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| 2. |
- 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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| 3. |
- 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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| 4. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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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. |
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| 7. |
- Song, Jun, et al.
(författare)
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Echelle grating demultiplexers with reduced return loss by using chirped diffraction order design
- 2006
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Ingår i: IEEE Photonics Technology Letters. - 1041-1135 .- 1941-0174. ; 18:14, s. 1506-1508
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Tidskriftsartikel (refereegranskat)abstract
- A design for echelle grating demultiplexers is presented to reduce the return loss. The input waveguide is placed on the minimal intensity position of the diffraction envelope. Then, by further chirping the diffraction order for each facet, we minimize the envelope intensity for other adjacent diffraction orders, which can contribute to a negligible return loss for a large spectral width. The present design is appropriate for multifrequency laser or multistage demultiplexer applications.
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| 8. |
- Song, Jun, et al.
(författare)
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Etched diffraction grating demultiplexers with large free-spectral range and large grating facets
- 2006
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Ingår i: IEEE Photonics Technology Letters. - 1041-1135 .- 1941-0174. ; 18:24, s. 2695-2697
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Tidskriftsartikel (refereegranskat)abstract
- A design for etched diffraction grating demultiplexers is presented to obtain both large grating facets and a larger free-spectral range (FSR) using the optimal chirped diffraction orders for different facets. The large grating facets by using a large diffraction order contribute to lowering the manufacturing difficulty, and can provide lower polarization-dependent loss. However, usually the large diffraction order must lower the FSR of the device by all means. Based on the present design, the FSR can overlay the whole diffraction envelop for a special order, but avoid the influence of the adjacent diffraction envelops. Calculations indicate that the extinction ratio between the operated order and adjacent orders can attain a 35 dB or so, which makes the crosstalk from channels in adjacent envelops to those in the operated diffraction envelop acceptable.
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| 9. |
- Song, Jun, et al.
(författare)
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Fast analysis method for polarization-dependent performance of a concave diffraction grating with total-internal-reflection facets
- 2005
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Ingår i: Journal of the Optical Society of America A: Optics and Image Science, and Vision. - 1084-7529. ; 22:9, s. 1947-1951
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Tidskriftsartikel (refereegranskat)abstract
- A fast simulation method for a waveguide-based concave grating with total-internal-reflection (TIR) facets is presented using the Kirchhoff-Huygens principle. Unlike the conventional scalar method, modifications are made to take into account the influence of the Goos-Hanchen (GH) shift. The simple method is in good agreement with a numerical method based on rigorous coupled-wave analysis for a wide range of practical device parameters and can provide an insightful physical explanation for the numerical results. It is shown that the GH shift is a main contributing factor for the loss and the polarization-dependent loss of an etched diffraction grating demultiplexer with TIR facets.
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| 10. |
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