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| 2. |
- 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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| 3. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 5. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 6. |
- Erzurumluoglu, A. Mesut, et al.
(författare)
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Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci
- 2020
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Ingår i: Molecular Psychiatry. - : Nature Publishing Group. - 1359-4184 .- 1476-5578. ; 25:10, s. 2392-2409
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Tidskriftsartikel (refereegranskat)abstract
- Smoking is a major heritable and modifiable risk factor for many diseases, including cancer, common respiratory disorders and cardiovascular diseases. Fourteen genetic loci have previously been associated with smoking behaviour-related traits. We tested up to 235,116 single nucleotide variants (SNVs) on the exome-array for association with smoking initiation, cigarettes per day, pack-years, and smoking cessation in a fixed effects meta-analysis of up to 61 studies (up to 346,813 participants). In a subset of 112,811 participants, a further one million SNVs were also genotyped and tested for association with the four smoking behaviour traits. SNV-trait associations with P < 5 × 10-8 in either analysis were taken forward for replication in up to 275,596 independent participants from UK Biobank. Lastly, a meta-analysis of the discovery and replication studies was performed. Sixteen SNVs were associated with at least one of the smoking behaviour traits (P < 5 × 10-8) in the discovery samples. Ten novel SNVs, including rs12616219 near TMEM182, were followed-up and five of them (rs462779 in REV3L, rs12780116 in CNNM2, rs1190736 in GPR101, rs11539157 in PJA1, and rs12616219 near TMEM182) replicated at a Bonferroni significance threshold (P < 4.5 × 10-3) with consistent direction of effect. A further 35 SNVs were associated with smoking behaviour traits in the discovery plus replication meta-analysis (up to 622,409 participants) including a rare SNV, rs150493199, in CCDC141 and two low-frequency SNVs in CEP350 and HDGFRP2. Functional follow-up implied that decreased expression of REV3L may lower the probability of smoking initiation. The novel loci will facilitate understanding the genetic aetiology of smoking behaviour and may lead to the identification of potential drug targets for smoking prevention and/or cessation.
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| 7. |
- Jian, Hong-lei, et al.
(författare)
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Influence of dehulling pretreatment on physicochemical properties of Gleditsia sinensis Lam. gum
- 2011
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Ingår i: Food Hydrocolloids. - : Elsevier BV. - 0268-005X. ; 25:5, s. 1337-1343
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Tidskriftsartikel (refereegranskat)abstract
- The seeds of Gleditsia sinensis Lam., widespread in China, are an important source of galactomannans. G. sinensis gum was extracted from whole seeds using baking, boiling water and acid dehulling pretreatment, respectively. The physicochemical properties of the three isolated G. sinensis gums were studied to evaluate three pretreatment methods. The results illustrated that the properties of G. sinensis gum were significantly influenced by dulling method (p < 0.05) including the yield, M/G ratio, viscosity, chemical composition and molecular weight. Power-law model (sigma = k.gamma(n)) was applied to the rheological measurements, which indicated that solutions of Gb, Gw and Ga gum behaved as pseudoplastic fluids at the concentration of 0.5% (w/v). The gum obtained by acid pretreatment (Ga) had the lowest yield of 20-24% (w/w). However Ga showed a pronounced shear-thinning behavior and particularly higher viscosity compared with the gums extracted by baking pretreatment (Gb) and boiling water dehulling method (Gw). The mannose to galactose ratios (M/G ratio) for Gb, Gw and Ga were found to be 4.5, 4.4 and 6.9, respectively. The highest molecular weight of 3.31 x 10(6) Da was observed for the galactomannans of Gb. (C) 2010 Elsevier Ltd. All rights reserved.
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| 8. |
- Jiang, Bin, et al.
