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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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| 7. |
- Ablikim, M., et al.
(författare)
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Measurement of branching fractions for psi(3686) -> gamma eta ', gamma eta, and gamma pi(0)
- 2017
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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 96:5
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Tidskriftsartikel (refereegranskat)abstract
- Using a data sample of 448 x 10(6) psi(3686) events collected with the BESIII detector operating at the BEPCII storage ring, the decays psi(3686) -> gamma eta and psi(3686) -> gamma pi(0) are observed with a statistical significance of 7.3 sigma and 6.7 sigma, respectively. The branching fractions are measured to be B(psi(3686) -> gamma eta) = (0.85 +/- 0.18 +/- 0.05) x 10(-6) and B(psi(3686) ->gamma pi(0)) = (0.95 +/- 0.16 +/- 0.05) x 10(-6). In addition, we measure the branching fraction of psi(3686) -> gamma eta' to be B(psi(3686) -> gamma eta') = (125.1 +/- 2.2 +/- 6.2)x10(-6), which represents an improvement of precision over previous results.
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| 8. |
- Ablikim, M., et al.
(författare)
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Measurements of absolute branching fractions for D mesons decays into two pseudoscalar mesons
- 2018
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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 97:7
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Tidskriftsartikel (refereegranskat)abstract
- Using a data sample of e(+)e(-) collision data with an integrated luminosity of 2.93 fb(-1) taken at the center-of-mass energy root s = 3.773 GeV with the BESIII detector operating at the BEPCII storage rings, we measure the absolute branching fractions of the two-body hadronic decays D+ -> pi(+)pi(0), K+pi(0), pi(+)eta., K+eta., pi(+)eta', K+eta', K-S(0)pi(+), (KSK+)-K-0, and D-0 -> pi(+)pi(-), K+ K-, K--/+pi(+/-), K-S(0)pi(0), K-S(0)eta, K-S(0)eta' Our results are consistent with previous measurements within uncertainties. Among them, the branching fractions for D+-> pi(+)pi(0), K+pi(0), pi(+)eta, pi(+)eta', (KSK+)-K-0, (KSK+)-K-0 and D-0 -> K-S(0)pi(0), K-S(0)eta, K-S(0)eta' are determined with improved precision compared to the world average values.
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| 9. |
- Ablikim, M., et al.
(författare)
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Observation of χc2→η′η′ and χc0,2→ηη′
- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:11
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Tidskriftsartikel (refereegranskat)abstract
- Using a sample of 448.1×106 ψ(3686) events collected with the BESIII detector in 2009 and 2012, we study the decays χc0,2→η′η′ and ηη′. The decays χc2→η′η′, χc0→ηη′ and χc2→ηη′ are observed for the first time with statistical significances of 9.6σ, 13.4σ and 7.5σ, respectively. The branching fractions are determined to be B(χc0→η′η′)=(2.19±0.03±0.14)×10−3, B(χc2→η′η′)=(4.76±0.56±0.38)×10−5, B(χc0→ηη′)=(8.92±0.84±0.65)×10−5 and B(χc2→ηη′)=(2.27±0.43±0.25)×10−5, where the first uncertainties are statistical and the second are systematic. The precision for the measurement of B(χc0→η′η′) is significantly improved compared to previous measurements. Based on the measured branching fractions, the role played by the doubly and singly Okubo-Zweig-Iizuka disconnected transition amplitudes for χc0,2 decays into pseudoscalar meson pairs can be clarified.
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| 10. |
- Ablikim, M., et al.
(författare)
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Precision Measurement of the e(+)e(-) -> Lambda(+)(c)(Lambda)over-bar(c)(-) Cross Section Near Threshold
- 2018
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 120:13
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Tidskriftsartikel (refereegranskat)abstract
- The cross section of the e(+)e(-) -> Lambda(+)(c)(Lambda) over bar (-)(c) process is measured with unprecedented precision using data collected with the BESIII detector at root s = 4574.5, 4580.0, 4590.0 and 4599.5 MeV. The nonzero cross section near the Lambda(+)(c)(Lambda) over bar (-)(c) production threshold is cleared. At center-of-mass energies root s = 4574.5 and 4599.5 MeV, the higher statistics data enable us to measure the Lambda(c) polar angle distributions. From these, the.c electric over magnetic form-factor ratios (vertical bar G(E)/G(M)vertical bar) are measured for the first time. They are found to be 1.14 +/- 0.14 +/- 0.07 and 1.23 +/- 0.05 +/- 0.03, respectively, where the first uncertainties are statistical and the second are systematic.
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