| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Akbari, Parsa, et al.
(author)
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Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity
- 2021
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 373:6550
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Journal article (peer-reviewed)abstract
- Large-scale human exome sequencing can identify rare protein-coding variants with a large impact on complex traits such as body adiposity. We sequenced the exomes of 645,626 individuals from the United Kingdom, the United States, and Mexico and estimated associations of rare coding variants with body mass index (BMI). We identified 16 genes with an exome-wide significant association with BMI, including those encoding five brain-expressed G protein-coupled receptors (CALCR, MC4R, GIPR, GPR151, and GPR75). Protein-truncating variants in GPR75 were observed in ∼4/10,000 sequenced individuals and were associated with 1.8 kilograms per square meter lower BMI and 54% lower odds of obesity in the heterozygous state. Knock out of Gpr75 in mice resulted in resistance to weight gain and improved glycemic control in a high-fat diet model. Inhibition of GPR75 may provide a therapeutic strategy for obesity.
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| 3. |
- Bischak, Connor G., et al.
(author)
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Liquid-like Interfaces Mediate Structural Phase Transitions in Lead Halide Perovskites
- 2020
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In: Matter. - : Elsevier BV. - 2590-2393 .- 2590-2385. ; 3:2, s. 534-545
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Journal article (peer-reviewed)abstract
- Microscopic pathways of structural phase transitions inmetal halide perovskites are difficult to probe because they occur over disparate time and length scales and because electron-based microscopies typically used to directly probe nanoscale dynamics of phase transitions often damage metal halide perovskite materials. Using in situ nanoscale cathodoluminescence microscopy with low electron beam exposure, we visualize nucleation and growth in the thermally driven transition to the perovskite phase in hundreds of non-perovskite phase nanowires. In combination with molecular dynamics simulations, we reveal that the transformation does not follow a simple martensitic mechanism, but proceeds despite a substantial energy barrier via ion diffusion through a liquid-like interface between the two structures. While cations are disordered in this liquid-like region, the halide ions retain substantial spatial correlations. This detailed picture not only reveals how phase transitions between disparate structures can proceed, but also opens the possibility to control such processes.
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| 4. |
- Leebens-Mack, James H., et al.
(author)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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In: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Journal article (peer-reviewed)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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| 5. |
- Li, Fay-Wei, et al.
(author)
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Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns
- 2014
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In: 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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Journal article (peer-reviewed)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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| 6. |
- Lin, Jia, et al.
(author)
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Thermochromic halide perovskite solar cells
- 2018
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In: Nature Materials. - : Springer Science and Business Media LLC. - 1476-1122 .- 1476-4660. ; 17:3, s. 261-267
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Journal article (peer-reviewed)abstract
- Smart photovoltaic windows represent a promising green technology featuring tunable transparency and electrical power generation under external stimuli to control the light transmission and manage the solar energy. Here, we demonstrate a thermochromic solar cell for smart photovoltaic window applications utilizing the structural phase transitions in inorganic halide perovskite caesium lead iodide/bromide. The solar cells undergo thermally-driven, moisture-mediated reversible transitions between a transparent non-perovskite phase (81.7% visible transparency) with low power output and a deeply coloured perovskite phase (35.4% visible transparency) with high power output. The inorganic perovskites exhibit tunable colours and transparencies, a peak device efficiency above 7%, and a phase transition temperature as low as 105 degrees C. We demonstrate excellent device stability over repeated phase transition cycles without colour fade or performance degradation. The photovoltaic windows showing both photoactivity and thermochromic features represent key stepping-stones for integration with buildings, automobiles, information displays, and potentially many other technologies.
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| 7. |
- Rothfels, Carl J., et al.
(author)
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The evolutionary history of ferns inferred from 25 low-copy nuclear genes
- 2015
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In: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 102:7, s. 1089-1107
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Journal article (peer-reviewed)abstract
- PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35 877 bp), along with rigorous alignment, orthology inference and model selection. KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to similar to 200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data. CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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