| 1. |
- Aksenova, Anna, et al.
(författare)
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Mismatch repair-independent increase in spontaneous mutagenesis in yeast lacking non-essential subunits of DNA polymerase ε
- 2010
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Ingår i: PLoS genetics. - : Public Library of Science. - 1553-7404. ; 6:11, s. e1001209-
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Tidskriftsartikel (refereegranskat)abstract
- Yeast DNA polymerase ε (Pol ε) is a highly accurate and processive enzyme that participates in nuclear DNA replication of the leading strand template. In addition to a large subunit (Pol2) harboring the polymerase and proofreading exonuclease active sites, Pol ε also has one essential subunit (Dpb2) and two smaller, non-essential subunits (Dpb3 and Dpb4) whose functions are not fully understood. To probe the functions of Dpb3 and Dpb4, here we investigate the consequences of their absence on the biochemical properties of Pol ε in vitro and on genome stability in vivo. The fidelity of DNA synthesis in vitro by purified Pol2/Dpb2, i.e. lacking Dpb3 and Dpb4, is comparable to the four-subunit Pol ε holoenzyme. Nonetheless, deletion of DPB3 and DPB4 elevates spontaneous frameshift and base substitution rates in vivo, to the same extent as the loss of Pol ε proofreading activity in a pol2-4 strain. In contrast to pol2-4, however, the dpb3Δdpb4Δ does not lead to a synergistic increase of mutation rates with defects in DNA mismatch repair. The increased mutation rate in dpb3Δdpb4Δ strains is partly dependent on REV3, as well as the proofreading capacity of Pol δ. Finally, biochemical studies demonstrate that the absence of Dpb3 and Dpb4 destabilizes the interaction between Pol ε and the template DNA during processive DNA synthesis and during processive 3' to 5'exonucleolytic degradation of DNA. Collectively, these data suggest a model wherein Dpb3 and Dpb4 do not directly influence replication fidelity per se, but rather contribute to normal replication fork progression. In their absence, a defective replisome may more frequently leave gaps on the leading strand that are eventually filled by Pol ζ or Pol δ, in a post-replication process that generates errors not corrected by the DNA mismatch repair system.
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| 2. |
- Lee, Craig M., et al.
(författare)
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A Framework for the Development, Design and Implementation of a Sustained Arctic Ocean Observing System
- 2019
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 6
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Forskningsöversikt (refereegranskat)abstract
- Rapid Arctic warming drives profound change in the marine environment that have significant socio-economic impacts within the Arctic and beyond, including climate and weather hazards, food security, transportation, infrastructure planning and resource extraction. These concerns drive efforts to understand and predict Arctic environmental change and motivate development of an Arctic Region Component of the Global Ocean Observing System (ARCGOOS) capable of collecting the broad, sustained observations needed to support these endeavors. This paper provides a roadmap for establishing the ARCGOOS. ARCGOOS development must be underpinned by a broadly endorsed framework grounded in high-level policy drivers and the scientific and operational objectives that stem from them. This should be guided by a transparent, internationally accepted governance structure with recognized authority and organizational relationships with the national agencies that ultimately execute network plans. A governance model for ARCGOOS must guide selection of objectives, assess performance and fitness-to-purpose, and advocate for resources. A requirements-based framework for an ARCGOOS begins with the Societal Benefit Areas (SBAs) that underpin the system. SBAs motivate investments and define the system's science and operational objectives. Objectives can then be used to identify key observables and their scope. The domains of planning/policy, strategy, and tactics define scope ranging from decades and basins to focused observing with near real time data delivery. Patterns emerge when this analysis is integrated across an appropriate set of SBAs and science/operational objectives, identifying impactful variables and the scope of the measurements. When weighted for technological readiness and logistical feasibility, this can be used to select Essential ARCGOOS Variables, analogous to Essential Ocean Variables of the Global Ocean Observing System. The Arctic presents distinct needs and challenges, demanding novel observing strategies. Cost, traceability and ability to integrate region-specific knowledge have to be balanced, in an approach that builds on existing and new observing infrastructure. ARCGOOS should benefit from established data infrastructures following the Findable, Accessible, Interoperable, Reuseable Principles to ensure preservation and sharing of data and derived products. Linking to the Sustaining Arctic Observing Networks (SAON) process and involving Arctic stakeholders, for example through liaison with the International Arctic Science Committee (IASC), can help ensure success.
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| 3. |
- Lett, Signe, et al.
(författare)
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Can bryophyte groups increase functional resolution in tundra ecosystems?
