| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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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.
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| 2. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 3. |
- Deng, Min, et al.
(författare)
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Genome-wide association analyses in Han Chinese identify two new susceptibility loci for amyotrophic lateral sclerosis
- 2013
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 45:6, s. 697-
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Tidskriftsartikel (refereegranskat)abstract
- To identify susceptibility genes for amyotrophic lateral sclerosis (ALS), we conducted a genome-wide association study (GWAS) in 506 individuals with sporadic ALS and 1,859 controls of Han Chinese ancestry. Ninety top SNPs suggested by the current GWAS and 6 SNPs identified by previous GWAS were analyzed in an independent cohort of 706 individuals with ALS and 1,777 controls of Han Chinese ancestry. We discovered two new susceptibility loci for ALS at 1q32 (CAMK1G, rs6703183, P-combined = 2.92 x 10(-8), odds ratio (OR) = 1.31) and 22p11 (CABIN1 and SUSD2, rs8141797, P-combined = 2.35 x 10(-9), OR = 1.52). These two loci explain 12.48% of the overall variance in disease risk in the Han Chinese population. We found no association evidence for the previously reported loci in the Han Chinese population, suggesting genetic heterogeneity of disease susceptibility for ALS between ancestry groups. Our study identifies two new susceptibility loci and suggests new pathogenic mechanisms of ALS.
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| 4. |
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| 5. |
- Chen, Zhi-Hui, et al.
(författare)
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Enhanced normal-direction excitation and emission of dual-emitting quantum dots on a cascaded photonic crystal surface
- 2014
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 6:24, s. 14708-14715
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Tidskriftsartikel (refereegranskat)abstract
- Large normal-direction excitation and emission of dual-emitting quantum dots (QDs) are essential for practical application of QD sensors based on the ratiometric fluorescence response. We have numerically demonstrated an all-dielectric four-layer cascaded photonic crystal (CPC) structure (alternating TiO2 and SiO2/SU8 layers with two dimensional nanoscale patterns in each layer) which is capable of providing normal-direction high Q-factor leaky modes at excitation wavelengths of QDs and two low Q-factor leaky modes coinciding with the two emission peaks of a dual-emitting QD. Normal-direction excitation and far-field emission of the dual-emitting QDs are enhanced significantly when QDs are distributed on/in the top TiO2 layer of the CPC structure, especially in the spatial distribution areas of the resonant leaky modes. QDs can be positioned differently depending on the applications. Positioning QDs on the top TiO2 layer will improve the signal-to-noise ratios of QD biomedical/chemical/temperature sensors, while embedding QDs in the top TiO2 layer will increase the light extraction from the QD light emitting device, making our CPC a versatile optical coupling structure. Our CPC-QD structure is experimentally feasible and robust against the parameter perturbation in real fabrication.
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| 9. |
- Wang, Congying, et al.
(författare)
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Adsorption of deoxyribonucleic acid (DNA) by willow wood biochars produced at different pyrolysis temperatures
- 2014
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Ingår i: Biology and Fertility of Soils. - : Springer Science and Business Media LLC. - 0178-2762 .- 1432-0789. ; 50:1, s. 87-94
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Tidskriftsartikel (refereegranskat)abstract
- Adsorption of DNA by biochars was investigated in the present study. Biochars were produced from air-dried willow wood chips at 300, 400, 500, and 600 A degrees C under limited oxygen supply. The resulting products, referred to as BC300, BC400, BC500, and BC600, respectively, were characterized for their elemental composition, cation exchange capacity (CEC), specific surface areas (SSA), and microporosity. According to a Langmuir isotherm, maximum DNA adsorption capacity of biochars was ranked as BC500 > BC600 > BC400 > BC300. Increasing solution pH (from 4.0 to 9.0) faintly decreased DNA adsorption onto biochars. The addition of Na+, Mg2+, and Ca2+ slightly increased the adsorption of DNA, and the effect decreased by increasing the pyrolysis temperature of biochars, indicating that electrostatic interaction was not the main driving force for DNA adsorption onto those biochars. Correlation analysis showed that SSA and micropore surface area were the main factors influencing DNA adsorption on biochars.
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| 10. |
- Wei, Tao, et al.
