| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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. |
- Chen, Peng, et al.
(author)
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Assembly of Graphene Oxide and Au(0.7)Ag(0.3) Alloy Nanoparticles on SiO(2): A New Raman Substrate with Ultrahigh Signal-to-Background Ratio
- 2011
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In: The Journal of Physical Chemistry C. - : American Chemical Society. - 1932-7447 .- 1932-7455. ; 115:49, s. 24080-24084
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Journal article (peer-reviewed)abstract
- Resonance Raman spectroscopy (RRS) often suffers from the large fluorescence background which obscures the much weaker Raman scattering. To address this fundamental problem, a novel Raman substrate has been fabricated by adsorption of Au(0.7)Ag(0.3) alloy nanoparticles (NPs) on a graphene oxide (GO) coated SiO(2) surface, which offers both excellent Raman enhancement and fluorescence quenching. Our experimental data reveal that a Raman to fluorescence background intensity ratio of 1.6 can be obtained for a highly fluorescent dye like Alexa fluor 488. Moreover, we demonstrate that the Raman enhancement mainly originates from the Au(0.7)Ag(0.3) alloy NPs and that the fluorescence quenching mainly arises from the underlying functionalized GO (FGO) substrate.
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| 4. |
- Chen, Zhiqiang, et al.
(author)
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Inheritance of growth and solid wood quality traits in a large Norway spruce population tested at two locations in southern Sweden
- 2014
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In: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 10:5, s. 1291-1303
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Journal article (peer-reviewed)abstract
- Unfavorable genetic correlations between growth and wood quality traits are one of the biggest challenges in advanced conifer breeding programs. To examine and deal with such correlation, increment cores were sampled at breast height from 5,618 trees in 524 open-pollinated families in two 21-year-old Norway spruce progeny trials in southern Sweden, and age trends of genetic variation, genetic correlation, and efficiency of selection were investigated. Wood quality traits were measured on 12-mm increment cores using SilviScan. Heritability was moderate (~0.4-0.5) for wood density and modulus of elasticity (MOE) but low (~0.2) for microfibril angle (MFA). Different age trends were observed for wood density, MFA, and MOE, and the lower heritability of MFA relative to wood density and MOE in Norway spruce contrasted with general trends of the three wood quality traits in pine. Genetic correlations among growth, wood density, MFA, and MOE increased to a considerably high value from pith to bark with unfavorable genetic correlations (−0.6 between growth and wood density, −0.74 between growth and MOE). Age-age genetic correlations reached 0.9 after ring 4 for diameter at breast height (DBH), wood density, MFA, and MOE traits. Early selections at ring 10 for diameter and at ring 6 or 7 for wood quality traits had similar effectiveness as selection conducted at reference ring 15. Selection based on diameter alone produced 19.0 % genetic gain in diameter but resulted in 4.8 % decrease in wood density, 9.4 % decrease in MOE, and 8.0 % increase in MFA. Index selection with a restriction of no change in wood density, MOE, and MFA, respectively, produced relatively lower genetic gains in diameter (16.4, 12.2, and 14.1 %, respectively), indicating such index selection could be implemented to maintain current wood density. Index selection using economic weights is, however, recommended for maximum economic efficiency
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| 5. |
- Cui, Wen, et al.
(author)
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Synthesis of alkali-metal-doped C60 nanotubes
- 2011
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In: Diamond and Related Materials. - : Elsevier BV. ; , s. 93-96
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Conference paper (peer-reviewed)abstract
- C60 nanotubes have been synthesized by a solution–solution method. After degassing in a dynamic vacuum, the C60 nanotubes were doped with alkali metals by means of vapor evaporation method. Different temperatures have been studied to evaporate the alkali metals for the doping experiments. Raman spectrum was further employed to analyze the doping concentration of the obtained samples. It was found that all three alkali metals (Li, Na and K) used can be efficiently doped into the C60 nanotubes, forming AxC60 nanotubes. The doping concentration of Li, Na changed from low to high level, depending on the experiment temperatures, while K doping always gave saturated doping. The melt points, the ionic sizes and vapor pressures of alkali metals were thought to affect the final doping results.
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| 6. |
- Gu, Dong, et al.
(author)
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Growth of Single-Crystal Mesoporous Carbons with Im(3)over-barm Symmetry
- 2010
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In: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 22:16, s. 4828-4833
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Journal article (peer-reviewed)abstract
- Highly ordered mesoporous carbon FDU-16 rhombic dodecahedral single crystals with body-centered cubic structure (space group Im (3) over barm) have been successfully synthesized by employing an organic-organic assembly of triblock copolymer Pluronic F127 (EO106PO70EO106) and phenol/formaldehyde resol in basic aqueous solution. Synthetic factors (including reaction time, temperature, and stirring rate) are explored for controlling the formation of rhombic dodecahedral single crystals. The optimal stirring rate and the reaction temperature are 300 +/- 10 rpm and similar to 66 degrees C, respectively. High-resolution scanning electron microscopy (HRSEM), scanning transmission electron microscopy (STEM), and ultramicrotomy are applied to study the fine structures of the carbon single crystals. The mesopores are arranged in body-centered cubic symmetry throughout the entire particle. Surface steps are clearly observed in the {110} surface, which suggests a layer-by-layer growth of the mesoporous carbon FDU-16 single crystals. Cryo-SEM results from the reactant solution confirm the formation of resol/F127 unit micelles, further supporting the layer-by-layer growth process. The mesoporous carbon FDU-16 single crystals grow up to the final size of 2-4 mu m within 2 days. These findings may have consequences for the growth mechanism of other carbon materials in aqueous solution; moreover, the high-quality single crystals also have potential applications in nanodevice technologies.
