| 1. |
- 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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| 2. |
- Jeon, Il, et al.
(författare)
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Lithium-Ion Endohedral Fullerene (Li+@C-60) Dopants in Stable Perovskite Solar Cells Induce Instant Doping and Anti-Oxidation
- 2018
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Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 57:17, s. 4607-4611
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Tidskriftsartikel (refereegranskat)abstract
- Herein, we report use of [Li+@C-60]TFSI- as a dopant for spiro-MeOTAD in lead halide perovskite solar cells. This approach gave an air stability nearly 10-fold that of conventional devices using Li+TFSI-. Such high stability is attributed to the hydrophobic nature of [Li+@C-60]TFSI- repelling moisture and absorbing intruding oxygen, thereby protecting the perovskite device from degradation. Furthermore, [Li+@C-60]TFSI- could oxidize spiro-MeOTAD without the need for oxygen. The encapsulated devices exhibited outstanding air stability for more than 1000h while illuminated under ambient conditions.
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| 3. |
- Sumi, Naoya, et al.
(författare)
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Direct Visualization of Nearly Free Electron States Formed by Superatom Molecular Orbitals in a Li@C-60 Monolayer
- 2021
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 12:32, s. 7812-7817
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Tidskriftsartikel (refereegranskat)abstract
- Using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, we directly determine the spatial and energetic distributions of superatom molecular orbitals (SAMOs) of an Li@C-60 monolayer adsorbed on a Cu(111) surface. Utilizing a weakly bonded [Li+@C-60] NTf2- (NTf2-: bis(trifluoromethanesulfonyl)imide) salt makes it possible to produce a Li@C-60 monolayer with high concentration of Li@C-60 molecules. Because of the very uniform adsorption geometry of Li@C-60 on Cu(111), the p(z)-SAMO, populated above the upper hemisphere of the molecule, exhibits an isotropic and delocalized nature, with an energy that is significantly lower compared to that of C-60. The isotropic overlapping of p(z)-SAMOs in the condensed monolayer of Li@C-60 results in a laterally homogeneous STM image contributing to the formation of a free-electron-like states. These findings make an important step toward further basic research and applicative utilization of Li@C-60 SAMOs.
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| 4. |
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| 5. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.
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| 6. |
- Kobayashi, Ryohei, et al.
(författare)
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Rotary catalysis of bovine mitochondrial F-1-ATPase studied by single-molecule experiments
- 2020
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:3, s. 1447-1456
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Tidskriftsartikel (refereegranskat)abstract
- The reaction scheme of rotary catalysis and the torque generation mechanism of bovine mitochondrial F-1 (bMF(1)) were studied in single-molecule experiments. Under ATP-saturated concentrations, high-speed imaging of a single 40-nm gold bead attached to the gamma subunit of bMF(1) showed 2 types of intervening pauses during the rotation that were discriminated by short dwell and long dwell. Using ATP gamma S as a slowly hydrolyzing ATP derivative as well as using a functional mutant beta E188D with slowed ATP hydrolysis, the 2 pausing events were distinctively identified. Buffer-exchange experiments with a nonhydrolyzable analog (AMP-PNP) revealed that the long dwell corresponds to the catalytic dwell, that is, the waiting state for hydrolysis, while it remains elusive which catalytic state short pause represents. The angular position of catalytic dwell was determined to be at +80 degrees from the ATP-binding angle, mostly consistent with other F(1)s. The position of short dwell was found at 50 to 60 degrees from catalytic dwell, that is, +10 to 20 degrees from the ATP-binding angle. This is a distinct difference from human mitochondrial F-1, which also shows intervening dwell that probably corresponds to the short dwell of bMF(1), at +65 degrees from the binding pause. Furthermore, we conducted stall-and-release experiments with magnetic tweezers to reveal how the binding affinity and hydrolysis equilibrium are modulated by the gamma rotation. Similar to thermophilic F-1, bMF(1) showed a strong exponential increase in ATP affinity, while the hydrolysis equilibrium did not change significantly. This indicates that the ATP binding process generates larger torque than the hydrolysis process.
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| 7. |
- Sakamoto, Kazuyuki, et al.
(författare)
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Core-level photoemission study of thallium adsorbed on a Si(111)-(7×7) surface : Valence state of thallium and the charge state of surface Si atoms
- 2006
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 74:7, s. 075335-
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Tidskriftsartikel (refereegranskat)abstract
- The coverage-dependent valence state of Tl adsorbed on a Si(111)-(7×7) surface and the coverage dependence of the charge states of surface Si atoms have been investigated by high-resolution core-level photoelectron spectroscopy. Although two different reconstructions were observed in low-energy electron diffraction at different coverages, a (1×1) pattern at a Tl coverage of 1 monolayer (ML) and a (√3×√3) pattern at a coverage of 1∕3 ML, the binding energy of the Tl 5d core-level was the same at Tl coverages up to 1 ML. Taking the valence state on a (1×1) surface reported in the literature into account, we conclude that the valence state of Tl is 1+, and that the 6s2 electrons of Tl are inactive as an inert pair in the Tl-Si bonding on a Si(111) surface at a coverage of 1 ML and below. In the Si 2p core-level spectra, one surface component was observed on the (1×1) surface, and three surface components were observed on the (√3×√3) surface. The binding energies and intensities of the Si 2p surface components indicate that the charge state of the surface Si atoms on Tl∕Si(111)-(1×1) is the same as that of the (√3×√3) surfaces induced by the other group III metals, but they are different on the Tl∕Si(111)-(√3×√3) surface.
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| 8. |
- Watanabe, Ryo R., et al.
(författare)
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Rotary properties of hybrid F1-ATPases consisting of subunits from different species
- 2023
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Ingår i: iScience. - 2589-0042. ; 26:5
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Tidskriftsartikel (refereegranskat)abstract
- F-1-ATPase (F-1) is an ATP-driven rotary motor protein ubiquitously found in many species as the catalytic portion of FoF1-ATP synthase. Despite the highly conserved amino acid sequence of the catalytic core subunits: alpha and beta, F-1 shows diversity in the maximum catalytic turnover rate V-max and the number of rotary steps per turn. To study the design principle of F-1, we prepared eight hybrid F(1)s composed of subunits from two of three genuine (F)1s: thermophilic Bacillus PS3 (TF1), bovine mitochondria (bMF(1)), and Paracoccus denitrificans (PdF1), differing in the V-max and the number of rotary steps. The V-max of the hybrids can be well fitted by a quadratic model highlighting the dominant roles of 0 and the couplings between alpha-beta. Although there exist no simple rules on which subunit dominantly determines the number of steps, our findings show that the stepping behavior is characterized by the combination of all subunits.
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