(författare)
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Molecular and catalytic characterization of a phi class glutathione transferase from Cathaya argyrophylla
- 2012
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Ingår i: Biochemical Systematics and Ecology. - Oxford : Pergamon Press. - 0305-1978 .- 1873-2925. ; 40, s. 75-85
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Tidskriftsartikel (refereegranskat)abstract
- Plant phi class glutathione transferases (GSTs) play important roles in stress tolerance and detoxification metabolism. This study reports the cloning, expression and biochemical characteristics of a phi GST gene (CaGSTF) from the endemic and endangered conifer Cathaya argyrophylla. The recombinant CaGSTF showed GSH-conjugating activity towards the substrate NED-Cl and CDNB. Kinetic analysis revealed low catalytic efficiency with a k(cat)/K-m(GSH) value of 9.82 mM(-1)S(-1). The CaGSTF proved to be a thermolabile enzyme, at 40 degrees C the enzyme's activity was nearly abolished. Site-directed mutagenesis revealed that Ser12, Lys42, Ile55, Glu67 and Ser68 of CaGSTF are critical components of glutathione-binding sites that contribute to the enzyme's catalytic activity. Compared to other plant phi GSTs and conifer tau GSTs, CaGSTF showed a narrow substrate spectrum, low catalytic efficiency and thermolability. These atypical properties suggest the enzyme may have a limited functional role in the organism's adaptation to environmental stresses in the subtropical regions. (C) 2011 Elsevier Ltd. All rights reserved.
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| 11. |
- Wang, Yuyu, et al.
(författare)
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Potential influence of water level changes on energy flows in a lake food web
- 2011
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Ingår i: Chinese Science Bulletin. - : Springer Science and Business Media LLC. - 1001-6538 .- 1861-9541. ; 56:26, s. 2794-2802
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Tidskriftsartikel (refereegranskat)abstract
- Large seasonal water-level fluctuations may influence isotopic signatures of primary producers and the types and amounts of these potential food sources accessible to aquatic fauna of Poyang Lake, the largest freshwater lake in China. In this study, the isotopic signatures of primary producers and consumers were determined, stable carbon and nitrogen isotope analysis and mixing models were combined to investigate the influence of water levels on the diet and isotopic composition of Poyang Lake fish and invertebrates. Five potential food sources (seston, benthic organic matter, aquatic macrophytes, attached algae, and terrestrial plants), 4 species of invertebrates, and 10 species of fish were collected from the lake area during dry and wet seasons between January 2009 and April 2010. The delta C-13 values of invertebrates and most fish were within the range of delta C-13 values of the potential food sources for both seasons. The delta C-13 values of invertebrates and most fish were lower in the dry season than in the wet season, whereas the delta N-15 values exhibited different patterns for different species. Mixing models indicated that the most important food sources for common lake fauna were seston in the dry season and aquatic macrophytes and terrestrial plants in the wet season. The fauna were more omnivorous in the wet season than in the dry season. The food web dynamics of Poyang Lake are strongly influenced by changes in the abundance and accessibility of different basal food sources that occur because of seasonal flood pulses. The trophic links within the aquatic communities of Poyang Lake are modified by water-level fluctuations.
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| 12. |
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| 13. |
- Zhao, Li Na, et al.
(författare)
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S100A9 induces aggregation-prone conformation in Abeta peptides : a combined experimental and simulation study
- 2013
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Ingår i: RSC Advances. - : RSC Publishing. - 2046-2069. ; 3:46, s. 24081-24089
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Tidskriftsartikel (refereegranskat)abstract
- Inflammation is one of the prominent pathological features in Alzheimer's disease (AD). Recently, there have been various proposed roles of neuroinflammation, such as the driving forces, bystander, byproduct or the neuroprotective response. Notwithstanding these diverse possible mechanisms, experiments have found that S100A9 is one of the pro-inflammatory proteins abundant and over-expressed in the inflammation sites of AD. In this paper, we examine the role of S100A9 in the oligomerization process of A beta peptides by means of replica exchange molecular dynamics simulation and experimental investigations. Our experiments, based on atomic force microscopy and Thioflavin T spectroscopic assays, have clearly indicated that the close interaction between S100A9 and A beta has significantly enhanced the A beta oligomerization. In line with the experimental observation, our simulation studies have revealed that the pro-inflammatory S100A9 protein interacts with the A beta peptides directly, mainly through hydrophobic interactions with the A beta central hydrophobic core region. In addition, the formation of hydrogen bonds between the residues of the S100A9 homodimer and the two ends of the A beta peptides is found to cause a straightening of the A beta(12-24) peptides. A more straight A beta(12-24) peptide with a higher beta-content then may function as a template to induce the folding of new incoming A beta peptides, which leads to the formation of aggregation-prone oligomers.
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