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| 7. |
- Jarvis, Erich D., et al.
(author)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Journal article (peer-reviewed)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 8. |
- Kilpeläinen, Tuomas O, et al.
(author)
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Physical activity attenuates the influence of FTO variants on obesity risk: a meta-analysis of 218,166 adults and 19,268 children.
- 2011
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In: PLoS medicine. - : Public Library of Science (PLoS). - 1549-1676 .- 1549-1277. ; 8:11
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Journal article (peer-reviewed)abstract
- BACKGROUND: The FTO gene harbors the strongest known susceptibility locus for obesity. While many individual studies have suggested that physical activity (PA) may attenuate the effect of FTO on obesity risk, other studies have not been able to confirm this interaction. To confirm or refute unambiguously whether PA attenuates the association of FTO with obesity risk, we meta-analyzed data from 45 studies of adults (n=218,166) and nine studies of children and adolescents (n=19,268). METHODS AND FINDINGS: All studies identified to have data on the FTO rs9939609 variant (or any proxy [r(2)>0.8]) and PA were invited to participate, regardless of ethnicity or age of the participants. PA was standardized by categorizing it into a dichotomous variable (physically inactive versus active) in each study. Overall, 25% of adults and 13% of children were categorized as inactive. Interaction analyses were performed within each study by including the FTO×PA interaction term in an additive model, adjusting for age and sex. Subsequently, random effects meta-analysis was used to pool the interaction terms. In adults, the minor (A-) allele of rs9939609 increased the odds of obesity by 1.23-fold/allele (95% CI 1.20-1.26), but PA attenuated this effect (p(interaction) =0.001). More specifically, the minor allele of rs9939609 increased the odds of obesity less in the physically active group (odds ratio =1.22/allele, 95% CI 1.19-1.25) than in the inactive group (odds ratio =1.30/allele, 95% CI 1.24-1.36). No such interaction was found in children and adolescents. CONCLUSIONS: The association of the FTO risk allele with the odds of obesity is attenuated by 27% in physically active adults, highlighting the importance of PA in particular in those genetically predisposed to obesity.
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| 9. |
- Li, Zhong-Yu, et al.
(author)
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Restricted Rotation of sigma-Bonds through a Rigidified Donor Structure to Increase the ICT Ability of Platinum-Acetylide-Based DSSCs
- 2013
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In: Chemistry - An Asian Journal. - : Wiley. - 1861-4728 .- 1861-471X. ; 8:11, s. 2660-2669
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Journal article (peer-reviewed)abstract
- A series of new triarylamine-based platinum-acetylide complexes (WYs) have been designed and synthesized as new sensitizers for applications in dye-sensitized solar cells (DSSCs). With the aim of investigating the effect of a rigidifying donor structure on the photoelectrical parameters of the corresponding DSSCs, two new sensitizers, WY1 and WY2, with rigid and coplanar fluorene units as an electron donor, were prepared. Moreover, two sensitizers that contained triphenylamine units as an electron donor, WY3 and WY4, were also synthesized for comparison. The photo- and electrochemical properties of all of these new complexes have been extensively explored. We found that the dimethyl-fluorene unit exhibited a stronger electron-donating ability and better photovoltaic performance compared to the triphenylamine unit, owing to its rigidifying structure, which restricted the rotation of sigma bonds, thus increasing the conjugation efficiency. Furthermore, WY2, which contained a dimethyl-fluorene unit as an electron donor and bithiophene as a bridge, showed a relatively high open-circuit voltage (V-oc) of 640mV and a PCE of 4.09%. This work has not only expanded the choice of platinum-acetylide sensitizers, but also demonstrates the advantages of restricted rotation of donor sigma bonds for improved behavior of the corresponding DSSCs.
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| 10. |
- Lock, Nina, et al.
(author)
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Scrutinizing negative thermal expansion in MOF-5 by scattering techniques and ab initio calculations
- 2013
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In: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9234. ; 42:6, s. 1996-2007
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Journal article (peer-reviewed)abstract
- Complementary experimental techniques and ab initio calculations were used to determine the origin and nature of negative thermal expansion (NTE) in the archetype metal-organic framework MOF-5 (Zn4O(1,4-benzenedicarboxylate) (3)). The organic linker was probed by inelastic neutron scattering under vacuum and at a gas pressure of 175 bar to distinguish between the pressure and temperature responses of the framework motions, and the local structure of the metal centers was studied by X-ray absorption spectroscopy. Multi-temperature powder-and single-crystal X-ray and neutron diffraction was used to characterize the polymeric nature of the sample and to quantify NTE over the large temperature range 4-400 K. Ab initio calculations complement the experimental data with detailed information on vibrational motions in the framework and their correlations. A uniform and comprehensive picture of NTE in MOF-5 has been drawn, and we provide direct evidence that the main contributor to NTE is translational transverse motion of the aromatic ring, which can be dampened by applying a gas pressure to the sample. The linker motion is highly correlated rather than local in nature. The relative energies of different framework vibrations populated in MOF-5 are suggested by analysis of neutron diffraction data. We note that the lowest-energy motion is a librational motion of the aromatic ring which does not contribute to NTE. The libration is followed by transverse motion of the linker and the carboxylate group. These motions result in unit-cell contraction with increasing temperature.
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