| 1. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
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.
|
|
| 2. |
- Zhang, S. N., et al.
(författare)
-
The high energy cosmic-radiation detection (HERD) facility onboard China's Space Station
- 2014
-
Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. - 9780819496126
-
Konferensbidrag (refereegranskat)abstract
- The High Energy cosmic-Radiation Detection (HERD) facility is one of several space astronomy payloads of the cosmic lighthouse program onboard China's Space Station, which is planned for operation starting around 2020 for about 10 years. The main scientific objectives of HERD are indirect dark matter search, precise cosmic ray spectrum and composition measurements up to the knee energy, and high energy gamma-ray monitoring and survey. HERD is composed of a 3-D cubic calorimeter (CALO) surrounded by microstrip silicon trackers (STKs) from five sides except the bottom. CALO is made of about 104 cubes of LYSO crystals, corresponding to about 55 radiation lengths and 3 nuclear interaction lengths, respectively. The top STK microstrips of seven X-Y layers are sandwiched with tungsten converters to make precise directional measurements of incoming electrons and gamma-rays. In the baseline design, each of the four side SKTs is made of only three layers microstrips. All STKs will also be used for measuring the charge and incoming directions of cosmic rays, as well as identifying back scattered tracks. With this design, HERD can achieve the following performance: energy resolution of 1% for electrons and gamma-rays beyond 100 GeV, 20% for protons from 100 GeV to 1 PeV; electron/proton separation power better than 10-5; effective geometrical factors of >3 m2sr for electron and diffuse gamma-rays, >2 m2sr for cosmic ray nuclei. R and D is under way for reading out the LYSO signals with optical fiber coupled to image intensified CCD and the prototype of one layer of CALO.
|
|
| 3. |
- Bryan, Samantha J., et al.
(författare)
-
Localisation and interaction of the Vipp1 protein in cyanobacteria
- 2014
-
Ingår i: Molecular Microbiology. - : John Wiley & Sons. - 0950-382X .- 1365-2958. ; 94:5, s. 1179-1195
-
Tidskriftsartikel (refereegranskat)abstract
- The Vipp1 protein is essential in cyanobacteria and chloroplasts for the maintenance of photosynthetic function and thylakoid membrane architecture. To investigate its mode of action we generated strains of the cyanobacteria Synechocystis sp. PCC6803 and Synechococcus sp. PCC7942 in which Vipp1 was tagged with green fluorescent protein at the C-terminus and expressed from the native chromosomal locus. There was little perturbation of function. Live-cell fluorescence imaging shows dramatic relocalisation of Vipp1 under high light. Under low light, Vipp1 is predominantly dispersed in the cytoplasm with occasional concentrations at the outer periphery of the thylakoid membranes. High light induces Vipp1 coalescence into localised puncta within minutes, with net relocation of Vipp1 to the vicinity of the cytoplasmic membrane and the thylakoid membranes. Pull-downs and mass spectrometry identify an extensive collection of proteins that are directly or indirectly associated with Vipp1 only after high-light exposure. These include not only photosynthetic and stress-related proteins but also RNA-processing, translation and protein assembly factors. This suggests that the Vipp1 puncta could be involved in protein assembly. One possibility is that Vipp1 is involved in the formation of stress-induced localised protein assembly centres, enabling enhanced protein synthesis and delivery to membranes under stress conditions.
|
|
| 4. |
- Chen, Mei-Qin, et al.
(författare)
-
Arabidopsis NMD3 is required for nuclear export of 60S ribosomal subunits and affects secondary cell wall thickening
- 2012
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:4, s. 35904-35904
-
Tidskriftsartikel (refereegranskat)abstract
- NMD3 is required for nuclear export of the 60S ribosomal subunit in yeast and vertebrate cells, but no corresponding function of NMD3 has been reported in plants. Here we report that Arabidopsis thaliana NMD3 (AtNMD3) showed a similar function in the nuclear export of the 60S ribosomal subunit. Interference with AtNMD3 function by overexpressing a truncated dominant negative form of the protein lacking the nuclear export signal sequence caused retainment of the 60S ribosomal subunits in the nuclei. More interestingly, the transgenic Arabidopsis with dominant negative interference of AtNMD3 function showed a striking failure of secondary cell wall thickening, consistent with the altered expression of related genes and composition of cell wall components. Observation of a significant decrease of rough endoplasmic reticulum (RER) in the differentiating interfascicular fiber cells of the transgenic plant stems suggested a link between the defective nuclear export of 60S ribosomal subunits and the abnormal formation of the secondary cell wall. These findings not only clarified the evolutionary conservation of NMD3 functions in the nuclear export of 60S ribosomal subunits in yeast, animals and plants, but also revealed a new facet of the regulatory mechanism underlying secondary cell wall thickening in Arabidopsis. This new facet is that the nuclear export of 60S ribosomal subunits and the formation of RER may play regulatory roles in coordinating protein synthesis in cytoplasm and transcription in nuclei.
|
|
| 5. |
- Du, Fang K., et al.
