| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Albert, F., et al.
(författare)
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Betatron x-ray radiation from laser-plasma accelerators driven by femtosecond and picosecond laser systems
- 2018
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Ingår i: Physics of Plasmas. - : AIP Publishing. - 1089-7674 .- 1070-664X. ; 25:5
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Tidskriftsartikel (refereegranskat)abstract
- A comparative experimental study of betatron x-ray radiation from laser wakefield acceleration in the blowout and self-modulated regimes is presented. Our experiments use picosecond duration laser pulses up to 150 J (self-modulated regime) and 60 fs duration laser pulses up to 10 J (blowout regime), for plasmas with electronic densities on the order of 1019cm-3. In the self-modulated regime, where betatron radiation has been very little studied compared to the blowout regime, electrons accelerated in the wake of the laser pulse are subject to both the longitudinal plasma and transverse laser electrical fields. As a result, their motion within the wake is relatively complex; consequently, the experimental and theoretical properties of the x-ray source based on self-modulation differ from the blowout regime of laser wakefield acceleration. In our experimental configuration, electrons accelerated up to about 250 MeV and betatron x-ray spectra with critical energies of about 10-20 keV and photon fluxes between 108and 1010photons/eV Sr are reported. Our experiments open the prospect of using betatron x-ray radiation for applications, and the source is competitive with current x-ray backlighting methods on multi-kilojoule laser systems.
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| 4. |
- Algaba, Juan-Carlos, et al.
(författare)
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Broadband Multi-wavelength Properties of M87 during the 2017 Event Horizon Telescope Campaign
- 2021
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Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 911:1
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Forskningsöversikt (refereegranskat)abstract
- In 2017, the Event Horizon Telescope (EHT) Collaboration succeeded in capturing the first direct image of the center of the M87 galaxy. The asymmetric ring morphology and size are consistent with theoretical expectations for a weakly accreting supermassive black hole of mass ∼6.5 × 109 M o˙. The EHTC also partnered with several international facilities in space and on the ground, to arrange an extensive, quasi-simultaneous multi-wavelength campaign. This Letter presents the results and analysis of this campaign, as well as the multi-wavelength data as a legacy data repository. We captured M87 in a historically low state, and the core flux dominates over HST-1 at high energies, making it possible to combine core flux constraints with the more spatially precise very long baseline interferometry data. We present the most complete simultaneous multi-wavelength spectrum of the active nucleus to date, and discuss the complexity and caveats of combining data from different spatial scales into one broadband spectrum. We apply two heuristic, isotropic leptonic single-zone models to provide insight into the basic source properties, but conclude that a structured jet is necessary to explain M87's spectrum. We can exclude that the simultaneous γ-ray emission is produced via inverse Compton emission in the same region producing the EHT mm-band emission, and further conclude that the γ-rays can only be produced in the inner jets (inward of HST-1) if there are strongly particle-dominated regions. Direct synchrotron emission from accelerated protons and secondaries cannot yet be excluded.
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| 5. |
- Velasquez, Nicolas, et al.
(författare)
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X-ray induced ultrafast charge transfer in thiophene-based conjugated polymers controlled by core-hole clock spectroscopy
- 2024
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Ingår i: Physical Chemistry Chemical Physics. - 1463-9076 .- 1463-9084. ; 26:2, s. 1234-1244
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Tidskriftsartikel (refereegranskat)abstract
- We explore ultrafast charge transfer (CT) resonantly induced by hard X-ray radiation in organic thiophene-based polymers at the sulfur K-edge. A combination of core-hole clock spectroscopy with real-time propagation time-dependent density functional theory simulations gives an insight into the electron dynamics underlying the CT process. Our method provides control over CT by a selective excitation of a specific resonance in the sulfur atom with monochromatic X-ray radiation. Our combined experimental and theoretical investigation establishes that the dominant mechanism of CT in polymer powders and films consists of electron delocalisation along the polymer chain occurring on the low-femtosecond time scale.
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| 6. |
- Martins, Ernane de Freitas, et al.
(författare)
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A multiscale approach for electronic transport simulation of carbon nanostructures in aqueous solvent
- 2022
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 24:39, s. 24404-24412
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Tidskriftsartikel (refereegranskat)abstract
- Theoretical works addressing electronic nano-devices operating in an aqueous environment often neglect solvent effects. In order to assess the role played by the polarization effects on the electronic transport properties of solvated graphene, for example in possible bio-sensing applications, we have used here a combination of polarizable force-field molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) approach, density functional theory, and non-equilibrium Green's function method. We considered different solvation conditions, the presence of defects in graphene, as well as various choices for the partitions between the quantum and classical regions in QM/MM, in which we explicitly account for polarization effects. Our results show that the polarization effects on graphene lead to changes in the structure of interfacial water molecules which are more pronounced in the vicinity of defects. The presence of water leads to increased scattering due to the long-range charge interactions with graphene. At the same time, changes in the conductance due to polarization or salt concentration are found to be small, paving the way for robust electronic nano-devices operating in aqueous environments.
