| 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. |
- Chen, Yong, et al.
(författare)
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A Vps21 endocytic module regulates autophagy
- 2014
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Ingår i: Molecular Biology of the Cell. - 1939-4586. ; 25:20, s. 3166-3177
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Tidskriftsartikel (refereegranskat)abstract
- In autophagy, the double-membrane autophagosome delivers cellular components for their degradation in the lysosome. The conserved Ypt/Rab GTPases regulate all cellular trafficking pathways, including autophagy. These GTPases function in modules that include guanine-nucleotide exchange factor (GEF) activators and downstream effectors. Rab7 and its yeast homologue, Ypt7, in the context of such a module, regulate the fusion of both late endosomes and autophagosomes with the lysosome. In yeast, the Rab5-related Vps21 is known for its role in early- to late-endosome transport. Here we show an additional role for Vps21 in autophagy. First, vps21Δ mutant cells are defective in selective and nonselective autophagy. Second, fluorescence and electron microscopy analyses show that vps21Δ mutant cells accumulate clusters of autophagosomal structures outside the vacuole. Third, cells with mutations in other members of the endocytic Vps21 module, including the GEF Vps9 and factors that function downstream of Vps21, Vac1, CORVET, Pep12, and Vps45, are also defective in autophagy and accumulate clusters of autophagosomes. Finally, Vps21 localizes to PAS. We propose that the endocytic Vps21 module also regulates autophagy. These findings support the idea that the two pathways leading to the lysosome—endocytosis and autophagy—converge through the Vps21 and Ypt7 GTPase modules.
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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. |
- Hudson, Thomas J., et al.
(författare)
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International network of cancer genome projects
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7291, s. 993-998
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Tidskriftsartikel (refereegranskat)abstract
- The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
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| 5. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)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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| 6. |
- Lu, Guo-Hui, et al.
(författare)
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Potential exposure of perfluorinated compounds to Chinese in Shenyang and Yangtze River Delta areas
- 2011
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Ingår i: Environmental Chemistry. - : CSIRO Publishing. - 1448-2517 .- 1449-8979. ; 8:4, s. 407-418
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Tidskriftsartikel (refereegranskat)abstract
- Environmental contextA total of 21 perfluorinated compounds (PFCs) including PFOS were quantified in river waters, sewage, sea waters, shallow ground waters as well as fish and domestic poultry, focussed on the main river basins in Shenyang and the Yangtze River Delta areas, China. The distribution characteristics of PFCs in the aquatic environment and evaluation of the potential risk for human health via the diet of fish was discussed. Comprehensive research was carried out using the world leading knowledge about PFOS-related chemicals in AIST, Japan to enable reliable evaluation of PFOS risk in Chinese environments, supported by ISO25101. AbstractA total of 21 perfluorinated compounds (PFCs) were quantified in water and biota samples collected from Shenyang in North-east China and the Yangtze River Delta area in East China. The human health risk owing to intake of perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) via fish and domestic poultry dietary was evaluated. The total PFC concentration (∑PFC) in water samples from the rivers in Shenyang averaged 5.32ngL-1, with PFOS and PFOA as the predominant compounds. The urban sewage could be the source of PFOS and perfluorohexane sulfonate (PFHxS) in the surface waters. The total PFCs in water samples from the Yangtze River Delta area ranged from 42.4 to 170ngL-1. The highest concentrations of most PFCs were observed in waters from the Shanghai section of the Yangtze River. In the biota samples, PFOS and PFUnDA (perfluoroundecanoic acid) were the most abundant. The acceptable daily intake (ADI) and hazard ratio (HR) values for PFOS and PFOA intake through the diet of fish and poultry in the studied areas were calculated, and showed that the HR values for PFOS and PFOA are all less than 1.0 for both the areas.
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| 7. |
- Qi, Qibin, et al.
(författare)
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FTO genetic variants, dietary intake and body mass index : insights from 177 330 individuals
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:25, s. 6961-6972
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Tidskriftsartikel (refereegranskat)abstract
- FTO is the strongest known genetic susceptibility locus for obesity. Experimental studies in animals suggest the potential roles of FTO in regulating food intake. The interactive relation among FTO variants, dietary intake and body mass index (BMI) is complex and results from previous often small-scale studies in humans are highly inconsistent. We performed large-scale analyses based on data from 177 330 adults (154 439 Whites, 5776 African Americans and 17 115 Asians) from 40 studies to examine: (i) the association between the FTO-rs9939609 variant (or a proxy single-nucleotide polymorphism) and total energy and macronutrient intake and (ii) the interaction between the FTO variant and dietary intake on BMI. The minor allele (A-allele) of the FTO-rs9939609 variant was associated with higher BMI in Whites (effect per allele = 0.34 [0.31, 0.37] kg/m(2), P = 1.9 × 10(-105)), and all participants (0.30 [0.30, 0.35] kg/m(2), P = 3.6 × 10(-107)). The BMI-increasing allele of the FTO variant showed a significant association with higher dietary protein intake (effect per allele = 0.08 [0.06, 0.10] %, P = 2.4 × 10(-16)), and relative weak associations with lower total energy intake (-6.4 [-10.1, -2.6] kcal/day, P = 0.001) and lower dietary carbohydrate intake (-0.07 [-0.11, -0.02] %, P = 0.004). The associations with protein (P = 7.5 × 10(-9)) and total energy (P = 0.002) were attenuated but remained significant after adjustment for BMI. We did not find significant interactions between the FTO variant and dietary intake of total energy, protein, carbohydrate or fat on BMI. Our findings suggest a positive association between the BMI-increasing allele of FTO variant and higher dietary protein intake and offer insight into potential link between FTO, dietary protein intake and adiposity.