(författare)
-
Direction and extent of organelle DNA introgression between two spruce species in the Qinghai-Tibetan Plateau
- 2011
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 192:4, s. 1024-1033
-
Tidskriftsartikel (refereegranskat)abstract
- A recent model has shown that, during range expansion of one species in a territory already occupied by a related species, introgression should take place preferentially from the resident species towards the invading species and genome components experiencing low rates of gene flow should introgress more readily than those experiencing high rates of gene flow. Here, we use molecular markers from two organelle genomes with contrasted rates of gene flow to test these predictions by examining genetic exchanges between two morphologically distinct spruce Picea species growing in the Qinghai-Tibetan Plateau. The haplotypes from both mitochondrial (mt) DNA and chloroplast (cp) DNA cluster into two distinct lineages that differentiate allopatric populations of the two species. By contrast, in sympatry, the species share the same haplotypes, suggesting interspecific genetic exchanges. As predicted by the neutral model, all sympatric populations of the expanding species had received their maternally inherited mtDNA from the resident species, whereas for paternally inherited cpDNA introgression is more limited and not strictly unidirectional. Our results underscore cryptic introgressions of organelle DNAs in plants and the importance of considering rates of gene flow and range shifts to predict direction and extent of interspecific genetic exchanges.
|
|
| 6. |
- Miao, Quan, et al.
(författare)
-
Dissociative X-ray Lasing
- 2012
-
Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 109:23, s. 233905-
-
Tidskriftsartikel (refereegranskat)abstract
- X-ray lasing is predicted to ensue when molecules are pumped into dissociative core-excited states by a free-electron-laser pulse. The lasing is due to the population inversion created in the neutral dissociation product, and the process features self-trapping of the x-ray pulse at the gain ridge. Simulations performed for the HCl molecule pumped at the 2p(1/2) -> 6 sigma resonance demonstrate that the scheme can be used to create ultrashort coherent x-ray pulses.
|
|
| 7. |
- Quan, Zhiyong, et al.
(författare)
-
Enhanced room temperature magnetoresistance and spin injection from metallic cobalt in Co/ZnO and Co/ZnAlO films
- 2013
-
Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 5:9, s. 3607-3613
-
Tidskriftsartikel (refereegranskat)abstract
- Co/ZnO and Co/ZnAlO films were prepared by depositing ultrathin cobalt layers and semiconductor layers on glass substrates at room temperature. The films consist of metallic Co particles, semiconductor matrix, and an interfacial magnetic semiconductor with the substitution of Co2+ for Zn 2+ in the ZnO lattice at the interface between Co particles and the semiconductor matrix. Large room temperature negative tunneling magnetoresistance was observed in the films. In addition, the magnetism and magnetoresistance were obviously enhanced by adding aluminum to the ZnO, and in one Co/ZnAlO sample, the room temperature negative magnetoresistance value reaches -12.3% at 18 kOe (compared with -8.4% of the corresponding Co/ZnO film) and the spin polarization of the tunneling electrons is about 37.5% which is characteristic of metallic Co. This enhancement of the tunneling spin polarization has been ascribed to the tunneling through an interfacial magnetic semiconductor, which causes the robust spin injection from cobalt metal into the semiconductors at room temperature resulting from the spin filter effect of the interfacial magnetic semiconductors.
|
|
| 8. |
- Sun, Xian-qiang, et al.
(författare)
-
Structure-based ensemble-QSAR model : a novel approach to the study of the EGFR tyrosine kinase and its inhibitors
- 2014
-
Ingår i: Acta Pharmacologica Sinica. - : Springer Science and Business Media LLC. - 1671-4083 .- 1745-7254. ; 35:2, s. 301-310
-
Tidskriftsartikel (refereegranskat)abstract
- Aim: To develop a novel 3D-QSAR approach for study of the epidermal growth factor receptor tyrosine kinase (EGFR TK) and its inhibitors. Methods: One hundred thirty nine EGFR TK inhibitors were classified into 3 clusters. Ensemble docking of these inhibitors with 19 EGFR TK crystal structures was performed. Three protein structures that showed the best recognition of each cluster were selected based on the docking results. Then, a novel QSAR (ensemble-QSAR) building method was developed based on the ligand conformations determined by the corresponding protein structures. Results: Compared with the 3D-QSAR model, in which the ligand conformations were determined by a single protein structure, ensemble-QSAR exhibited higher R2 (0.87) and Q2 (0.78) values and thus appeared to be a more reliable and better predictive model. Ensemble-QSAR was also able to more accurately describe the interactions between the target and the ligands. Conclusion: The novel ensemble-QSAR model built in this study outperforms the traditional 3D-QSAR model in rationality, and provides a good example of selecting suitable protein structures for docking prediction and for building structure-based QSAR using available protein structures.
|
|
| 9. |
- Zhu, Xuefeng, et al.
(författare)
-
Histone modifications influence mediator interactions with chromatin.
- 2011
-
Ingår i: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 39:19, s. 8342-54
-
Tidskriftsartikel (refereegranskat)abstract
- The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator-histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization.
|
|
