| 1. |
|
|
| 2. |
|
|
| 3. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
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.
|
|
| 4. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
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.
|
|
| 5. |
- Ablikim, M., et al.
(författare)
-
Analysis of D+ -> (K)over-bar(0)e(+)nu(e) and D+ -> pi(0)e(+)nu(e) semileptonic decays
- 2017
-
Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 96:1
-
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.
|
|
| 6. |
-
- 2019
-
Tidskriftsartikel (refereegranskat)
|
|
| 7. |
- Ablikim, M., et al.
(författare)
-
Observation of electromagnetic Dalitz decays J/\psi \to P e^+e^-
- 2014
-
Ingår i: PHYSICAL REVIEW D. - 2470-0010 .- 1550-7998 .- 1550-2368. ; 89:9
-
Tidskriftsartikel (refereegranskat)abstract
- Based on a sample of (225.3\pm2.8)\times 10^{6} J/\psi events collected with the BESIII detector, the electromagnetic Dalitz decays of J/\psi \to P e^+e^-(P=\eta'/\eta/\pi^0) are studied. By reconstructing the pseudoscalar mesons in various decay modes, the decays J/\psi \to \eta' e^+e^-, J/\psi \to \eta e^+e^- and J/\psi \to \pi^0 e^+e^- are observed for the first time. The branching fractions are determined to be \mathcal{B}(J/\psi\to \eta' e^+e^-) = (5.81\pm0.16\pm0.31)\times10^{-5}, \mathcal{B}(J/\psi\to \eta e^+e^-) = (1.16\pm0.07\pm0.06)\times10^{-5}, and \mathcal{B}(J/\psi\to \pi^0 e^+e^-)=(7.56\pm1.32\pm0.50)\times10^{-7}, where the first errors are statistical and the second ones systematic.
|
|
| 8. |
- Ablikim, M., et al.
(författare)
-
Precision measurements of $B(D^+ \rightarrow \mu^+ \nu_{\mu})$, the pseudoscalar decay constant $f_{D^+}$, and the quark mixing matrix element $|V_{\rm cd}|$
- 2014
-
Ingår i: PHYSICAL REVIEW D. - 2470-0010 .- 1550-7998 .- 1550-2368. ; 89:5
-
Tidskriftsartikel (refereegranskat)abstract
- We report a measurement of the branching fraction $B(D^+ \rightarrow \mu^+ \nu_{\mu}) = [3.71 \pm 0.19 (\rm stat) \pm 0.06 (\rm sys)]\times 10^{-4}$ based on 2.92 ${\rm fb^{-1}}$ of data accumulated at $\sqrt{s}=3.773$ GeV with the BESIII detector at the BEPCII collider. This measurement, in conjunction with the Cabibbo-Kobayashi-Maskawa matrix element $|V_{\rm cd}|$ determined from a global Standard Model fit, implies a value for the weak decay constant $f_{D^+}=(203.2 \pm 5.3 \pm 1.8)$ MeV. Additionally, using this branching fraction measurement together with a Lattice QCD prediction for $f_{D^+}$, we find $|V_{\rm cd}|=0.2210\pm 0.0058 \pm 0.0047$. In either case, these are the most precise results for these quantities to date.
|
|
| 9. |
- Ablikim, M., et al.
(författare)
-
Study of J/psi and psi(3686) -> Sigma(1385)(0)(Sigma)over-bar(1385)(0) and Xi(0)(Xi)over-bar(0) : Study of J/ψ and ψ(3686) → (1385)0( ¯ 1385)0 and 0¯ 0
- 2017
-
Ingår i: Physics Letters B. - : ELSEVIER SCIENCE BV. - 0370-2693 .- 1873-2445. ; 770, s. 217-225
-
Tidskriftsartikel (refereegranskat)abstract
- We study the decays of J/psi and psi(3686) to the final states Sigma(1385)(0)(Sigma) over bar (1385)(0) and Xi(0)(Xi) over bar (0) based on a single baryon tag method using data samples of (1310.6 +/- 7.0) x 10(6) J/psi and (447.9 +/- 2.9) x 10(6) psi(3686) events collected with the BESIII detector at the BEPCII collider. The decays to Sigma(1385)(0)(Sigma) over bar (1385)(0) are observed for the first time. The measured branching fractions of J/psi and psi(3686) to Xi(0)(Xi) over bar (0) are in good agreement with, and much more precise than, the previously published results. The angular parameters for these decays are also measured for the first time. The measured angular decay parameter for J/psi -> Sigma(1385)(0)(Sigma) over bar (1385)(0), alpha = -0.64 +/- 0.03 +/- 0.10, is found to be negative, different to the other decay processes in this measurement. In addition, the "12% rule" and isospin symmetry in the decays of J/psi and psi(3686) to Xi(Xi) over bar and Sigma(1385)(Sigma) over bar (1385) are tested.
|
|
| 10. |
- Aad, G., et al.
(författare)
-
- 2016
-
Ingår i: Physical Review D. Particles and fields. - : American Physical Society. - 0556-2821 .- 1089-4918. ; 93:1
-
Tidskriftsartikel (refereegranskat)
|
|
