| 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. |
- 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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| 3. |
- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 4. |
- Li, Fay-Wei, et al.
(författare)
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Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns
- 2014
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 111:18, s. 6672-6677
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Tidskriftsartikel (refereegranskat)abstract
- Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor-neochrome-that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.
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| 5. |
- Lin, Yuze, et al.
(författare)
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Mapping Polymer Donors toward High-Efficiency Fullerene Free Organic Solar Cells
- 2017
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Ingår i: Advanced Materials. - : WILEY-V C H VERLAG GMBH. - 0935-9648 .- 1521-4095. ; 29:3
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Tidskriftsartikel (refereegranskat)abstract
- Five polymer donors with distinct chemical structures and different electronic properties are surveyed in a planar and narrow-bandgap fused-ring electron acceptor (IDIC)-based organic solar cells, which exhibit power conversion efficiencies of up to 11%.
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| 6. |
- Wei, Yanan, et al.
(författare)
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A universal method for constructing high efficiency organic solar cells with stacked structures
- 2021
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Ingår i: Energy & Environmental Science. - : ROYAL SOC CHEMISTRY. - 1754-5692 .- 1754-5706. ; 14:4, s. 2314-2321
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Tidskriftsartikel (refereegranskat)abstract
- The construction of organic solar cells with stacked structures by the sequential deposition (SD) of donor and acceptor films has great potential in industrial production, as it demonstrates little dependence on the ratio of donor and acceptor materials, solvents, and additives. Herein, we present an eco-friendly solvent protection (ESP) method for the fabrication of high-performance OSCs with stacked structures. Several non-aromatic and non-halogenated solvents are employed as protective agents to build SD devices with a configuration of indium tin oxide (ITO)/poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS Clevios P VP Al 4083)/donor/protective solvent/acceptor/perylene diimide functionalized with amino N-oxide (PDINO)/Al, which shows that n-octane is the optimal choice for SD devices. Nine different SD systems including the fullerene and nonfullerene ones present comparable photovoltaic performance to their BC counterparts, which proves the universality of this ESP method. Significantly, the device of ITO/PEDOT:PSS/D18/N3/PDINO/Al with n-octane as the protective solvent achieves a maximum PCE of 17.52%, which is the record efficiency of SD devices. Furthermore, a protective factor (delta) is proposed to demonstrate the quantitative relationship between delta and PCE after experimental and theoretical investigation, which presents an idea to understand the mechanism and provides a guideline for solvent choices.
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| 7. |
- Zhang, Xin, et al.
(författare)
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Side-Chain Engineering for Enhancing the Molecular Rigidity and Photovoltaic Performance of Noncovalently Fused-Ring Electron Acceptors
- 2021
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Ingår i: Angewandte Chemie International Edition. - : WILEY-V C H VERLAG GMBH. - 1433-7851 .- 1521-3773. ; 60:32, s. 17720-17725
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Tidskriftsartikel (refereegranskat)abstract
- Side-chain engineering is an effective strategy to regulate the solubility and packing behavior of organic materials. Recently, a unique strategy, so-called terminal side-chain (T-SC) engineering, has attracted much attention in the field of organic solar cells (OSCs), but there is a lack of deep understanding of the mechanism. Herein, a new noncovalently fused-ring electron acceptor (NFREA) containing two T-SCs (NoCA-5) was designed and synthesized. Introduction of T-SCs can enhance molecular rigidity and intermolecular pi-pi stacking, which is confirmed by the smaller Stokes shift value, lower reorganization free energy, and shorter pi-pi stacking distance in comparison to NoCA-1. Hence, the NoCA-5-based device exhibits a record power conversion efficiency (PCE) of 14.82 % in labs and a certified PCE of 14.5 %, resulting from a high electron mobility, a short charge-extraction time, a small Urbach energy (E-u), and a favorable phase separation.
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| 8. |
- Zhou, Ruimin, et al.
(författare)
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All-small-molecule organic solar cells with over 14% efficiency by optimizing hierarchical morphologies
- 2019
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- The high efficiency all-small-molecule organic solar cells (OSCs) normally require optimized morphology in their bulk heterojunction active layers. Herein, a small-molecule donor is designed and synthesized, and single-crystal structural analyses reveal its explicit molecular planarity and compact intermolecular packing. A promising narrow bandgap small-molecule with absorption edge of more than 930 nm along with our home-designed small molecule is selected as electron acceptors. To the best of our knowledge, the binary all-small-molecule OSCs achieve the highest efficiency of 14.34% by optimizing their hierarchical morphologies, in which the donor or acceptor rich domains with size up to ca. 70 nm, and the donor crystals of tens of nanometers, together with the donor-acceptor blending, are proved coexisting in the hierarchical large domain. All-small-molecule photovoltaic system shows its promising for high performance OSCs, and our study is likely to lead to insights in relations between bulk heterojunction structure and photovoltaic performance.
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| 9. |
- Zou, Zhixiang, et al.
(författare)
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Design of Filter-Based Stabilizing Control for PLL-Synchronized Converters
- 2024
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Ingår i: IEEE Transactions on Industrial Electronics. - : Institute of Electrical and Electronics Engineers (IEEE). - 0278-0046 .- 1557-9948. ; , s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- The phase-locked loop (PLL) has an important effect on the system stability of grid-connected converters in weak grids. In the literature, parameter tuning methods and stabilizing control strategies have been proposed to deal with this problem. However, most of them target at tuning parameters of PLL or mitigating the negative damping as well as the phase lag introduced by the PLL, while the interactions between the PLL and the current control and the cross coupling effects are still not fully explored in the design procedure of stabilizing control. To address this issue, this article extends the study of the interaction between the PLL and the current control using a multiple-input multiple-output (MIMO) model, and then proposes a design criterion of the stabilizing control using design-oriented analysis from the perspective of MIMO impedance model. A category of stabilizing control schemes that uses different types of biquad filters is proposed following the criterion, which not only improves system stability but also removes the coupling between the PLL and the current control according to the sensitivity analysis. Hardware-in-the-loop and experimental results are provided to verify the effectiveness of the proposed control schemes.
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