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- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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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| 4. |
- Ablikim, M., et al.
(author)
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Branching fraction measurement of J/ψ→KSKL and search for J/ψ→KSKS
- 2017
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In: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:11
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Journal article (peer-reviewed)abstract
- Using a sample of 1.31 x 10(9) J/Psi events collected with the BESIII detector at the BEPCII collider, we study the decays of J/Psi -> KSKL and KSKS. The branching fraction of J/Psi -> KSKL is determined to be B(J/Psi -> KSKL) = (1.93 +/- 0.01 (stat) +/- 0.05 (syst)) x 10(-4), which significantly improves on previous measurements. No clear signal is observed for the J/Psi -> KSKS process, and the upper limit at the 95% confidence level for its branching fraction is determined to be B(J/Psi -> KSKS) < 1.4 x 10(-8), which improves on the previous searches by 2 orders in magnitude and reaches the order of the Einstein-Podolsky-Rosen expectation.
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| 5. |
- Ablikim, M., et al.
(author)
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Observation of h(1)(1380) in the J/psi -> eta ' K(K)over-bar pi decay
- 2018
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In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 98:7
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Journal article (peer-reviewed)abstract
- Using 1.31 x 10(9) J/psi events collected by the BESIII detector at the BEPCII e(+)e(-) collider, we report the first observation of the h(1)(1380) in J/psi -> eta'h(1)(1380) with a significance of more than ten standard deviations. The mass and width of the possible axial-vector strangeonium candidate h(1)(1380) are measured to be M = (1423.2 +/- 2.1 +/- 7.3) MeV/c(2) and Gamma = (90.3 +/- 9.8 +/- 17.5) MeV. The product branching fractions, assuming no interference, are determined to be B(J/psi -> eta'h(1)(1380)) x B(h(1)(1380) -> K*(892)K-+(-)+c.c.) = (1.51 +/- 0.09 +/- 0.21) x 10(-4) in eta'K+K-pi(0) mode and B(J/psi -> eta'h(1)(1380)) x B(h(1)(1380) -> K*(892)(K) over bar +c.c.) =(2.16 +/- 0.12 +/- 0.29) x 10(-4) in eta'(KSK +/-)-K-0 pi(-/+) mode. The first uncertainties are statistical and the second are systematic. Isospin symmetry violation is observed in the decays h(1)(1380) K*(892)K-+(-) + c.c. and h(1)(1380) -> K*(892)(0)(K) over bar (0) + c.c.. Based on the measured h(1)(1380) mass, the mixing angle between the states h(1)(1170) and h(1)(1380) is determined to be (35.9 +/- 2.6)degrees, consistent with theoretical expectations.
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| 6. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 7. |
- Ablikim, M., et al.
(author)
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Amplitude analysis of the KSKS system produced in radiative J /psi decays
- 2018
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In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 98:7
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Journal article (peer-reviewed)abstract
- An amplitude analysis of the KSKS system produced in radiative J/psi decays is performed using the (1310.6 +/- 7.0) x 10(6) nip decays collected by the BESIII detector. Two approaches are presented. A mass-dependent analysis is performed by parametrizing the KSKS invariant mass spectrum as a sum of Breit-aligner line shapes. Additionally, a mass-independent analysis is performed to extract a piecewise function that describes the dynamics of the KSKS system while making minimal assumptions about the properties and number of poles in the amplitude. The dominant amplitudes in the mass-dependent analysis include the f(0)(1710), f(0)(2200), and f(2)'(1525). The mass-independent results, which are made available as input for further studies, are consistent with those of the mass-dependent analysis and are useful for a systematic study of hadronic interactions. The branching fraction of radiative J/psi decays to KSKS is measured to be (8.1 +/- 0.4) x 10(-4), where the uncertainty is systematic and the statistical uncertainty is negligible.
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| 8. |
- Ablikim, M., et al.
(author)
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Improved measurements of X-cJ -> Sigma(+) (Sigma)over-bar(-) and Sigma(0)(Sigma)over-bar(0) decays
- 2018
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In: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 97:5
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Journal article (peer-reviewed)abstract
- Using a data sample of (448.1 +/- 2.9) x 10(6) psi (3686) events collected with the BESIII detector at the BEPCII collider, we present measurements of branching fractions for the decays X-cJ -> Sigma(+) (Sigma) over bar (-) and Sigma(0) (Sigma) over bar (0) The decays X-c1.2 -> Sigma(+) (Sigma) over bar (-) and Sigma (Sigma) over bar (0) are observed for the first time, and the branching fractions for X-c0 -> Sigma(+) (Sigma) over bar (-) and Sigma(0) (Sigma) over bar (0) decays are measured with improved precision. The branching fraction ratios between the charged and neutral modes are consistent with the prediction of isospin symmetry.
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| 9. |
- Ablikim, M., et al.
(author)
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Measurement of e(+)e(-) -> K(K)over-barJ/psi cross sections at center-of-mass energies from 4.189 to 4.600 GeV
- 2018
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In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 97:7
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Journal article (peer-reviewed)abstract
- We investigate the process e(+)e(-) -> K (K) over barJ/psi at center-of-mass energies from 4.189 to 4.600 GeV using 4.7 fb(-1) of data collected by the BESIII detector at the BEPCII collider. The Born cross sections for the reactions e(+)e(-) -> K(+)K(-)J/psi and K(S)(0)K(S)(0)J/psi are measured as a function of center-of-mass energy. The energy dependence of the cross section for e(+)e(-) -> K(+)K(-)J/psi is shown to differ from that for pi(+)pi(-)J/psi in the region around the Y(4260). In addition, there is evidence for a structure around 4.5 GeV in the e(+)e(-) -> K(+)K(-)J/psi cross section that is not present in pi(+)pi(-)J/psi.
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| 10. |
- Ablikim, M., et al.
(author)
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Measurement of singly Cabibbo-suppressed decays D-0 → π0π0π0, π0π0η, π0ηη and ηηη
- 2018
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In: Physics Letters B. - : ELSEVIER SCIENCE BV. - 0370-2693 .- 1873-2445. ; 781, s. 368-375
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Journal article (peer-reviewed)abstract
- Using a data sample of e(+)e(-) collision data corresponding to an integrated luminosity of 2.93 fb(-1) collected with the BESIII detector at a center-of-mass energy of root s = 3.773 GeV, we search for the singly Cabibbo-suppressed decays D-0 -> pi(0)pi(0)pi(0), pi(0)pi(0)eta, pi(0)eta eta and eta eta eta using the double tag method. The absolute branching fractions are measured to be B(D-0 -> pi(0)pi(0)pi(0)) = (2.0 +/- 0.4 +/- 0.3) x 10(-4), B(D-0 -> pi(0)pi(0)eta) = (3.8 +/- 1.1 +/- 0.7) x 10(-4) and B(D-0 -> pi(0)eta eta) = (7.3 +/- 1.6 +/- 1.5) x 10(-4) with the statistical significances of 4.8 sigma, 3.8 sigma and 5.5 sigma, respectively, where the first uncertainties are statistical and the second ones systematic. No significant signal of D-0 -> eta eta eta is found, and the upper limit on its decay branching fraction is set to be B(D-0 -> eta eta eta) < 1.3 x 10(-4) at the 90% confidence level.
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