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- 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. |
- 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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| 6. |
- Yuan, Shuai, et al.
(författare)
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Continuous Variation of Lattice Dimensions and Pore Sizes in Metal-Organic Frameworks
- 2020
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 142:10, s. 4732-4738
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Tidskriftsartikel (refereegranskat)abstract
- The continuous variation of the lattice metric in metal-organic frameworks (MOFs) allows precise control over their chemical and physical properties. This has been realized herein by a series of mixed-linker and Zr-6-cluster-based MOFs, namely, continuously variable MOFs (CVMOFs). Similar to the substitutional solid solutions, organic linkers with different lengths and various ratios were homogeneously incorporated into a framework rather than being allowed to form separate phases or domains, which was manifested by single-crystal X-ray diffraction, powder X-ray diffraction, fluorescence quenching experiments, and molecular simulations. The unit cell dimension, surface area, and pore size of CVMOFs were precisely controlled by adopting different linker sets and linker ratios. We demonstrate that CVMOFs allow the continuous and fine tailoring of cell-edge lengths from 17.83 to 32.63 angstrom, Brunauer-Emmett-Teller (BET) surface areas from 585 to 3791 m(2)g(-1), and pore sizes up to 15.9 angstrom. Furthermore, this synthetic strategy can be applied to other MOF systems with various metal nodes thus allowing for a variety of CVMOFs with unprecedented tunability.
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| 7. |
- Yuan, Shuai, et al.
(författare)
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[Ti8Zr2O12(COO)(16)] Cluster : An Ideal Inorganic Building Unit for Photoactive Metal-Organic Frameworks
- 2018
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Ingår i: Acs Central Science. - : American Chemical Society (ACS). - 2374-7943 .- 2374-7951. ; 4:1, s. 105-111
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Tidskriftsartikel (refereegranskat)abstract
- Metal-organic frameworks (MOFs) based on Ti-oxo clusters (Ti-MOFs) represent a naturally self-assembled superlattice of TiO2 nanoparticles separated by designable organic linkers as antenna chromophores, epitomizing a promising platform for solar energy conversion. However, despite the vast, diverse, and well-developed Ti-cluster chemistry, only a scarce number of Ti-MOFs have been documented. The synthetic conditions of most Ti-based clusters are incompatible with those required for MOF crystallization, which has severely limited the development of Ti-MOFs. This challenge has been met herein by the discovery of the [Ti8Zr2O12(COO)(16)] cluster as a nearly ideal building unit for photoactive MOFs. A family of isoreticular photoactive MOFs were assembled, and their orbital alignments were fine-tuned by rational functionalization of organic linkers under computational guidance. These MOFs demonstrate high porosity, excellent chemical stability, tunable photoresponse, and good activity toward photocatalytic hydrogen evolution reactions. The discovery of the [Ti8Zr2O12(COO)(16)] cluster and the facile construction of photoactive MOFs from this cluster shall pave the way for the development of future Ti-MOF-based photocatalysts. GRAPHICS
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