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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. |
- 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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| 4. |
- Feng, Jia-Jin, et al.
(författare)
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Quantum Computing by Coherent Cooling
- 2022
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - 2469-9926 .- 2469-9934. ; 105:5
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Tidskriftsartikel (refereegranskat)abstract
- Interesting problems in quantum computation take the form of finding low-energy states of (pseudo)spin systems with engineered Hamiltonians that encode the problem data. Motivated by the practical possibility of producing very low-temperature spin systems, we propose and exemplify the possibility to compute by coupling the computational spins to a quantum coherent bath that serves as a heat sink. The quantum tunneling effect provides additional cooling channels to accelerate the cooling process. We demonstrate both analytically and numerically that this strategy can achieve a quantum advantage in the unstructured search problem.
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| 5. |
- Gu, Shi-Ran, et al.
(författare)
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Phylogeny and re-circumscription of Cheniella (Leguminosae: Cercidoideae) based on plastome data and morphology, with description of three new species
- 2024
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Ingår i: TAXON. - 0040-0262 .- 1996-8175. ; 73:2, s. 475-502
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Tidskriftsartikel (refereegranskat)abstract
- Subfamily Cercidoideae is an early-diverging lineage of Leguminosae, within which the number and classification of genera have been controversial. Cheniella is a recently described genus in the Cercidoideae which requires revision and testing of its monophyly and circumscription. Here we infer the phylogenetic position and infrageneric relationships of Cheniella as well as the intergeneric relationships of Cercidoideae using 48 newly sequenced plastid genomes, including 34 individuals representing all species of Cheniella. Our phylogenetic analyses yield a well-resolved tree of Cercidoideae with robust support at most nodes. We also present morphological studies through field work and herbarium studies to re-assess the classification and circumscription of the genus. Based on the results of molecular analyses and morphological studies combined with distribution data, we broaden the circumscription of Cheniella to comprise a total of 15 species and 3 subspecies, including three new species (C. hechiensis, C. longistaminea, C. pubicarpa), one new combination (C. tianlinensis) and one new status and combination (C. longipes).
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| 6. |
- Peng, Xu-Biao, et al.
(författare)
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Application of topological soliton in modeling protein folding : Recent progress and perspective
- 2020
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Ingår i: Chinese Physics B. - : IOP Publishing. - 1674-1056. ; 29:10
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Forskningsöversikt (refereegranskat)abstract
- Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one of the main tasks in modern biophysics. Coarse-grained methods play an increasingly important role in the simulation of protein folding, especially for large proteins. In recent years, we proposed a novel coarse-grained method derived from the topological soliton model, in terms of the backbone C(alpha)chain. In this review, we will first systematically address the theoretical method of topological soliton. Then some successful applications will be displayed, including the thermodynamics simulation of protein folding, the property analysis of dynamic conformations, and the multi-scale simulation scheme. Finally, we will give a perspective on the development and application of topological soliton.
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| 7. |
- Xu, Buqing, et al.
(författare)
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Compound-Specific Radiocarbon Analysis of Low Molecular Weight Dicarboxylic Acids in Ambient Aerosols Using Preparative Gas Chromatography : Method Development
- 2021
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Ingår i: Environmental Science and Technology Letters. - : American Chemical Society (ACS). - 2328-8930. ; 8:2, s. 135-141
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Tidskriftsartikel (refereegranskat)abstract
- Low molecular weight dicarboxylic acids constitute a large fraction of atmospheric organic aerosols, which impact atmospheric radiative forcing and hence Earth's climate. Radiocarbon (C-14) is a unique approach to unambiguously distinguishing the relative contributions of biomass-derived and fossil sources. Here, we developed a compound-specific radiocarbon analysis (CSRA) method for individual dicarboxylic acids in atmospheric particulates. Specifically, the method starts with a dibutyl ester derivatization technique, followed by separation and harvesting of single compounds employing AIMS a preparative capillary gas chromatography in sufficient amounts for offline C-14 measurement with accelerator mass spectrometry. The optimized preparative steps yielded recoveries of >60% and purities of >99% for target molecules. The radiocarbon isotope compositions determined for reference standards taken through the entire method agree well with the original composition of each standard (R-2 = 0.9998). The applicability of the approach was demonstrated with ambient aerosol samples representing contrasting air mass regimes. This yielded two radically different yet system-consistent precursor sources. A minimum size of 50 mu g of C of ambient dicarboxylic acids is needed for credible C-14 measurement. The established method for CSRA of dicarboxylic acids demonstrates a new analytical dimension for studies of the source and evolution of atmospheric secondary organic aerosols.
