| 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. |
- 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.
|
|
| 4. |
- Fenstermacher, M.E., et al.
(författare)
-
DIII-D research advancing the physics basis for optimizing the tokamak approach to fusion energy
- 2022
-
Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:4
-
Tidskriftsartikel (refereegranskat)abstract
- DIII-D physics research addresses critical challenges for the operation of ITER and the next generation of fusion energy devices. This is done through a focus on innovations to provide solutions for high performance long pulse operation, coupled with fundamental plasma physics understanding and model validation, to drive scenario development by integrating high performance core and boundary plasmas. Substantial increases in off-axis current drive efficiency from an innovative top launch system for EC power, and in pressure broadening for Alfven eigenmode control from a co-/counter-I p steerable off-axis neutral beam, all improve the prospects for optimization of future long pulse/steady state high performance tokamak operation. Fundamental studies into the modes that drive the evolution of the pedestal pressure profile and electron vs ion heat flux validate predictive models of pedestal recovery after ELMs. Understanding the physics mechanisms of ELM control and density pumpout by 3D magnetic perturbation fields leads to confident predictions for ITER and future devices. Validated modeling of high-Z shattered pellet injection for disruption mitigation, runaway electron dissipation, and techniques for disruption prediction and avoidance including machine learning, give confidence in handling disruptivity for future devices. For the non-nuclear phase of ITER, two actuators are identified to lower the L-H threshold power in hydrogen plasmas. With this physics understanding and suite of capabilities, a high poloidal beta optimized-core scenario with an internal transport barrier that projects nearly to Q = 10 in ITER at ∼8 MA was coupled to a detached divertor, and a near super H-mode optimized-pedestal scenario with co-I p beam injection was coupled to a radiative divertor. The hybrid core scenario was achieved directly, without the need for anomalous current diffusion, using off-axis current drive actuators. Also, a controller to assess proximity to stability limits and regulate β N in the ITER baseline scenario, based on plasma response to probing 3D fields, was demonstrated. Finally, innovative tokamak operation using a negative triangularity shape showed many attractive features for future pilot plant operation.
|
|
| 5. |
- Allakhverdiev, Suleyman I., et al.
(författare)
-
Vyacheslav (Slava) Klimov (1945-2017) : A scientist par excellence, a great human being, a friend, and a Renaissance man
- 2018
-
Ingår i: Photosynthesis Research. - : Springer. - 0166-8595 .- 1573-5079. ; 136:1, s. 1-16
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Vyacheslav Vasilevich (V.V.) Klimov (or Slava, as most of us called him) was born on January 12, 1945 and passed away on May 9, 2017. He began his scientific career at the Bach Institute of Biochemistry of the USSR Academy of Sciences (Akademy Nauk (AN) SSSR), Moscow, Russia, and then, he was associated with the Institute of Photosynthesis, Pushchino, Moscow Region, for about 50 years. He worked in the field of biochemistry and biophysics of photosynthesis. He is known for his studies on the molecular organization of photosystem II (PSII). He was an eminent scientist in the field of photobiology, a well-respected professor, and, above all, an outstanding researcher. Further, he was one of the founding members of the Institute of Photosynthesis in Pushchino, Russia. To most, Slava Klimov was a great human being. He was one of the pioneers of research on the understanding of the mechanism of light energy conversion and of water oxidation in photosynthesis. Slava had many collaborations all over the world, and he is (and will be) very much missed by the scientific community and friends in Russia as well as around the World. We present here a brief biography and some comments on his research in photosynthesis. We remember him as a friendly and enthusiastic person who had an unflagging curiosity and energy to conduct outstanding research in many aspects of photosynthesis, especially that related to PSII.
|
|
| 6. |
- Han, Guangye, et al.
(författare)
-
Hydration of the oxygen-evolving complex of photosystem II probed in the dark-stable S1 state using proton NMR dispersion profiles
- 2014
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; :16, s. 11924-11935
-
Tidskriftsartikel (refereegranskat)abstract
- The hydration of the oxygen-evolving complex (OEC) was characterized in the dark stable S1 state of photosystem II using water R1(ω) NMR dispersion (NMRD) profiles. The R1(ω) NMRD profiles were recorded over a frequency range from 0.01 MHz to 40 MHz for both intact and Mn-depleted photosystem II core complexes from Thermosynechococcus vulcanus (T. vulcanus). The intact-minus-(Mn)-depleted difference NMRD profiles show a characteristic dispersion from approximately 0.03 MHz to 1 MHz, which is interpreted on the basis of the Solomon-Bloembergen-Morgan (SBM) and the slow motion theories as being due to a paramagnetic enhanced relaxation (PRE) of water protons. Both theories are qualitatively consistent with the ST = 1, g = 4.9 paramagnetic state previously described for the S1 state of the OEC; however, an alternative explanation involving the loss of a separate class of long-lived internal waters due to the Mn-depletion procedure can presently not be ruled out. Using a point-dipole approximation the PRE-NMRD effect can be described as being caused by 1-2 water molecules that are located about 10 Å away from the spin center of the Mn4CaO5 cluster in the OEC. The application of the SBM theory to the dispersion observed for PSII in the S1 state is questionable, because the parameters extracted do not fulfil the presupposed perturbation criterion. In contrast, the slow motion theory gives a consistent picture indicating that the water molecules are in fast chemical exchange with the bulk (τw < 1 μs). The modulation of the zero-field splitting (ZFS) interaction suggests a (restricted) reorientation/structural equilibrium of the Mn4CaO5 cluster with a characteristic time constant of τZFS = 0.6-0.9 μs.
|
|
| 7. |
- Huang, Meng, et al.
(författare)
-
Fiber Integrated Wavelength Converter Based on a Silicon Core Fiber With a Nano-Spike Coupler
- 2019
-
Ingår i: IEEE Photonics Technology Letters. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 1041-1135 .- 1941-0174. ; 31:19, s. 1561-1564
-
Tidskriftsartikel (refereegranskat)abstract
- An all-fiber integrated nonlinear silicon photonic wavelength converter has been proposed and fabricated using the silicon core fiber platform. The silicon fiber was spliced directly to a conventional single mode fiber, facilitated via an inverse tapered nano-spike that helped to reduce the mode mismatch between the different core materials. Four-wave mixing-based wavelength conversion with an efficiency as high as -22.1 dB has been achieved for selected wavelengths across the C-band in a device length of only similar to 1 cm. Successful conversion of quadrature phase-shift keying signals at a 20-Gb/s bitrate, with a 1 to 2 dB penalty level at the bit error ratio (BER) = 3.8 x 10(-3), was used to demonstrate the suitability of the silicon fiber device for the construction of ultra-compact, all-fiber-based optical signal processing systems.
|
|
| 8. |
- Lensink, Marc F., et al.
(författare)
-
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
-
Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
-
Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
|
|
| 9. |
- Messinger, Johannes, et al.
(författare)
-
Photosynthesis : from natural to artificial
- 2014
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 16:24, s. 11810-11811
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
|
|
| 10. |
|
|