- 2022
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Ingår i: Arctic Science. - Ottawa : Canadian Science Publishing. - 2368-7460. ; 8:3, s. 609-637
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Tidskriftsartikel (refereegranskat)abstract
- The relative contribution of bryophytes to plant diversity, primary productivity, and ecosystem functioning increases towards colder climates. Bryophytes respond to environmental changes at the species level, but because bryophyte species are relatively difficult to identify, they are often lumped into one functional group. Consequently, bryophyte function remains poorly resolved. Here, we explore how higher resolution of bryophyte functional diversity can be encouraged and implemented in tundra ecological studies. We briefly review previous bryophyte functional classifications and the roles of bryophytes in tundra ecosystems and their susceptibility to environmental change. Based on shoot morphology and colony organization, we then propose twelve easily distinguishable bryophyte functional groups. To illustrate how bryophyte functional groups can help elucidate variation in bryophyte effects and responses, we compiled existing data on water holding capacity, a key bryophyte trait. Although plant functional groups can mask potentially high interspecific and intraspecific variability, we found better separation of bryophyte functional group means compared with previous grouping systems regarding water holding capacity. This suggests that our bryophyte functional groups truly represent variation in the functional roles of bryophytes in tundra ecosystems. Lastly, we provide recommendations to improve the monitoring of bryophyte community changes in tundra study sites.
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| 4. |
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| 5. |
- Sekretareva, Alina, et al.
(författare)
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Total phenol analysis of water using a laccase-based microsensor array
- 2015
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Ingår i: Program of the XXIII International Symposium on Bioelectrochemistry and Bioenergetics of the Bioelectrochemical Society. 14-18 June, 2015. Malmö, Sweden. - Lausanne : Bioelectrochemical Society. ; , s. 155-155
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The monitoring of phenolic compounds in raw waters and wastewaters is of great importance for environmental control. Use of biosensors for rapid, specific and simple detection of phenolic compounds is a promising approach. A number of biosensors have been developed for phenol detection. A general drawback of previously reported biosensors is their insufficient detection limits for phenols in water samples. One way to improve the detection limit is by the use of microelectrodes.Microband design of the microelectrodes combines convergent mass transport due to the microscale width and high output currents due to the macroscopic length. Among the various techniques available for microband electrode fabrication, we have chosen screen-printing which is a cost-effective production method.In this study, we report on the development of a laccase-based microscale biosensor operating under a convergent diffusion regime. Screen-printing followed by simple cutting was utilized for the fabrication of graphite microbands as a platform for further covalent immobilization of laccase. Numerical simulations, utilizing the finite element method with periodic boundary conditions, were used for modeling the voltammetric response of the developed microband electrodes. Anodization followed by covalent immobilization was used for the electrode modification with laccase. Direct and mediated laccase bioelectrocatalytic oxidation of phenols was studied on macro- and microscale graphite electrodes. Significant enhancement of the analytical performance was achieved by the establishment of convergent diffusion in the microscale sensor. Finally, the developed microsensor was utilized to monitor phenolic compounds in real waste water.
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| 6. |
- Sekretaryova, Alina N., et al.
(författare)
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Evaluation of the Electrochemically Active Surface Area of Microelectrodes by Capacitive and Faradaic Currents
- 2019
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Ingår i: ChemElectroChem. - : WILEY-V C H VERLAG GMBH. - 2196-0216. ; 6:17, s. 4411-4417
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Tidskriftsartikel (refereegranskat)abstract
- Two experimental methods to estimate the electrochemically active surface area (EASA) of microelectrodes are investigated. One method is based on electrocapacitive measurements and depends significantly on the surface roughness as well as on other parameters. The other method is based on faradaic current measurements and depends on the geometric surface area. The experimental results are supplemented with numerical modeling of electrodes with different surface roughness. A systematic study reveals a strong influence of the scale and arrangement of the surface roughness, the measurement potential and the electrolyte concentration on the EASA of microelectrodes estimated from the electrocapacitive measurements. The results show that electrocapacitive measurements should not be used to estimate the faradaic EASA of microelectrodes with a non-negligible surface roughness.
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| 7. |
- Sekretaryova, Alina, et al.
(författare)
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Total phenol analysis of weakly supported water using a laccase-based microband biosensor.
- 2016
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Ingår i: Analytica Chimica Acta. - : Elsevier. - 0003-2670 .- 1873-4324. ; 907, s. 45-53
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Tidskriftsartikel (refereegranskat)abstract
- The monitoring of phenolic compounds in wastewaters in a simple manner is of great importance for environmental control. Here, a novel screen printed laccase-based microband array for in situ, total phenol estimation in wastewaters and for water quality monitoring without additional sample pre-treatment is presented. Numerical simulations using the finite element method were utilized for the characterization of micro-scale graphite electrodes. Anodization followed by covalent modification was used for the electrode functionalization with laccase. The functionalization efficiency and the electrochemical performance in direct and catechol-mediated oxygen reduction were studied at the microband laccase electrodes and compared with macro-scale electrode structures. The reduction of the dimensions of the enzyme biosensor, when used under optimized conditions, led to a significant improvement in its analytical characteristics. The elaborated microsensor showed fast responses towards catechol additions to tap water – a weakly supported medium – characterized by a linear range from 0.2 to 10 μM, a sensitivity of 1.35 ± 0.4 A M−1 cm−2 and a dynamic range up to 43 μM. This enhanced laccase-based microsensor was used for water quality monitoring and its performance for total phenol analysis of wastewater samples from different stages of the cleaning process was compared to a standard method.