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| 7. |
- Martins, Ernane de Freitas, et al.
(författare)
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Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates
- 2019
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Ingår i: Molecules. - : MDPI. - 1431-5157 .- 1420-3049. ; 24:5
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes in the electronic transport properties of graphene interacting with DNA strands under the effect of the solvent. To investigate these systems, we applied a hybrid methodology, combining quantum and classical mechanics (QM/MM) coupled to non-equilibrium Green's functions, allowing for the calculations of electronic transport. Our results show that the proposed device has high sensitivity towards the presence of DNA, and, combined with the presence of a specific DNA probe in the form of a single-strand, it presents good selectivity towards specific nucleotide sequences.
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| 8. |
- Martins, Ernane de Freitas, et al.
(författare)
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The role of water on the electronic transport in graphene nanogap devices designed for DNA sequencing
- 2020
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Ingår i: Carbon. - : Elsevier BV. - 0008-6223 .- 1873-3891. ; 158, s. 314-319
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Tidskriftsartikel (refereegranskat)abstract
- Innovative methodologies for reliably and inexpensively sequencing DNA can lead to a new era of personalized medicine. In this work, we performed a theoretical investigation of a nanogap-based all electronic DNA sequencing device. To do so, we used a nitrogen-terminated nanogap on a graphene sheet with the aqueous environment fully taken into account. Our investigation is performed using a hybrid methodology combining quantum and classical mechanics coupled to non-equilibrium Green's functions for solving the electron transport across the device. The obtained results show that the DNA nucleotides can be both detected and distinguished in such a device, which indicates that it can be used as a DNA sequencing device providing very high sensitivity and selectivity. Furthermore, our results show that water plays a major role in electronic transport in nanoscopic tunneling devices, not only from an electrostatics point of view, but also by providing states that significantly increase the conductance in nanogap-based DNA sequencing devices.
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| 9. |
- Prasongkit, Jariyanee, et al.
(författare)
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Topological Line Defects Around Graphene Nanopores for DNA Sequencing
- 2018
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Ingår i: The Journal of Physical Chemistry C. - : AMER CHEMICAL SOC. - 1932-7447 .- 1932-7455. ; 122:13, s. 7094-7099
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Tidskriftsartikel (refereegranskat)abstract
- Topological line defects in graphene represent an ideal way to produce highly controlled structures with reduced dimensionality that can be used in electronic devices. In this work, we propose using extended line defects in graphene to improve nucleobase selectivity in nanopore-based DNA sequencing devices. We use a combination of quantum mechanics/molecular mechanics and nonequilibrium Green's function methods to investigate the conductance modulation, fully accounting for solvent effects. By sampling over a large number of different orientations generated from molecular dynamics simulations, we theoretically demonstrate that distinguishing between the four nucleobases using line defects in a graphene-based electronic device appears possible. The changes in conductance are associated with transport across specific molecular states near the Fermi level and their coupling to the pore. Through the application of a specifically tuned gate voltage, such a device would be able to discriminate the four types of nucleobases more reliably than that of graphene sensors without topological line defects.
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| 10. |
- Velasquez, Nicolas, et al.
(författare)
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Generalization of the post-collision interaction effect from gas-phase to solid-state systems demonstrated in thiophene and its polymers
- 2023
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Ingår i: Physical Review Research. - : American Physical Society. - 2643-1564. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate experimentally and theoretically the presence of the post-collision interaction (PCI) effect in sulfur KL2,3L2,3 Auger electron spectra measured in the gas-phase thiophene and in solid-state organic polymers: polythiophene (PT) and poly(3-hexylthiophene-2,5-diyl), commonly known as P3HT. PCI manifests itself through a distortion and a blueshift of the normal Auger S KL2,3L2,3 spectrum when S 1s ionization occurs close to the ionization threshold. Our investigation shows that the PCI-induced shift of the Auger spectra is stronger in the solid-state polymers than in the gas-phase organic molecule. Theoretical modeling within the framework of the eikonal approximation provides good agreement with the experimental observations. In a solid medium, two effects influence the interaction between the photoelectron and the Auger electron. In detail, stronger PCI in the polymers is attributed to the photoelectron scattering in the solid, which overcompensates the polarization screening of electron charges which causes a reduction of the interaction. Our paper demonstrates the general nature of the PCI effect occurring in different media.
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