| 1. |
|
|
| 2. |
- 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.
|
|
| 3. |
|
|
| 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. |
-
- 2019
-
Tidskriftsartikel (refereegranskat)
|
|
| 6. |
- Ablikim, M., et al.
(författare)
-
Observation of the Semileptonic Decay D-0 -> a(0)(980)(-)e(+)nu(e) and Evidence for D+ -> a(0)(980)(0)e(+)nu(e)
- 2018
-
Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 121:8
-
Tidskriftsartikel (refereegranskat)abstract
- Using an e(+)e(-) collision data sample of 2.93 fb(-1) collected at a center-of-mass energy of 3.773 GeV by the BESIII detector at BEPCII, we report the observation of D-0 -> a(0)(980)(-)e(+)nu(e) and evidence for D+ -> a(0)(980)(0)e(+)nu(e) with significances of 6.4 sigma and 2.9 sigma, respectively. The absolute branching fractions are determined to be B(D-0 -> a(0)(980)(-)e(+)nu(e)) x B(a(0)(980)(-) -> eta pi(-)) = [1.33(-0.29)(+0.33)(stat) +/- 0.09(syst)] x 10(-4) and B(D+ -> a(0)(980)(0)e(+)nu(e)) x B(a(0)(980)(0) -> eta pi(0)) = [1.66(-0.66)(+0.81)(stat) +/- 0.11(syst) x 10(-4). This is the first time the a(0)(980) meson has been measured in a D-0 semileptonic decay, which would open one more interesting page in the investigation of the nature of the puzzling a(0)(980) states.
|
|
| 7. |
- Ablikim, M., et al.
(författare)
-
Amplitude analysis of the KSKS system produced in radiative J /psi decays
- 2018
-
Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 98:7
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 8. |
- Ablikim, M., et al.
(författare)
-
Amplitude analysis of the pi(0)pi(0) system produced in radiative J/psi decays
- 2015
-
Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 92:5
-
Tidskriftsartikel (refereegranskat)abstract
- An amplitude analysis of the pi(0)pi(0) system produced in radiative J/psi decays is presented. In particular, a piecewise function that describes the dynamics of the pi(0)pi(0) system is determined as a function of M pi(0)pi(0) from an analysis of the (1.311 +/- 0.011) x 10(9) J/psi decays collected by the BESIII detector. The goal of this analysis is to provide a description of the scalar and tensor components of the pi(0)pi(0) system while making minimal assumptions about the properties or number of poles in the amplitude. Such a model-independent description allows one to integrate these results with other related results from complementary reactions in the development of phenomenological models, which can then be used to directly fit experimental data to obtain parameters of interest. The branching fraction of J/psi -> pi(0)pi(0) is determined to be (1.15 +/- 0.05) x 10(-3), where the uncertainty is systematic only and the statistical uncertainty is negligible.
|
|
| 9. |
- 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.
|
|
| 10. |
- Ablikim, M., et al.
(författare)
-
Dark photon search in the mass range between 1.5 and 3.4 GeV/c
- 2017
-
Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 774, s. 252-257
-
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.
|
|