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| 8. |
- Stavrinidou, Eleni, et al.
(författare)
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In vivo polymerization and manufacturing of wires and supercapacitors in plants
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:11, s. 2807-2812
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Tidskriftsartikel (refereegranskat)abstract
- Electronic plants, e-Plants, are an organic bioelectronic platform that allows electronic interfacing with plants. Recently we have demonstrated plants with augmented electronic functionality. Using the vascular system and organs of a plant, we manufactured organic electronic devices and circuits in vivo, leveraging the internal structure and physiology of the plant as the template, and an integral part of the devices. However, this electronic functionality was only achieved in localized regions, whereas new electronic materials that could be distributed to every part of the plant would provide versatility in device and circuit fabrication and create possibilities for new device concepts. Here we report the synthesis of such a conjugated oligomer that can be distributed and form longer oligomers and polymer in every part of the xylem vascular tissue of a Rosa floribunda cutting, forming long-range conducting wires. The plant’s structure acts as a physical template, whereas the plant’s biochemical response mechanism acts as the catalyst for polymerization. In addition, the oligomer can cross through the veins and enter the apoplastic space in the leaves. Finally, using the plant’s natural architecture we manufacture supercapacitors along the stem. Our results are preludes to autonomous energy systems integrated within plants and distribute interconnected sensor-actuator systems for plant control and optimization
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| 9. |
- Volkov, Anton, 1989-
(författare)
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Ionic and electronic transport in electrochemical and polymer based systems
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Electrochemical systems, which rely on coupled phenomena of the chemical change and electricity, have been utilized for development an interface between biological systems and conventional electronics. The development and detailed understanding of the operation mechanism of such interfaces have a great importance to many fields within life science and conventional electronics. Conducting polymer materials are extensively used as a building block in various applications due to their ability to transduce chemical signal to electrical one and vice versa. The mechanism of the coupling between the mass and charge transfer in electrochemical systems, and particularly in conductive polymer based system, is highly complex and depends on various physical and chemical properties of the materials composing the system of interest.The aims of this thesis have been to study electrochemical systems including conductive polymer based systems and provide knowledge for future development of the devices, which can operate with both chemical and electrical signals. Within the thesis, we studied the operation mechanism of ion bipolar junction transistor (IBJT), which have been previously utilized to modulate delivery of charged molecules. We analysed the different operation modes of IBJT and transition between them on the basis of detailed concentration and potential profiles provided by the model.We also performed investigation of capacitive charging in conductive PEDOT:PSS polymer electrode. We demonstrated that capacitive charging of PEDOT:PSS electrode at the cyclic voltammetry, can be understood within a modified Nernst-Planck-Poisson formalism for two phase system in terms of the coupled ion-electron diffusion and migration without invoking the assumption of any redox reactions.Further, we studied electronic structure and optical properties of a self-doped p-type conducting polymer, which can polymerize itself along the stem of the plants. We performed ab initio calculations for this system in undoped, polaron and bipolaron electronic states. Comparison with experimental data confirmed the formation of undoped or bipolaron states in polymer film depending on applied biases.Finally, we performed simulation of the reduction-oxidation reaction at microband array electrodes. We showed that faradaic current density at microband array electrodes increases due to non-linear mass transport on the microscale compared to the corresponding macroscale systems. The studied microband array electrode was used for developing a laccase-based microband biosensor. The biosensor revealed improved analytical performance, and was utilized for in situ phenol detection.
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| 10. |
- Volkov, Anton, et al.
