| 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. |
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| 3. |
- Ai, Yuejie, 1982-, et al.
(författare)
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Exploring concerted effects of base pairing and stacking on the excited-state nature of DNA oligonucleotides by DFT and TD-DFT studies
- 2011
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 111:10, s. 2366-2377
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Tidskriftsartikel (refereegranskat)abstract
- We have taken (dA)5, (dT)5, and (dA)5•(dT)5 as model systems to study concerted effects of base pairing and stacking on excited-state nature of DNA oligonucleotides using density functional theory (DFT) and time dependent DFTmethods. The spectroscopic states are determined to be of a partial A →A charge transfernature in the A•T oligonucleotides. The T → T charge-transfer transitionsproduce dark states, which are hidden in the energy region of the steady-stateabsorption spectra. This is different from the previous assignment that the T → Tcharge-transfer transition is responsible for a shoulder at the red side of the first strongabsorption band. The A →T charge-transfer states were predicted to have relativelyhigh energies in the A•T oligonucleotides. The present calculations predict that the T→A charge-transfer states are not involved in the spectra and excited-state dynamics ofthe A•T oligonucleotides. In addition, the influence of base pairing and stacking on thenature of the 1nΠ* and 1ΠΠ* states are discussed in detail.
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| 4. |
- Ai, Yuejie, et al.
(författare)
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Importance of the Intramolecular Hydrogen Bond on the Photochemistry of Anionic Hydroquinone (FADH-) in DNA Photolyase
- 2010
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Ingår i: The Journal of Physical Chemistry Letters. - U. S. A. : American Chemical Society. - 1948-7185. ; 1, s. 743-747
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Tidskriftsartikel (refereegranskat)abstract
- The design of a proper molecular model with a good balance between the size of the model system and the computational capacity is essential for theoretical modeling of biological systems. We have shown in this letter that the often used model system, a lumiflavin (7,8-dimethy-10-methyl-isoalloxazine), can not correctly describe geometrical and electronic structures of FADH− in DNA photolyase. The intramolecular hydrogen bond between the isoalloxazine ring and the ribityl moiety is found to play a significant role in controlling photochemical properties of FADH− in DNA photolyase
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| 5. |
- 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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| 6. |
- Ai, Yue-Jie, et al.
(författare)
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Role of non-Condon vibronic coupling and conformation change on two-photon absorption spectra of green fluorescent protein
- 2013
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Ingår i: Molecular Physics. - : Informa UK Limited. - 0026-8976 .- 1362-3028. ; 111:9-11, s. 1316-1321
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Tidskriftsartikel (refereegranskat)abstract
- Two-photon absorption spectra of green fluorescent proteins (GFPs) often show a blue-shift band compared to their conventional one-photon absorption spectra, which is an intriguing feature that has not been well understood. We present here a systematic study on one- and two-photon spectra of GFP chromophore by means of the density functional response theory and complete active space self-consistent field (CASSCF) methods. It shows that the popular density functional fails to provide correct vibrational progression for the spectra. The non-Condon vibronic coupling, through the localised intrinsic vibrational modes of the chromophore, is responsible for the blue-shift in the TPA spectra. The cis to trans isomerisation can be identified in high-resolution TPA spectra. Our calculations demonstrate that the high level ab initio multiconfigurational CASSCF method, rather than the conventional density functional theory is required for investigating the essential excited-state properties of the GFP chromophore.
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| 7. |
- Ai, Yue-Jie, et al.
(författare)
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Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:44, s. 14096-14102
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Tidskriftsartikel (refereegranskat)abstract
- The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.
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| 8. |
- Ai, Yue-Jie, et al.
(författare)
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Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore
- 2012
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 14:38, s. 13409-13414
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Tidskriftsartikel (refereegranskat)abstract
- We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.
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| 9. |
- Ai, Yue-Jie, et al.
(författare)
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Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair : Similarities and differences
- 2010
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 133:6, s. 064302-
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Tidskriftsartikel (refereegranskat)abstract
- 2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized (1)pi pi(*) excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3464485]
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| 10. |
- Ai, Yuejie, 1982-
(författare)
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Theoretical studies on photophysics and photochemistry of DNA
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Theoretical studies on biological systems like nucleic acid and protein have been widely developed in the past 50 years and will continue to be a topic of interest in forefronts of natural science. In addition to experimental science, computational modeling can give useful information and help us to understand biochemical issues at molecular, atomic and even electronic levels. Deoxyribonucleic acid (DNA), the hereditary basis of life’s genetic identity, has always been major topic of discussions since its structure was built in 1953. However, harmful UV radiation from sunlight can make damage to DNA molecules and eventually give rise to DNA damaging biological consequences, like mutagenesis, carcinogenesis, and cell death. Photostability, photodamage, and photorepair are of vital importance in the photophysics and photochemistry of DNA. In this thesis, we have applied high level computer-aided theoretical methods to explore the underlying mechanisms for these three critical issues of DNA. Special attentions are paid to the following aspects: the properties of the excited states, the design of relevant computational models and the effects of biological environments. We have systematically studied the excited state properties of DNA from single base to base pair and oligonucleotides, where the concerted base pairing and base stacking effects was found to play important roles in DNA photostability. The UV-light induced isomerization mechanism between two photoproducts of DNA photodamage has been revealed in different biological environments. In association with DNA photodamage, the related photorepair processes have been proposed for different lesions in photolyase which is a catalytic enzyme for DNA, and the calculated results well explained the experimental observations. In particular, the internal and external properties of flavin cofactors have been extensively studied by combining the electronic structure and spectroscopic calculations. We have examined the effects of the intramolecular hydrogen bond on spectroscopic properties of flavins. The good agreements with the experimental spectra indicated that the biological self-regulation acted critical role in these biological systems.
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