| 1. |
- 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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| 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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| 4. |
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| 5. |
- Fu, Kai, 1981-
(författare)
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Growth Dynamics of Semiconductor Nanostructures by MOCVD
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Semiconductors and related low-dimensional nanostructures are extremely important in the modern world. They have been extensively studied and applied in industry/military areas such as ultraviolet optoelectronics, light emitting diodes, quantum-dot photodetectors and lasers. The knowledge of growth dynamics of semiconductor nanostructures by metalorganic chemical vapour deposition (MOCVD) is very important then. MOCVD, which is widely applied in industry, is a kind of chemical vapour deposition method of epitaxial growth for compound semiconductors. In this method, one or several of the precursors are metalorganics which contain the required elements for the deposit materials. Theoretical studies of growth mechanism by MOCVD from a realistic reactor dimension down to atomic dimensions can give fundamental guidelines to the experiment, optimize the growth conditions and improve the quality of the semiconductor-nanostructure-based devices. Two main types of study methods are applied in the present thesis in order to understand the growth dynamics of semiconductor nanostructures at the atomic level: (1) Kinetic Monte Carlo method which was adopted to simulate film growths such as diamond, Si, GaAs and InP using the chemical vapor deposition method; (2) Computational fluid dynamics method to study the distribution of species and temperature in the reactor dimension. The strain energy is introduced by short-range valence-force-field method in order to study the growth process of the hetero epitaxy. The Monte Carlo studies show that the GaN film grows on GaN substrate in a two-dimensional step mode because there is no strain over the surface during homoepitaxial growth. However, the growth of self-assembled GaSb quantum dots (QDs) on GaAs substrate follows strain-induced Stranski-Krastanov mode. The formation of GaSb nanostructures such as nanostrips and nanorings could be determined by the geometries of the initial seeds on the surface. Furthermore, the growth rate and aspect ratio of the GaSb QD are largely determined by the strain field distribution on the growth surface.
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| 6. |
- Fu, Kai, et al.
(författare)
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Kinetic Monte Carlo study of metal organic chemical vapor deposition growth dynamics of GaN thin film at microscopic level
- 2008
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 103:10, s. 103524-
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Tidskriftsartikel (refereegranskat)abstract
- Group III nitrides, especially gallium nitride (GaN), have many applications. The materials are usually grown by metal organic chemical vapor deposition (MOCVD) technology. By combining the computational fluid dynamics and kinetic Monte Carlo method, we present a multiscale modeling of fluid dynamics, thermodynamics, and molecular dynamics to study the chemical and physical growth process of GaN in a standard MOCVD reactor, which shows a general agreement with experimental results. The theoretical model thus provides us with a fundamental guideline for optimizing GaN MOCVD growth at the microscopic level.
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| 7. |
- Fu, Kai, et al.
(författare)
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Kinetic Monte Carlo study of metal organic chemical vapor deposition growth mechanism of GaSb quantum dots
- 2008
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 93:101906
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Tidskriftsartikel (refereegranskat)abstract
- The growth dynamics of self-assembled GaSb quantum dots (QDs) on GaAs substrate in the strain-induced Stranski-Krastanov mode was investigated using kinetic Monte Carlo method. The strain induced by the lattice mismatch between the epitaxial material and the substrate was shown to be directly responsible for the QD formation and the transition of growth mode from two dimensional to three dimensional.
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| 8. |
- Fu, Kai, et al.
(författare)
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Strain-induced Stranski-Krastanov three dimensional growth mode of GaSb quantum dot on GaAs substrate
- 2009
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 94:181913
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Tidskriftsartikel (refereegranskat)abstract
- The growth dynamics of self-assembled GaSb quantum dots (QDs) on GaAs substrate was investigated using kinetic Monte Carlo method. The strain induced by the lattice mismatch between the epitaxial material and the substrate was shown to be directly responsible for the three-dimensional QD formation. Different geometries of the initial seeds on the surface which are equally favorable from an energy point of view can result in different GaSb nanostructures (nanostrips and nanoring).
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| 9. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Tidskriftsartikel (refereegranskat)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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| 10. |
- Yang, Xifeng, et al.
(författare)
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Strain effect in determining the geometric shape of self-assembled quantum dot
- 2009
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Ingår i: Journal of Physics D. - : IOP Publishing. - 0022-3727 .- 1361-6463. ; 42:125414
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Tidskriftsartikel (refereegranskat)abstract
- The geometric shape of a self-assembled quantum dot (QD) formed by the strain-induced Stranski-Krastanov mode has been studied as a function of strain energy by the short-range valence-force-field approach. It has been shown by dynamic bond relaxation through strain energy minimization that for the most commonly used InAs QD in GaAs and InP matrices and Ge QD in Si matrix, a pyramidal shape is energy favoured over an hemispherical shape when the QD is not capped due to the lattice relaxation at the QD surface. When the QD becomes totally embedded in the background material, the elastic strain energy of a hemispherical InAs QD is minimal. The results agree with experimental observations. We further studied the coupling of strain fields of QDs in adjacent QD layers which shows that QDs in multiply stacked QD layers can be aligned along the layer growth direction in order to minimize the strain energy.
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