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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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- 2019
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Tidskriftsartikel (refereegranskat)
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| 7. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 8. |
- Jiang, Shi, et al.
(författare)
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Fe-S complexes containing five-membered heterocycles : novel models for the active site of hydrogenases with unusual low reduction potential
- 2007
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; :8, s. 896-902
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Tidskriftsartikel (refereegranskat)abstract
- Three biomimetic 2Fe2S complexes [{(mu-SCH2)(2)NCH2(2-C4H3O)}](Fe-2(CO)(6)) (6a), [{(mu-SCH2)(2) NCH2(2-C4H3S)}](Fe-2(CO)(6)) (6b) and [{(mu-SCH2)(2)NCH2(5-Br-2-C4H2S)}Fe-2(CO)(6)] (6c) were prepared as models for the active site of Fe-only hydrogenase by the convergent process from [(mu-S-2)Fe-2(CO)(6)] and N,N-bis(hydromethyl)-2-furan and thiophene. The structures of these complexes were identified spectroscopically and crystallographically. The electrochemical behavior of the complexes 6a and 6c was unique as they showed catalytic proton reduction with a low reduction potential at -1.13 and -1.09 V vs Fc/Fc(+), respectively, in the presence of HClO4.
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| 9. |
- Jiang, Shi, et al.
(författare)
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Preparation, characteristics and crystal structures of novel N-heterocyclic carbene substituted furan- and pyridine-containing azadithiolate Fe-S complexes
- 2007
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Ingår i: Polyhedron. - : Elsevier BV. - 0277-5387 .- 1873-3719. ; 26:7, s. 1499-1504
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Tidskriftsartikel (refereegranskat)abstract
- Two novel N-heterocyclic carbene disubstituted furan- and pyridine-containing azadithiolate Fe-only hydrogenase models (2 and 4) have been synthesized, and characterized by IR and H-1 NMR spectra and X-ray single crystal diffraction. Cyclic voltammetry (CV) experiments indicate that they show more negative reductive potentials at -2.53 V and -2.49 V, respectively versus the ferrocene/ferrocenium couple (Fc/Fc(+)) and are easier to capture proton attributing to the strong electron-donating ligand NHC. After the protonation under F3CCO2H the reductive potentials of 2 and 4 have 1.02 V and 0.77 V shifts, indicating the formation of Fe-H-Fe bond. The results also are confirmed by the data changes in IR spectra and the negative H signals are detected by 1H NMR spectra at -27 ppm and -55 ppm.
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| 10. |
- Ai, Yue-Jie, 1982-, et al.
(författare)
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Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase
- 2011
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 115:37, s. 10976-10982
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Tidskriftsartikel (refereegranskat)abstract
- Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.
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