| 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. |
- Weinstein, John N., et al.
(författare)
-
The cancer genome atlas pan-cancer analysis project
- 2013
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
-
Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
|
|
| 3. |
- Li, Yu, et al.
(författare)
-
In situ analysis of Na and K in a laminar premixed flame by laser-induced breakdown spectroscopy
- 2013
-
Ingår i: Chemical Research in Chinese Universities. - : Springer Science and Business Media LLC. - 1005-9040 .- 2210-3171. ; 29:6, s. 1149-1152
-
Tidskriftsartikel (refereegranskat)abstract
- Laser-induced breakdown spectroscopy(LIBS) was used to in situ monitor the concentration of alkali elements in combustion environments. Particular efforts were made to optimize the temporally resolved spectra of Na and K elements. Calibration curves were constructed by relating the intensities of the specific lines to the corresponding elemental concentrations. The detection limits of Na and K elements were found to be temperature-dependent. The results indicate that LIBS can be a powerful tool for in situ monitoring Na and K concentrations in combustion environments.
|
|
| 4. |
- Du, Chun, et al.
(författare)
-
9-Alkylidene-9H-Fluorene-Containing Polymer for High-Efficiency Polymer Solar Cells
- 2011
-
Ingår i: Macromolecules. - : American Chemical Society. - 0024-9297 .- 1520-5835. ; 44:19, s. 7617-7624
-
Tidskriftsartikel (refereegranskat)abstract
- A novel donor-acceptor copolymer containing 9-alkylidene-9H-fluorene unit in the main chain, poly[9-(1-hexylheptylidene)-2,7-fluorene-alt-5, 5-(4,7-di-2-thienyl-5,6-dialkoxy-2,1,3-benzothiadiazole)] (PAFDTBT), has been synthesized and evaluated in bulk heterojunction polymer solar cells (BHJ PSCs). The polymer possesses a low band gap of 1.84 eV, a low-lying HOMO energy level (5.32 eV), and excellent solubility in common organic solvents. PSCs based on PAFDTBT and (6,6)-phenyl-C(71)-butyric add methyl ester (PC(71)BM) demonstrate a power conversion efficiency (PCE) of 6.2% with a high fill factor (FF) of 0.70, which indicates that 9-alkylidene-9H-fluorene can be a very useful building block for constructing narrow band gap conjugated polymers for high-efficiency BHJ PSCs.
|
|
| 5. |
- Lu, Lu, et al.
(författare)
-
Crystal structure of tubulin folding cofactor A from Arabidopsis thaliana and its beta-tubulin binding characterization
- 2010
-
Ingår i: FEBS Letters. - : Wiley. - 1873-3468 .- 0014-5793. ; 584:16, s. 9-3533
-
Tidskriftsartikel (refereegranskat)abstract
- Microtubules are composed of polymerized alpha/beta-tubulin heterodimers. Biogenesis of assembly-competent tubulin dimers is a complex multistep process that requires sequential actions of distinct molecular chaperones and cofactors. Tubulin folding cofactor A (TFCA), which captures beta-tubulin during the folding pathway, has been identified in many organisms. Here, we report the crystal structure of Arabidopsis thaliana TFC A (KIESEL, KIS), which forms a monomeric three-helix bundle. The functional binding analysis demonstrated that KIS interacts with beta-tubulin in plant. Furthermore, mutagenesis studies indicated that the alpha-helical regions of KIS participate in beta-tubulin binding. Unlike the budding yeast TFC A, the two loop regions of KIS are not required for this interaction suggesting a distinct binding mechanism of TFC A to beta-tubulin in plants.
|
|
| 6. |
- Lu, Lu, et al.