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| 8. |
- Shen, Yong-Feng, et al.
(författare)
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Deformation mechanisms of a 20Mn TWIP steel investigated by in situ neutron diffraction and TEM
- 2013
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Ingår i: Acta Materialia. - : Elsevier. - 1359-6454 .- 1873-2453. ; 61:16, s. 6093-6106
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Tidskriftsartikel (refereegranskat)abstract
- The deformation mechanisms and associated microstructure changes during tensile loading of an annealed twinning-induced plasticity steel with chemical composition Fe-20Mn-3Si-3Al-0.045C (wt.%) were systematically investigated using in situ time-of-flight neutron diffraction in combination with post mortem transmission electron microscopy (TEM). The initial microstructure of the investigated alloy consists of equiaxed gamma grains with the initial alpha'-phase of similar to 7% in volume. In addition to dislocation slip, twinning and two types of martensitic transformations from the austenite to alpha'- and epsilon-martensites were observed as the main deformation modes during the tensile deformation. In situ neutron diffraction provides a powerful tool for establishing the deformation mode map for elucidating the role of different deformation modes in different strain regions. The critical stress is 520 MPa for the martensitic transformation from austenite to alpha'-martensite, whereas a higher stress (>600 MPa) is required for actuating the deformation twin and/or the martensitic transformation from austenite to epsilon-martensite. Both epsilon- and alpha'-martensites act as hard phases, whereas mechanical twinning contributes to both the strength and the ductility of the studied steel. TEM observations confirmed that the twinning process was facilitated by the parent grains oriented with < 1 1 1 > or < 1 1 0 > parallel to the loading direction. The nucleation and growth of twins are attributed to the pole and self-generation formation mechanisms, as well as the stair-rod cross-slip mechanism.
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| 9. |
- Wang, Yawei, et al.
(författare)
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Distribution of perfluorooctane sulfonate and other perfluorochemicals in the ambient environment around a manufacturing facility in China
- 2010
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 44:21, s. 8062-8067
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Tidskriftsartikel (refereegranskat)abstract
- Perfluorinated compounds (PFCs) can be released to the surrounding environment during manufacturing and usage of PFC containing products, which are considered as main direct sources of PFCs in the environment. This study evaluates the release of perfluorooctane sulfonate (PFOS) and other PFCs to the ambient environment around a manufacturing plant. Among the nine PFCs analyzed, only PFOS, perfluorooctanoic acid (PFOA), and perfluorohexane sulfonate (PFHxS) were found in dust, water, soil, and chicken eggs. Very high concentrations of PFOS and PFOA were found in dust from the production storage, raw material stock room, and sulfonation workshop in the manufacturing facility, with the highest value at 4962 μg/g (dry weight) for PFOS and 160 μg/g for PFOA. A decreasing trend of the three PFCs concentrations in soils, water, and chicken eggs with increasing distance from the plant was found, indicating the production site to be the primary source of PFCs in this region. Risk quotients (RQs) assessment for surface water >500 m away from the plant were less than unity. Risk assessment of PFOS using predicted no-effect concentration (PNEC, 3.23 ng/g on a logarithmic scale) indicated no immediate ecological risk of a reduction in offspring survival. PFOS concentrations in most egg samples did not exceed the benchmark concentration derived in setting a reference dose for noncancer health effects (0.025 μg/(kgxd)).
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| 10. |
- Zhou, Zhen, et al.
(författare)
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Highly elevated serum concentrations of perfluoroalkyl substances in fishery employees from tangxun lake, China.
- 2014
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 48:7, s. 3864-3874
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Tidskriftsartikel (refereegranskat)abstract
- Increasing production and use of per- and polyfluoroalkyl substances (PFASs) has been reported from China, and a few studies have shown there are subpopulations in China with high and increasing exposure to these chemicals. In this paper, we present a comprehensive exposure assessment of PFASs in fishery employees from Tangxun Lake, China. Exceptionally high serum concentrations of C4 to C12 PFASs were observed in fishery employees (n = 39, median perfluorooctanesulfonic acid (PFOS) 10 400 ng/mL) compared to a reference group from the same city (n = 9, median PFOS 18.7 ng/mL). On the basis of the comparison of different exposure pathways, it was concluded that contaminated fish from Tangxun Lake was the primary source of PFAS exposure to fishery employees, and there was a positive association between serum PFAS concentrations and time of employment in the fishery. PFOS isomer profiles in fishery employees showed a significantly higher proportion of linear PFOS (78.4%) compared to the background-exposed reference group (66.8%), reflecting the highly linear PFOS isomer profile (>90%) of lake fish. Median renal clearance rates (CLrenal) of C4 to C10 perfluoroalkyl carboxylic acids (PFCAs) and perfluoroalkanesulfonic acids (PFSAs) ranged from 0.020 to 16.5 mL/day/kg and 0.013 to 9.43 mL/day/kg, respectively. PFCAs with less than eight perfluoroalkyl carbons were primarily eliminated via urine, whereas other routes of excretion may have contributed to the elimination for long-chain PFCAs and PFSAs. Calculated daily PFOS exposures of fishery employees significantly exceeded tolerable daily intake limits, but clinical blood chemistry parameters were mostly within normal reference ranges. However, additional epidemiological studies are needed to address potential associations between PFAS exposure and health effects in the Tangxun Lake area.
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