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- 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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- Lensink, Marc F., et al.
(författare)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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- Chr Germs, W., et al.
(författare)
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Unusual Thermoelectric Behavior Indicating a Hopping to Bandlike Transport Transition in Pentacene
- 2012
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 109:1
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Tidskriftsartikel (refereegranskat)abstract
- An unusual increase in the Seebeck coefficient with increasing charge carrier density is observed in pentacene thin film transistors. This behavior is interpreted as being due to a transition from hopping transport in static localized states to bandlike transport, occurring at temperatures below similar to 250 K. Such a transition can be expected for organic materials in which both static energetic disorder and dynamic positional disorder are important. While clearly visible in the temperature and density dependent Seebeck coefficient, the transition hardly shows up in the charge carrier mobility.
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- Guo, J.-H., et al.
(författare)
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How the phenyle rings (benzene) act as building blocks in pi conjugated polymers
- 1998
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Ingår i: Advanced Light Source. - Berkeley : Ernest Orlando Lawrence Berkeley National Laboratory, University of California Berkeley, California, USA. ; , s. 129-132
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Organic conjugated polymers have the electronic structure of semiconductors and can be doped to become good conductors (1). Conjugated polymers are now used as active materials in a wide variety of prototype applications such as light emitting diodes [2] and organic transistors [3,4]. Most of the interesting chemistry and physics of conjugated polymers is associated with the details of the electronic structure at the valence and conduction band edges and, in this connection, various electron spectroscopies can be used as tools for diagnosis of the relevant electronic and geometric properties....
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- Guo, J.-H., et al.
(författare)
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Resonant and nonresonant x-ray scattering spectra of some poly(phenylenevinylene)s
- 1998
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 108:14, s. 5990-5996
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Tidskriftsartikel (refereegranskat)abstract
- The electronic structure of some poly(phenylenevinylene)s have been investigated by resonant and nonresonant x-ray inelastic scattering spectroscopies. The nonresonant as well as all resonant spectra for each polymer demonstrate benzene-like features, indicating a local character of the x-ray emission in which the phenyl ring acts as a building block. Theoretical simulations of x-ray energies and intensities taking the repeat unit as a model molecule of the polymer agree with the experimental spectra fairly well. The edges of the occupied bands have been identified in the nonresonant spectra of each polymer. By subtracting the emission energy of the highest occupied molecular orbital in the nonresonant spectrum from the core excitation energy in the resonant spectrum an alternative way to determine the optical band gap is obtained. As for free benzene the outer π band in the polymer spectra show a depletion of the emission going from the nonresonant to the resonant x-ray emission spectra. It is demonstrated that this transition, which is strictly symmetry forbidden for free benzene, becomes effectively forbidden in the polymer case as a result of strong interference effects, and it is argued that this is the general case for resonant x-ray emission of conjugated polymers as far as the frozen orbital approximation holds.
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- Tong, Chuan, et al.
(författare)
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Annual CO2 and CH4 fluxes in coastal earthen ponds with Litopenaeus vannamei in southeastern China
- 2021
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Ingår i: Aquaculture. - : ELSEVIER. - 0044-8486 .- 1873-5622. ; 545
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Tidskriftsartikel (refereegranskat)abstract
- Small-scale aquaculture operation is being increasing practised around the world, particularly in the developing countries, but the greenhouse gas (GHG) dynamics and fluxes from small aquaculture ponds are still poorly assessed. In this study, the dissolved concentrations and fluxes of CO2 and CH4 were determined in three coastal earthen shrimp ponds over one whole year, covering both the farming and non-farming periods, in the Min River Estuary, southeastern China. Both ebullitive and diffusive CH4 fluxes were measured, which were rarely done in previous studies. The average concentrations of dissolved CO2 and CH4 in water column in the farming period varied between 18.1 +/- 0.1 and 79.6 +/- 1.1 mu mol L-1, and 1.3 +/- 0.1 and 55.9 +/- 3.2 mu mol L-1, respectively. When averaged across the whole year, the mean CO2 and CH4 fluxes from the ponds were - 18.4 +/- 7.4 and 22.6 +/- 6.9 mg m- 2 h-1, respectively, suggesting that the shrimp ponds acted as a CO2 sink and a CH4 source. Based on the sustained-flux global warming potential (SGWP) and sustained-flux global cooling potential (SGCP) models, the annual warming potential was estimated to be 7.1 x 103 g CO2-eq m- 2 yr- 1, with approximately 90% of this arising from the farming period. Ebullition was the dominant emission pathway for CH4, accounting for over 90% of the total CH4 emission during the farming period. This full-year study improves our understanding of carbon cycling in coastal aquaculture ponds and provides a scientific basis for updating the GHG inventories.
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