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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. |
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| 7. |
- Wang, Shi Zhi, et al.
(författare)
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Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds
- 2024
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 41:7
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Tidskriftsartikel (refereegranskat)abstract
- The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3′UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.
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| 8. |
- Zhu, Liang-Liang, et al.
(författare)
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Photolockable Ratiometric Viscosity Sensitivity of Cyclodextrin Polypseudorotaxane with Light-Active Rotor Graft
- 2009
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 25:6, s. 3482-3486
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Tidskriftsartikel (refereegranskat)abstract
- A prototype, based on light-active fluorescent rotor grafted to beta-cyclodextrin, shows a good solvent viscosity-sensitive behavior due to the environment-dependent nonradiative decay. With the reversible photoisomerization of the cyanostilbene unit, the viscosity sensitivity of the molecular rotor could be locked and activated, and the two switchable states can be distinguished by fluorescent signals. This cyclodextrin derivative was threaded to form a novel polypseudorotaxane. Such supramolecular assembly displays a lockable ratiometric fluorescent viscosity sensitivity with two emission channels: one aroused by fluorophore's intramolecular excimer without influenced by viscosity is used to gauge the concentration of the compound, while the other corresponding to the monomer's rotor fluorescence acts as a viscosity-sensitive signal and it can be shut off by UV irradiation.
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| 9. |
- Zou, Linqing, et al.
(författare)
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Assessing the upper elevational limits of vegetation growth in global high-mountains
- 2023
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Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257. ; 286
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Tidskriftsartikel (refereegranskat)abstract
- The upper elevational limits of vegetation growth in global high-mountains have been the focus for monitoring and assessment of climate change impacts on terrestrial ecosystems. However, existing studies have relied on field surveys that do not allow for large-scale analysis. Although remote sensing data have been used for local and regional monitoring of the vegetation upper boundaries, a global synthesis of the treeline and vegetation line (the upper altitudinal threshold for the existence of trees and the transition line from vegetation to bare land or permanent snow cover, respectively) in high-mountain ecosystems is still missing. To fill this gap, we developed two independent methods based on (1) the relationship between a Sentinel-2 vegetation index and elevation and (2) the European Space Agency's 10 m resolution land cover dataset (WorldCover), respectively, to automatically identify the upper elevational limits of treeline and vegetation line for each one-quarter degree grid across the global high-mountain areas. We obtained highly consistent results from the two methods, both of which are spatially consistent with ground surveyed treeline elevations. Our results are in line with the current understanding of the global distributions of tree and vegetation lines, which are observed at the highest elevations in the Tibetan plateau and decreasing for increasing latitudes. We find that the tree and vegetation lines are aspect-dependent, reaching higher elevations on the equatorial-facing slopes than on the polar-facing slopes in high latitudes, and the opposite in the middle latitudes. Our analysis shows that mountain height is the dominant factor in determining the upper elevational limits of tree and vegetation lines across the globe, while climatic conditions and soil properties also play important roles at regional scales. Our study provides a framework for monitoring the tree and vegetation lines in global high-mountains and provides an important benchmark for further examining their long-term changes in response to climate change.
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