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| 2. |
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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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- 2019
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Tidskriftsartikel (refereegranskat)
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| 5. |
- Ablikim, M., et al.
(författare)
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Analysis of D+ -> (K)over-bar(0)e(+)nu(e) and D+ -> pi(0)e(+)nu(e) semileptonic decays
- 2017
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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 96:1
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Tidskriftsartikel (refereegranskat)abstract
- Using 2.93 fb(-1) of data taken at 3.773 GeV with the BESIII detector operated at the BEPCII collider, we study the semileptonic decays D+ -> (K) over bar (0)e(+)nu(e) and D+ -> pi(0)e(+)nu(e). We measure the absolute decay branching fractions B(D+ -> (K) over bar (0)e(+)nu(e)) = (8.60 +/- 0.06 +/- 0.15) x 10(-2) and B(D+ -> pi(0)e(+)nu(e)) = (3.63 +/- 0.08 +/- 0.05) x 10(-3), where the first uncertainties are statistical and the second systematic. We also measure the differential decay rates and study the form factors of these two decays. With the values of |V-cs| and |V-cd| from Particle Data Group fits assuming Cabibbo-Kobayashi-Maskawa (CKM) unitarity, we obtain the values of the form factors at q(2) = 0, f(+)(K)(0) = 0.725 +/- 0.004 +/- 0.012, and f(+)(pi)(0) = 0.622 +/- 0.012 +/- 0.003. Taking input from recent lattice QCD calculations of these form factors, we determine values of the CKM matrix elements |V-cs| = 0.944 +/- 0.005 +/- 0.015 +/- 0.024 and |V-cd| = 0.210 +/- 0.004 +/- 0.001 +/- 0.009, where the third uncertainties are theoretical.
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| 6. |
- Ablikim, M., et al.
(författare)
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Dark photon search in the mass range between 1.5 and 3.4 GeV/c
- 2017
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 774, s. 252-257
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Tidskriftsartikel (refereegranskat)abstract
- Using a data set of 2.93 fb taken at a center-of-mass energy root s = 3.773 GeV with the BESIII detector at the BEPCII collider, we perform a search for an extra U(1) gauge boson, also denoted as a dark photon. We examine the initial state radiation reactions e(+)e(-) -> e(+)e(-) gamma(ISR) and e(+)e(-) -> mu(+)mu(-) gamma(ISR) for this search, where the dark photon would appear as an enhancement in the invariant mass distribution of the leptonic pairs. We observe no obvious enhancement in the mass range between 1.5 and 3.4 GeV/c(2) and set a 90% confidence level upper limit on the mixing strength of the dark photon and the Standard Model photon. We obtain a competitive limit in the tested mass range.
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| 7. |
- Ablikim, M., et al.
(författare)
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Measurement of the leptonic decay width of J/psi using initial state radiation
- 2016
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 761, s. 98-103
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Tidskriftsartikel (refereegranskat)abstract
- Using a data set of 2.93 fb(-1) taken at a center-of-mass energy of root s = 3.773 GeV with the BESIII detector at the BEPCII collider, we measure the process e(+) e(-) -> J/psi gamma -> mu(+)mu(-)gamma and determine the product of the branching fraction and the electronic width B-mu mu . Gamma(ee) = (333.4 +/- 2.5(stat) +/- 4.4(sys)) eV. Using the earlier-published BESIII result for B-mu mu = (5.973 +/- 0.007(stat) +/- 0.037(sys))%, we derive the J/psi electronic width Gamma(ee) = (5.58 +/- 0.05(stat) +/- 0.08(sys)) keV. (C) 2016 The Author(s). Published by Elsevier B.V.
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| 8. |
- Ablikim, M., et al.
(författare)
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Study of dynamics of D-0 -> K(-)e(+)nu(e) and D-0 -> pi(-)e(+)nu(e) decays
- 2015
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 92:7
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Tidskriftsartikel (refereegranskat)abstract
- In an analysis of a 2.92 fb(-1) data sample taken at 3.773 GeV with the BESIII detector operated at the BEPCII collider, we measure the absolute decay branching fractions B(D-0 -> K(-)e(+)nu(e)) = (3.505 +/- 0.014 +/- 0.033)% and B(D-0 -> pi(-)e(+)nu(e)) = (0.295 +/- 0.004 +/- 0.003)%. From a study of the differential decay rates we obtain the products of hadronic form factor and the magnitude of the Cabibbo-Kobayashi-Maskawa (CKM) matrix element f(+)(K)(0)vertical bar V-cs vertical bar = 0.7172 +/- 0.0025 +/- 0.0035 and f(+)(pi)(0)vertical bar V-cd vertical bar = 0.1435 +/- 0.0018 +/- 0.0009. Combining these products with the values of vertical bar V-cs(d)vertical bar from the SM constraint fit, we extract the hadronic form factors f(+)(K)(0) = 0.7368 +/- 0.0026 +/- 0.0036 and f(+)(pi)(0) = 0.6372 +/- 0.0080 +/- 0.0044, and their ratio f(+)(pi)(0)/f(+)(K)(0) = 0.8649 +/- 0.0112 +/- 0.0073. These form factors and their ratio are used to test unquenched lattice QCD calculations of the form factors and a light cone sum rule (LCSR) calculation of their ratio. The measured value of f(+)(K(pi))(0)vertical bar V-cs(d)vertical bar and the lattice QCD value for f(+)(K(pi))(0) are used to extract values of the CKM matrix elements of vertical bar V-cs vertical bar = 0.9601 +/- 0.0033 +/- 0.0047 +/- 0.0239 and vertical bar V-cd vertical bar = 0.2155 +/- 0.0027 +/- 0.0014 +/- 0.0094, where the third errors are due to the uncertainties in lattice QCD calculations of the form factors. Using the LCSR value for f(+)(pi)(0)/f(+)(K)(0), we determine the ratio vertical bar V-cd vertical bar/vertical bar V-cs vertical bar = 0.238 +/- 0.004 +/- 0.002 +/- 0.011, where the third error is from the uncertainty in the LCSR normalization. In addition, we measure form factor parameters for three different theoretical models that describe the weak hadronic charged currents for these two semileptonic decays. All of these measurements are the most precise to date.
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| 9. |
- 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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| 10. |
- Ablikim, M., et al.
(författare)
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Amplitude analysis of D0 → K -π+π+π-
- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 95:7
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Tidskriftsartikel (refereegranskat)abstract
- We present an amplitude analysis of the decay D0 → K -π+π+π- based on a data sample of 2.93 fb−1 acquired by the BESIII detector at the ψ(3770) resonance. With a nearly background free sample of about 16000 events, we investigate the substructure of the decay and determine the relative fractions and the phases among the different intermediate processes. Our amplitude model includes the two-body decays D0 → ¯K*0ρ0, D0 → K−a+1(1260) and D0 → K−1(1270)π+, the three-body decays D0 →¯K*0π+π− and D0 → K−π+ρ0, as well as the four-body nonresonant decay D0 → K−π+π+π−. The dominant intermediate process is D0 → K−a+1(1260), accounting for a fit fraction of 54.6%.
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