(författare)
-
Crystallization and preliminary X-ray analysis of tubulin-folding cofactor A from Arabidopsis thaliana
- 2010
-
Ingår i: Acta Crystallographica. Section F: Structural Biology and Crystallization Communications. - 2053-230X. ; 66:Pt 8, s. 6-954
-
Tidskriftsartikel (refereegranskat)abstract
- Tubulin-folding cofactor A (TFC A) is a molecular post-chaperonin that is involved in the beta-tubulin-folding pathway. It has been identified in many organisms including yeasts, humans and plants. In this work, Arabidopsis thaliana TFC A was expressed in Escherichia coli and purified to homogeneity. After thrombin cleavage, a well diffracting crystal was obtained by the sitting-drop vapour-diffusion method at 289 K. The crystal diffracted to 1.6 A resolution using synchrotron radiation and belonged to space group I4(1), with unit-cell parameters a=55.0, b=55.0, c=67.4 A.
|
|
| 7. |
- Stajich, Jason E., et al.
(författare)
-
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
- 2010
-
Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 107:26, s. 11889-11894
-
Tidskriftsartikel (refereegranskat)abstract
- The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.
|
|
| 8. |
- Sui, Jiong-Ming, et al.
(författare)
-
Isolation and characterization of a stress responsive small GTP-binding protein AhRabG3b in peanut (Arachis hypogaea L.)
- 2013
-
Ingår i: Euphytica. - : Springer Science and Business Media LLC. - 0014-2336 .- 1573-5060. ; 189:2, s. 161-172
-
Tidskriftsartikel (refereegranskat)abstract
- Rab7 is a member of small GTP-binding protein family involved in intracellular vesicle trafficking from late endosome to vacuole, some of them are found to be responsive by different environmental stresses. Here we report the isolation of a Rab7 (RabG3b) cDNA from peanut (Arachis hypogaea). Overexpression of the open reading frame (ORF) of Rab7 cDNA encoding 205 amino acids in E. coli conferred the cells tolerance to various abiotic stresses. Transcription of AhRabG3b was differentially up-regulated by different environmental stimuli such as cold, dehydration, NaCl and the plant hormone ABA. Overexpression of the AhRabG3b exhibited enhanced tolerance to drought and salinity stresses in transgenic peanut. These results suggested that the AhRabG3b be a potential candidate gene responsible for both salinity and dehydration tolerance in cultivated peanut.
|
|
| 9. |
- Chen, Han, et al.
(författare)
-
LTBP-2 confers pleiotropic suppression and promotes dormancy in a growth factor permissive microenvironment in nasopharyngeal carcinoma
- 2012
-
Ingår i: Cancer Letters. - : Elsevier. - 0304-3835 .- 1872-7980. ; 325:1, s. 89-98
-
Tidskriftsartikel (refereegranskat)abstract
- This study identified LTBP-2 as a pleiotropic tumor suppressor in nasopharyngeal carcinoma, which safeguards against critical malignant behaviors of tumor cells. LTBP-2 expression was significantly decreased or lost in up to 100% of NPC cell lines (7/7) and 80% of biopsies (24/30). Promoter hypermethylation was found to be involved in LTBP-2 silencing. Using a tetracycline-regulated inducible expression system, we unveiled functional roles of LTBP-2 in suppressing colony formation, anchorage-independent growth, cell migration, angiogenesis, VEGF secretion, and tumorigenicity. Three-dimensional culture studies suggested the involvement of LTBP-2 in maintenance of tumor cell dormancy in a growth factor favorable microenvironment.
|
|
| 10. |
- Hsu, Chih-Wei, et al.
(författare)
-
Optical properties of functionalized GaN nanowires
- 2011
-
Ingår i: JOURNAL OF APPLIED PHYSICS. - : American Institute of Physics. - 0021-8979 .- 1089-7550. ; 109:5, s. 053523-
-
Tidskriftsartikel (refereegranskat)abstract
- The evolution of the optical properties of GaN nanowires (NWs) with respect to a sequence of surface functionalization processes is reported; from pristine hydroxylated to finally, 3-mercaptopropyltrimethoxysilane (MPTMS) functionalized GaN NWs. Photoluminescence, Raman, stationary, and time-resolved photoluminescence measurements were applied to investigate the GaN NWs with different surface conditions. A documented surface passivation effect of the GaN NWs induced by the MPTMS functionalization is determined based on our characterization results. A hypothesis associated with the surface band bending and the defect levels near the band edges is proposed to explain the observed experimental results.
|
|
