| 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. |
- Shen, Xi, et al.
(författare)
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REV3 and REV1 play major roles in recombination-independent repair of DNA interstrand cross-links mediated by monoubiquitinated proliferating cell nuclear antigen (PCNA).
- 2006
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Ingår i: The Journal of biological chemistry. - 0021-9258. ; 281:20, s. 13869-72
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Tidskriftsartikel (refereegranskat)abstract
- DNA interstrand cross-links (ICLs) are the most cytotoxic lesions to eukaryotic genome and are repaired by both homologous recombination-dependent and -independent mechanisms. To better understand the role of lesion bypass polymerases in ICL repair, we investigated recombination-independent repair of ICLs in REV3 and REV1 deletion mutants constructed in avian DT40 cells and mouse embryonic fibroblast cells. Our results showed that Rev3 plays a major role in recombination-independent ICL repair, which may account for the extreme sensitivity of REV3 mutants to cross-linking agents. This result raised the possibility that the NER gap synthesis, when encountering an adducted base present in the ICL repair intermediate, can lead to recruitment of Rev3, analogous to the recruitment of polymerase eta during replicative synthesis. Indeed, the monoubiquitination-defective Proliferating Cell Nuclear Antigen (PCNA) mutant exhibits impaired recombination-independent ICL repair as well as drastically reduced mutation rate, indicating that the PCNA switch is utilized to enable lesion bypass during DNA repair synthesis. Analyses of a REV1 deletion mutant also revealed a significant reduction in recombination-independent ICL repair, suggesting that Rev1 cooperates with Rev3 in recombination-independent ICL repair. Moreover, deletion of REV3 or REV1 significantly altered the spectrum of mutations resulting from ICL repair, further confirming their involvement in mutagenic repair of ICLs.
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| 3. |
- Allison, J, et al.
(författare)
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Geant4 developments and applications
- 2006
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Ingår i: IEEE TRANSACTIONS ON NUCLEAR SCIENCE. - 0018-9499. ; 53:1, s. 270-278
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 4. |
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| 5. |
- Christensen, Kirsten E, et al.
(författare)
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A germanate built from 68126 cavity co-templated by a (H2O)16 water cluster and 2-methylpiperazine
- 2008
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Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 47:41, s. 7868-7871
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Tidskriftsartikel (refereegranskat)abstract
- Totally tubular: A new tubular germanate is cotemplated by 2-methylpiperazine and an (H2O)16 cluster in a hydro(solvo)thermal synthesis. The germanate features a large, highly symmetric 68126 cavity (see picture; yellow sphere) built from 12 Ge7X19 (X=O, OH, F) clusters (GeX6 red, GeX5 yellow, GeX4 green).
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| 6. |
- Christensen, Kirsten E., et al.
(författare)
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An open-framework silicogermanate with 26-ring channels built from seven-coordinated (Ge,Si)10(O, OH)28 clusters
- 2008
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 130:12, s. 3758-3759
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Tidskriftsartikel (refereegranskat)abstract
- We report a new open-framework silicogermanate SU-61 containing 26-ring channels with a low framework density. It can be seen as a crystalline analogue to the mesoporous silica MCM-41. The structure is built from the assembly of (Ge,Si)10(O,OH)28 clusters. It is the first time that silicon has been successfully introduced in the Ge10 cluster in significant amounts (21% of the tetrahedral sites). Five- and six-coordinated Ge10 clusters have previously been observed in other germanate compounds leading to either dense or open structures. In SU-61, the seven-coordinated clusters fall onto yet another underlying net, the osf net. SU-61, along with other Ge10 based frameworks, shows the versatility of the germanate system to adopt defined topologies playing on the connectivity of the clusters following the principles of net decoration and scale chemistry.
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| 7. |
- Christensen, Kirsten E., et al.
(författare)
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Open-framework germanates formed by the flexible Ge10 cluster
- 2008
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Ingår i: Zeolites and related materials: Trends, targets and challenges. - Amsterdam : Elsevier. - 9780444532978 ; , s. 317-320
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Konferensbidrag (refereegranskat)abstract
- Open-framework germanates have shown promising results in achieving extra-large pores and channels. Pores that extend to the mesoporous range (>20Å) were reported in SU-M. The structure of SU-M is built by the Ge10X28 (Ge10, X = O, OH, F) clusters. This cluster is also found in Ge-pharmacosiderite, Na4Ge9O20, ICMM-7 and SU-61. The Ge10 cluster has a flexibility to form compounds with both high and very low framework densities.
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| 8. |
- Coulter, John E., et al.
(författare)
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Environment as the stage for economic actors
- 2007
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Ingår i: Chinese Journal of Population, Resources and Environment. - 1004-2857. ; 5:1, s. 3-8
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The relative importance of economics and environment in debate may soon be reversed due to the influence of three factors. Firstly, in the global economy it is hard to hide the unwanted products of economic processes. Secondly, huge advances in science will reduce the imperfect knowledge of markets, making some monitoring and analyzing tools show the design of sensible and equitable livelihood in communities, which is more important than the motivation of maximising profits for some individuals or firms. Thirdly, China, as the last major player on the planet to take on economic growth, comes from traditions fundamentally different from those economies that have experienced the Industrial Revolution previously. Its challenges with sustainability and environmental conservation predate Western economics by millennia, and it is implementing policies domestically and starting to work on the world stage that acknowledges that the surroundings are the host for any economic and socio-political system.
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| 9. |
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| 10. |
- Nascimento, V. B., et al.
(författare)
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Procedure for LEED I-V structural analysis of metal oxide surfaces : Ca1.5Sr0.5RuO4(001)
- 2007
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 75:3, s. 035408-
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Tidskriftsartikel (refereegranskat)abstract
- Transition metal oxides (TMOs) are famous for the intimate coupling between the lattice, electrons, and spin, creating exotic functionality. Creating a surface, breaking the symmetry, should result in lattice distortions that due to the close coupling could create different "surface phases." Historically it has been very difficult to use low energy electron diffraction I-V to quantitatively determine the surface structure of TMOs. A signature of this problem is the large values commonly reported in the literature of the Pendry reliability factor (R-P), which is used to quantify the agreement between experimental data and calculated diffraction. In this paper we describe a consistent procedure for determining the phase shifts using an optimized muffin-tin potential approach combined with an energy-dependent real and imaginary inner potential. This procedure is used to determine the surface structure of the layered TMO Ca1.5Sr0.5RuO4. An acceptable Pendry reliability factor is achieved (R-P=0.28).
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