| 1. |
- 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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| 2. |
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| 3. |
- Li, Zhenyu, et al.
(författare)
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How Graphene is Cut upon Oxidation?
- 2009
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 131:18, s. 6320-6321
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Tidskriftsartikel (refereegranskat)abstract
- Our first principles calculations reveal that an oxidative cut of graphene is realized by forming epoxy and then carbonyl pairs. Direct formation of a carbonyl pair to tear graphene up from an edge position is not favorable in energy. This atomic picture is valuable for developing effective means of graphene manipulation. The proposed epoxy pairs may be related to some long puzzling experimental observations on graphene oxide.
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| 4. |
- Shegai, Timur, et al.
(författare)
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Managing light polarization via plasmon-molecule interactions within an asymmetric metal nanoparticle trimer
- 2008
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 105:43, s. 16448-16453
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Tidskriftsartikel (refereegranskat)abstract
- The interaction of light with metal nanoparticles leads to novel phenomena mediated by surface plasmon excitations. In this article we use single molecules to characterize the interaction of surface plasmons with light, and show that such interaction can strongly modulate the polarization of the emitted light. The simplest nanostructures that enable such polarization modulation are asymmetric silver nanocrystal trimers, where individual Raman scattering molecules are located in the gap between two of the nanoparticles. The third particle breaks the dipolar symmetry of the two-particle junction, generating a wavelength-dependent polarization pattern. Indeed, the scattered light becomes elliptically polarized and its intensity pattern is rotated in the presence of the third particle. We use a combination of spectroscopic observations on single molecules, scanning electron microscope imaging, and generalized Mie theory calculations to provide a full picture of the effect of particles on the polarization of the emitted light. Furthermore, our theoretical analysis allows us to show that the observed phenomenon is very sensitive to the size of the trimer particles and their relative position, suggesting future means for precise control of light polarization on the nanoscale.
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| 5. |
- Wang, Wei, et al.
(författare)
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Ag@SiO2 Core-Shell Nanoparticles for Probing Spatial Distribution of Electromagnetic Field Enhancement via Surface-Enhanced Raman Scattering
- 2009
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-086X .- 1936-0851. ; 3:11, s. 3493-3496
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Tidskriftsartikel (refereegranskat)abstract
- We show that the spatial distribution of the electromagnetic (EM) field enhancement can be probed directly via dynamic evolution of surface-enhanced Raman scattering (SERS) of rhodamine 6G (R6G) molecules as they diffuse into Ag@SiO2 core-shell nanoparticles. The porous silica shell limits the diffusion of R6G molecules toward Inner Ag cores, thereby allowing direct observation and quantification of the spatial distribution of SERS enhancement as molecules migrate from the low to high EM fields inside the dielectric silica shell. Our experimental evidence is validated by the generalized Mie theory, and the approach can potentially offer a novel platform for further investigating the site and spatial distribution of the EM fields and the EM versus chemical enhancement of SERS due to molecular confinement within the Ag@SiO2 nanoshell.
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| 6. |
- Zhang, Wenhua, 1981-, et al.
(författare)
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A first-principles study of NO adsorption and oxidation on Au(111) surface
- 2008
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 129:13, s. 134708-
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Tidskriftsartikel (refereegranskat)abstract
- Density functional theory and slab models are employed to study NO molecule adsorption and reaction on clean and atomic oxygen precovered Au(111) surfaces. While clean Au(111) surface is catalytically inert and can only weakly adsorb NO, an atomic oxygen precovered Au(111) surface is found to be very active to NO. On the clean surface, NO prefers to bond at the onefold on-top surface site with a tilted geometry. On 0.33 ML (monolayer) oxygen precovered surface NO reacts with chemisorbed oxygen to form chemisorbed NO2 by conquering a small energy barrier about 0.18 eV, and the desorption energy of NO 2 is 0.64 eV. On 1.0 ML oxygen coverage surface, no barrier is found while NO reacts with precovered oxygen. The desorption energy of NO2 is 0.03 eV. The desorption of NO2 is the rate determining step on both surfaces and the overall reaction barriers are 0.64 and 0.03 eV, respectively. The activation energies depend on the initial coverage of oxygen, which compare favorably with experiments on Au surface with different oxygen coverages.
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| 7. |
- Zhang, Wenhua, 1981-, et al.
(författare)
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Density Functional Study on the Mechanism of CO Oxidation with Activated Water on O/Au(111) Surface
- 2009
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Ingår i: Chinese Science Bulletin. - : Elsevier BV. - 1001-6538 .- 1861-9541 .- 2095-9273 .- 2095-9281. ; 54:11, s. 1973-1977
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Tidskriftsartikel (refereegranskat)abstract
- With density functional theory, the mechanism of water-enhanced CO oxidation on oxygen pre-covered Au (111) surface is theoretically studied. First, water is activated by the pre-covered oxygen atom and dissociates to OHads group. Then, OHads reacts with COads to form chemisorbed HOCOads. Finally, with the aid of water, HOCO ads dissociates to CO2. The whole process can be described as 1/2H2O ads + H2Oads + 1/2O ads + COads → H3Oads + CO 2, gas. One CO2 is formed with only 1/2 pre-covered oxygen atom. That is why more CO2 is observed when water is present on oxygen pre-covered Au (111) surface. Activation energy of each elementary step is low enough to allow the reaction to proceed at low temperature
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| 8. |
- Zhang, Wenhua, et al.
(författare)
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First Principles Study on the Geometric and Electronic Structures of the FeO/Pt(111) Surface
- 2009
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 113:19, s. 8302-8305
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Tidskriftsartikel (refereegranskat)abstract
- The geometric, electronic, and magnetic properties of the FeO monolayer on a Pt(111) surface are investigated by first principles calculations. Generally, antiferromagnetic (AFM) structures are more stable than that of the ferromagnetic one. On the basis of a specific AFM structure, the long puzzling scanning tunneling microscopy (STM) experimental observations can be well explained. In this AFM model, the Fe-O layer distance at the fee region is larger than the hcp region, in contrast to previous theoretical results. The STM images at the field-emission regime are explained by local surface potential.
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| 9. |
- Zhang, Wenhua, et al.
(författare)
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Oxidation states of graphene : Insights from computational spectroscopy
- 2009
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 131:24
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Tidskriftsartikel (refereegranskat)abstract
- When it is oxidized, graphite can be easily exfoliated forming graphene oxide (GO). GO is a critical intermediate for massive production of graphene, and it is also an important material with various application potentials. With many different oxidation species randomly distributed on the basal plane, GO has a complicated nonstoichiometric atomic structure that is still not well understood in spite of intensive studies involving many experimental techniques. Controversies often exist in experimental data interpretation. We report here a first principles study on binding energy of carbon 1s orbital in GO. The calculated results can be well used to interpret experimental x-ray photoelectron spectroscopy (XPS) data and provide a unified spectral assignment. Based on the first principles understanding of XPS, a GO structure model containing new oxidation species epoxy pair and epoxy-hydroxy pair is proposed. Our results demonstrate that first principles computational spectroscopy provides a powerful means to investigate GO structure.
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