(författare)
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Experimental observation of non-Abelian topological acoustic semimetals and their phase transitions
- 2021
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Ingår i: Nature Physics. - : Springer Science and Business Media LLC. - 1745-2473 .- 1745-2481. ; 17, s. 1239-1246
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Tidskriftsartikel (refereegranskat)abstract
- Topological phases of matter connect mathematical principles to real materials, and may shape future electronic and quantum technologies. So far, this discipline has mostly focused on single-gap topology described by topological invariants such as Chern numbers. Here, based on a tunable kagome model, we observe non-Abelian band topology and its transitions in acoustic semimetals, in which the multi-gap Hilbert space plays a key role. In non-Abelian semimetals, the topological charges of band nodes are converted through the braiding of nodes in adjacent gaps, and their behaviour cannot be captured by conventional topological band theory. Using kagome acoustic metamaterials and pump–probe measurements, we demonstrate the emergence of non-Abelian topological nodes, identify their dispersions and observe the induced multi-gap topological edge states. By controlling the geometry of the metamaterials, topological transitions are induced by the creation, annihilation, merging and splitting of band nodes. This reveals the underlying rules for the conversion and transfer of non-Abelian topological charges in multiple bandgaps. The resulting laws that govern the evolution of band nodes in non-Abelian multi-gap systems should inspire studies on multi-band topological semimetals and multi-gap topological out-of-equilibrium systems.
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| 9. |
- Jiang, Bin, et al.
(författare)
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Observation of an acoustic topological Euler insulator with meronic waves
- 2024
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Ingår i: Science Bulletin. - : Elsevier BV. - 2095-9273. ; 69:11, s. 1653-1659
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Tidskriftsartikel (refereegranskat)abstract
- Topological band theory has conventionally been concerned with the topology of bands around a single gap. Only recently non-Abelian topologies that thrive on involving multiple gaps were studied, unveiling a new horizon in topological physics beyond the conventional paradigm. Here, we report on the first experimental realization of a topological Euler insulator phase with unique meronic characterization in an acoustic metamaterial. We demonstrate that this topological phase has several nontrivial features: First, the system cannot be described by conventional topological band theory, but has a nontrivial Euler class that captures the unconventional geometry of the Bloch bands in the Brillouin zone. Second, we uncover in theory and probe in experiments a meronic configuration of the bulk Bloch states for the first time. Third, using a detailed symmetry analysis, we show that the topological Euler insulator evolves from a non-Abelian topological semimetal phase via. the annihilation of Dirac points in pairs in one of the band gaps. With these nontrivial properties, we establish concretely an unconventional bulk-edge correspondence which is confirmed by directly measuring the edge states via. pump-probe techniques. Our work thus unveils a nontrivial topological Euler insulator phase with a unique meronic pattern and paves the way as a platform for non-Abelian topological phenomena.
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| 10. |
- Jiang, Jian-xin, et al.
(författare)
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Structural and thermal characterization of galactomannans from genus Gleditsia seeds as potential food gum substitutes
- 2011
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Ingår i: Journal of the Science of Food and Agriculture. - : Wiley. - 1097-0010 .- 0022-5142. ; 91:4, s. 732-737
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Seed galactomannans are preferred hydrocolloids since they are comparatively cheap, non-toxic, eco-friendly and non-polluting during production and application. Galactomannans from seeds of three species of Gleditsia, namely G. sinensis, G. microphylla and G. melanacantha, were characterized in terms of structural and thermal properties. RESULTS: Gleditsia polysaccharides were characterized using both chemical and chromatographic methods, as well as Fourier transform infrared, H-1 nuclear magnetic resonance (NMR) and C-13 NMR spectroscopy, and it was shown that they consist of D-mannopyranose and D-galactopyranose residues. The mannose/galactose (M/G) ratio of galactomannans was 3.25, 3.31 and 2.30, respectively. It was also found that these polysaccharides differ from one another in values of M-w, M-n and polydispersity. X-ray diffraction confirmed the amorphous nature of Gleditsia galactomannans, although G. sinensis galactomannan showed a high crystallinity. Thermal analysis of the galactomannans by differential scanning calorimetry illustrated that their endothermic peaks ranged from 290 to 320 degrees C. CONCLUSION: Gleditsia polysaccharides are neutral galactomannans. The higher value of M/G ratio from G. sinensis and G. microphylla indicates that their gums offer an excellent alternative for locus bean gum. (C) 2011 Society of Chemical Industry
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