    Available from: 2017-12-06 Created: 2017-12-06 Last updated: 2019-07-26Bibliographically approved
    2. Subcellular fractionation of human liver reveals limits in global proteomic quantification from isolated fractions
    Open this publication in new window or tab >>Subcellular fractionation of human liver reveals limits in global proteomic quantification from isolated fractions
    2016 (English)In: Analytical Biochemistry, ISSN 0003-2697, E-ISSN 1096-0309, Vol. 509, p. 82-88Article in journal (Refereed) Published
    Abstract [en]

    The liver plays an important role in metabolism and elimination of xenobiotics, including drugs. Determination of concentrations of proteins involved in uptake, distribution, metabolism, and excretion of xenobiotics is required to understand and predict elimination mechanisms in this tissue. In this work, we have fractionated homogenates of snap -frozen human liver by differential centrifugation and performed quantitative mass spectrometry -based proteomic analysis of each fraction. Concentrations of proteins were calculated by the "total protein approach". A total of 4586 proteins were identified by at least five peptides and were quantified in all fractions. We found that the xenobiotics transporters of the canalicular and basolateral membranes were differentially enriched in the subcellular fractions and that phase I and II metabolizing enzymes, the cytochrome P450s and the UDP glucuronyl transferases, have complex subcellular distributions. These findings show that there is no simple way to scale the data from measurements in arbitrarily selected membrane fractions using a single scaling factor for all the proteins of interest. This study also provides the first absolute quantitative subcellular catalog of human liver proteins obtained from frozen tissue specimens. Our data provide quantitative insights into the sub cellular distribution of proteins and can be used as a guide for development of fractionation procedures.

    Keywords
    Human liver, Subcellular fractionation, Absolute quantitative proteomics, Total protein approach, Drug metabolism, Drug transport
    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-303255 (URN)10.1016/j.ab.2016.06.006 (DOI)000380866800013 ()27311553 (PubMedID)
    Funder
    Swedish Research Council, 2822
    Available from: 2016-09-16 Created: 2016-09-15 Last updated: 2019-07-26Bibliographically approved
    3. Bridging differences in CYP activity between donor-matched human liver microsomes and hepatocytes
    Open this publication in new window or tab >>Bridging differences in CYP activity between donor-matched human liver microsomes and hepatocytes
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    (English)Manuscript (preprint) (Other academic)
    Keywords
    Human liver microsomes, Human hepatocytes, Proteomics, Kpuu, Clearance
    National Category
    Pharmaceutical Sciences
    Research subject
    Pharmaceutical Science
    Identifiers
    urn:nbn:se:uu:diva-389737 (URN)
    Available from: 2019-07-23 Created: 2019-07-23 Last updated: 2019-07-26
    4. Global expression variability of proteins across and within human tissues
    Open this publication in new window or tab >>Global expression variability of proteins across and within human tissues
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    (English)In: Article in journal (Other academic) Submitted
    Place, publisher, year, edition, pages
    Uppsala:
    Keywords
    Expression variability, Human liver, Human jejunum, Proteomics, Transcriptomics, Reference genes
    National Category
    Cell and Molecular Biology
    Research subject
    Pharmaceutical Science
    Identifiers
    urn:nbn:se:uu:diva-389738 (URN)
    Available from: 2019-07-23 Created: 2019-07-23 Last updated: 2019-07-26
    5. Effects of obesity and weight loss on global protein expression in human liver and jejunum
    Open this publication in new window or tab >>Effects of obesity and weight loss on global protein expression in human liver and jejunum
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    (English)Manuscript (preprint) (Other academic)
    Keywords
    Proteomics, Obesity, Gastric bypass, Human liver, Human jejunum
    National Category
    Cell and Molecular Biology
    Research subject
    Pharmaceutical Science
    Identifiers
    urn:nbn:se:uu:diva-389739 (URN)