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| 8. |
- Zhang, Jing, et al.
(författare)
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Adaptive Laboratory Evolution of Halomonas bluephagenesis Enhances Acetate Tolerance and Utilization to Produce Poly(3-hydroxybutyrate)
- 2022
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Ingår i: Molecules. - : MDPI AG. - 1420-3049 .- 1420-3049. ; 27:9
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Tidskriftsartikel (refereegranskat)abstract
- Acetate is a promising economical and sustainable carbon source for bioproduction, but it is also a known cell-growth inhibitor. In this study, adaptive laboratory evolution (ALE) with acetate as selective pressure was applied to Halomonas bluephagenesis TD1.0, a fast-growing and contamination-resistant halophilic bacterium that naturally accumulates poly(3-hydroxybutyrate) (PHB). After 71 transfers, the evolved strain, B71, was isolated, which not only showed better fitness (in terms of tolerance and utilization rate) to high concentrations of acetate but also produced a higher PHB titer compared with the parental strain TD1.0. Subsequently, overexpression of acetyl-CoA synthetase (ACS) in B71 resulted in a further increase in acetate utilization but a decrease in PHB production. Through whole-genome resequencing, it was speculated that genetic mutations (single-nucleotide variation (SNV) in phaB, mdh, and the upstream of OmpA, and insertion of TolA) in B71 might contribute to its improved acetate adaptability and PHB production. Finally, in a 5 L bioreactor with intermittent feeding of acetic acid, B71 was able to produce 49.79 g/L PHB and 70.01 g/L dry cell mass, which were 147.2% and 82.32% higher than those of TD1.0, respectively. These results highlight that ALE provides a reliable method to harness H. bluephagenesis to metabolize acetate for the production of PHB or other high-value chemicals more efficiently.
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| 9. |
- Zhang, Li, et al.
(författare)
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Characterization of anti-BCG benz[α]anthraquinones and new siderophores from a Xinjiang desert-isolated rare actinomycete Nocardia sp. XJ31
- 2020
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 104:19, s. 8267-8278
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Tidskriftsartikel (refereegranskat)abstract
- The current global demand for novel anti-TB drugs has drawn urgent attention on the discovery of natural product compounds with anti-TB activity. Lots of efforts have emphasized on environmental samples from unexplored or underexplored natural habits and identified numerous rare actinomycete taxa producing structurally diverse bioactive natural products. Herein, we report a survey of the rare actinobacteria diversity in Xinjiang region together with the discovery of anti-TB active natural products from these strains. We have collected 17 soil samples at different sites with different environmental conditions, from which 39 rare actinobacteria were identified by using a selective isolation strategy with 5 media variations. Among those isolated strains, XJ31 was identified as a new Nocardia sp. based on 16S rRNA gene analysis. Through one strain-many compounds (OSMAC) strategy combined with anti-Bacillus Calmette-Guérin bioassay-guided isolation, two groups of compounds were identified. They were twelve siderophores (nocardimicins, 1-12) and two anthraquinones (brasiliquinones, 13 and 14) and ten of them were identified as new compounds. The structures of the purified compounds were elucidated using HR-ESI-MS, 1D NMR, and 2D NMR techniques. The anti-TB bioassays revealed that the two benz[α]anthraquinones have potent activity against BCG (MICs = 25 μM), which can be used as a promising start point for further anti-TB drug development.
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