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- 2019
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Tidskriftsartikel (refereegranskat)
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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. |
- 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. |
- Cao, Zhi-Guo, et al.
(författare)
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Particle size : A missing factor in risk assessment of human exposure to toxic chemicals in settled indoor dust
- 2012
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Ingår i: Environment International. - : Elsevier. - 0160-4120 .- 1873-6750. ; 49, s. 24-30
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Tidskriftsartikel (refereegranskat)abstract
- For researches on toxic chemicals in settled indoor dust, selection of dust fraction is a critical influencing factor to the accuracy of human exposure risk assessment results. However, analysis of the selection of dust fraction in recent studies revealed that there is no consensus. This study classified and presented researches on distribution of toxic chemicals according to dust particle size and on relationship between dust particle size and human exposure possibility. According to the literature, beyond the fact that there were no consistent conclusions on particle size distribution of adherent fraction, dust with particle size less than 100 mu m should be paid more attention and that larger than 250 mu m is neither adherent nor proper for human exposure risk assessment. Calculation results based on literature data show that with different selections of dust fractions, analytical results of toxic chemicals would vary up to 10-fold, which means that selecting dust fractions arbitrarily will lead to large errors in risk assessment of human exposure to toxic chemicals in settled dust. Taking into account the influence of dust particle size on risk assessment of human exposure to toxic chemicals, a new methodology for risk assessment of human exposure to toxic chemicals in settled indoor dust is proposed and human exposure parameter systems to settled indoor dust are advised to be established at national and regional scales all over the world.
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| 6. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 7. |
- Zhang, Chao-Zhi, et al.
(författare)
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NONLINEAR OPTICAL PROPERTIES OF NOVEL AND EFFECTIVE H-SHAPED CHROMOPHORES CONTAINING THREE PARALLEL AND NON-CONJUGATED D-pi-A UNITS
- 2011
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Ingår i: Journal of nonlinear optical physics and materials. - 0218-8635. ; 20:3, s. 327-339
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Tidskriftsartikel (refereegranskat)abstract
- H-shaped chromophores containing three parallel non-conjugated D-pi-A units are effective chromophores with high hyperpolarizability and good optical transparency. The semi-empirical methods ZINDO, AM1, MNDO and PM3 were employed to study the effect of strength of acceptors and donors, and steric repulsion between substituents on static first hyperpolarizabilities (beta(0)) and enhancements of beta(0) of the H-shaped chromophores. The results show that the H-shaped chromophore would exhibit the largest beta(0) and/or the largest enhancement of beta(0) of the chromophore when combination of a donor (D) and an acceptor (A) in a D-pi-A unit is suitable.
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| 8. |
- Zhang, Chao-Zhi, et al.
(författare)
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Theoretical study of macroscopic optical nonlinearities of "parallel connection" chromophores containing PNA units
- 2013
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Ingår i: Journal of nonlinear optical physics and materials. - 0218-8635. ; 22:2, s. 1350014-
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Tidskriftsartikel (refereegranskat)abstract
- The semi-empirical method ZINDO was employed to study relationship between macroscopic optical nonlinear parameter mu beta/MW (where mu is the dipole moment, beta is the first hyperpolarizability, and MW is molecular weight) and the number of parallel non-conjugated D-pi-A units in a chromophore. The computational results show that macroscopic optical nonlinear parameter mu beta/MW value increases remarkably from 1.64 to 2.53 with increasing the number of parallel and non-conjugated p-Nitroaniline (PNA) units in a chromophore from 1 to 3. Then the mu beta/MW value decreases rapidly from 2.53 to 0.43 with increasing the number of PNA units in a chromophore from 3 to 5. It suggests that design of chromophores containing two or three parallel non-conjugated D-pi-A units would be an effective strategy for increasing the first hyperpolarizability and macroscopic optical nonlinearity of designed NLO materials.
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| 9. |
- Abbafati, Cristiana, et al.
(författare)
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- 2020
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Tidskriftsartikel (refereegranskat)
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