(författare)
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Modeling of Charge Transport in Ion Bipolar Junction Transistors
- 2014
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 30:23, s. 6999-7005
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Tidskriftsartikel (refereegranskat)abstract
- Spatiotemporal control of the complex chemical microenvironment is of great importance to many fields within life science. One way to facilitate such control is to construct delivery circuits, comprising arrays of dispensing outlets, for ions and charged biomolecules based on ionic transistors. This allows for addressability of ionic signals, which opens up for spatiotemporally controlled delivery in a highly complex manner. One class of ionic transistors, the ion bipolar junction transistors (IBJTs), is especially attractive for these applications because these transistors are functional at physiological conditions and have been employed to modulate the delivery of neurotransmitters to regulate signaling in neuronal cells. Further, the first integrated complementary ionic circuits were recently developed on the basis of these ionic transistors. However, a detailed understanding of the device physics of these transistors is still lacking and hampers further development of components and circuits. Here, we report on the modeling of IBJTs using Poissons and Nernst-Planck equations and the finite element method. A two-dimensional model of the device is employed that successfully reproduces the main characteristics of the measurement data. On the basis of the detailed concentration and potential profiles provided by the model, the different modes of operation of the transistor are analyzed as well as the transitions between the different modes. The model correctly predicts the measured threshold voltage, which is explained in terms of membrane potentials. All in all, the results provide the basis for a detailed understanding of IBJT operation. This new knowledge is employed to discuss potential improvements of ion bipolar junction transistors in terms of miniaturization and device parameters.
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| 11. |
- Volkov, Anton, et al.
(författare)
-
Spectroelectrochemistry and Nature of Charge Carriers in Self-Doped Conducting Polymer
- 2017
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Ingår i: Advanced Electronic Materials. - : Wiley-VCH Verlagsgesellschaft. - 2199-160X. ; 3:8
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Tidskriftsartikel (refereegranskat)abstract
- A recently developed water-soluble self-doped sodium salt of bis[3,4-ethylenedioxythiophene] 3thiophene butyric acid (ETE-S) is electropolymerized and characterized by means of spectroelectrochemistry, electron paramagnetic resonance spectroscopy, and cyclic voltammetry, combined with the density functional theory (DFT) and time-dependent DFT calculations. The focus of the studies is to underline the nature of the charge carriers when the electrochemically polymerized ETE-S films undergo a reversible transition from reduced to electrically conductive oxidized states. Spectroelectrochemistry shows clear distinctions between absorption features from reduced and charged species. In the reduced state, the absorption spectrum of ETE-S electropolymerized film shows a peak that is attributed to HOMO. LUMO transition. As the oxidation level increases, this peak diminishes and the absorption of the film is dominated by spinless bipolaronic states with some admixture of polaronic states possessing a magnetic momentum. For fully oxidized samples, the bipolaronic states fully dominate, and the features in the absorption spectra are related to the drastic changes of the band structure, exhibiting a strong decrease of the band gap when a polymeric film undergoes oxidation.
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| 12. |
- Volkov, Anton, et al.
(författare)
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Understanding the Capacitance of PEDOT:PSS
- 2017
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Ingår i: Advanced Functional Materials. - : WILEY-V C H VERLAG GMBH. - 1616-301X .- 1616-3028. ; 27:28
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Tidskriftsartikel (refereegranskat)abstract
- Poly(3,4-ethylenedioxythiophene): polystyrene sulfonate (PEDOT:PSS) is the most studied and explored mixed ion-electron conducting polymer system. PEDOT: PSS is commonly included as an electroactive conductor in various organic devices, e.g., supercapacitors, displays, transistors, and energy-converters. In spite of its long-term use as a material for storage and transport of charges, the fundamentals of its bulk capacitance remain poorly understood. Generally, charge storage in supercapacitors is due to formation of electrical double layers or redox reactions, and it is widely accepted that PEDOT: PSS belongs to the latter category. Herein, experimental evidence and theoretical modeling results are reported that significantly depart from this commonly accepted picture. By applying a two-phase, 2D modeling approach it is demonstrated that the major contribution to the capacitance of the two-phase PEDOT: PSS originates from electrical double layers formed along the interfaces between nanoscaled PEDOT-rich and PSS-rich interconnected grains that comprises two phases of the bulk of PEDOT: PSS. This new insight paves a way for designing materials and devices, based on mixed ion-electron conductors, with improved performance.
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| 13. |
- Volkov, A. V., et al.
(författare)
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Interaction-induced enhancement of g-factor in graphene
- 2012
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - : American Physical Society. - 1098-0121 .- 1550-235X. ; 86:15, s. 155440-
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Tidskriftsartikel (refereegranskat)abstract
- We study the effect of electron interaction on the spin-splitting and the g-factor in graphene in perpendicular magnetic field using the Hartree and Hubbard approximations within the Thomas-Fermi model. We found that the g-factor is enhanced in comparison to its free electron value g = 2 and oscillates as a function of the filling factor ѵ in the range 2 ≤ g∗ < 4 reaching maxima at even ѵ and minima at odd ѵ. We outline the role of charged impurities in the substrate, which are shown to suppress the oscillations of the g∗-factor. This effect becomes especially pronounced with the increase of the impurity concentration, when the effective g-factor becomes independent of the filling factor reaching a value of g∗ ≈ 2.3. A relation to the recent experiment is discussed.
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