| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- 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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| 3. |
- Li, Xinyi, et al.
(författare)
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Phylogenetic analysis and functional characterization of norcoclaurine synthase involved in benzylisoquinoline alkaloids biosynthesis in Stephania tetrandra
- 2023
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Ingår i: Journal of Cellular Physiology. - 1097-4652 .- 0021-9541. ; In Press
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Tidskriftsartikel (refereegranskat)abstract
- Benzylisoquinoline alkaloids (BIAs) are a class of secondary metabolites that possess diverse pharmaceutical properties and are exclusively accumulated in specific plant genera. The Pictet–Spengler condensation, catalyzed by norcoclaurine synthase (NCS), represents a key enzymatic reaction in the biosynthetic pathway of BIAs. While NCS genes have been identified in several plant families such as Papaveraceae, Berberidaceae, and Ranunculaceae, no NCS genes have been reported in Menispermaceae, which is another genus known to accumulate BIAs. Here, NCSs were isolated and functionally characterized from the Menispermaceae family plant Stephania tetrandra. In vitro enzyme assay identified two functional StNCSs which could catalyze the formation of (S)-norcoclaurine. These functionally characterized genes were then integrated into engineered yeast to enable the production of norcoclaurine. Phylogenetic analysis of the NCS enzymes revealed that the StNCSs predominantly clustered into two clades. The functional StNCSs clustered with known NCSs, highlighting the presence of a specific NCS catalytic domain. This study not only provides additional genetic components for the synthetic biology-based production of BIAs in yeast but also contributes to the understanding of the phylogenetic relationships and structure–function relationship of NCS genes involved in the origin and production of BIAs.
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| 4. |
- Nowak, Michael D., et al.
(författare)
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The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic
- 2021
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; :3, s. 661-676
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Tidskriftsartikel (refereegranskat)abstract
- The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome-scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.
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| 5. |
- Tan, Xiaoqin, et al.
(författare)
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Band gap tailoring in a low toxicity and low-cost solar cell absorber Cu3SbS4 through Na alloying : A first-principles study
- 2023
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Ingår i: Journal of Crystal Growth. - : Elsevier BV. - 0022-0248 .- 1873-5002. ; 607
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Tidskriftsartikel (refereegranskat)abstract
- High power conversion efficiency, high stability, low cost, and environmentally friendly manufacturing are the main requirements for a commercializable photovoltaic device. Cu3SbS4 is an eco-friendly and earth-abundant compound that is studied as a potential solar cell absorber. However, its band gap is smaller than the ideal value. In this work, the possibility to modulate and improve the band gap by sodium alloying has been investigated by means of the first-principles density functional theory with the HSE06 hybrid functional. Our results demonstrate that the Cu3-xNaxSbS4 alloy with a high alloying concentration should be possible to realize, and that the Na incorporation widens the gap. An alloy concentration of x approximate to 0.64 yields the desired gap for a solar light absorber, which can then lead to a more efficient solar cell.
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| 6. |
- Zhang, Xiaotian, et al.
(författare)
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Delafossite NaYTe2 as a transparent conductive material with bipolar conductivity: A first-principles prediction
- 2024
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Ingår i: Journal of Physics and Chemistry of Solids. - : Elsevier BV. - 0022-3697 .- 1879-2553. ; 190
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Tidskriftsartikel (refereegranskat)abstract
- Doping asymmetry is a long-standing issue for the progress of wide-bandgap semiconductors, including also several transparent conductors. However, a few compounds exhibit bipolar conductivity, implying a desired band gap in combination with proper energy positions of the band edges according to the empirical doping limit rule. The present first-principles study of delafossite NaYTe2 reveals that the compound is thermodynamic stable with an optical gap energy of ∼3.0 eV and an ionization potential of 6.2 eV, and the electronic structure is thus in the range for realizing bipolar character as a transparent conductive material. In addition, the analysis of the defect properties strengthens this prediction, especially for high free carrier concentration in NaYTe2, obtained by either extrinsic doping or intrinsic defects under suitable growth conditions.
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| 7. |
- Zhong, Jia, et al.
(författare)
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B vitamins attenuate the epigenetic effects of ambient fine particles in a pilot human intervention trial
- 2017
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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. ; 114:13, s. 3503-3508
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Tidskriftsartikel (refereegranskat)abstract
- Acute exposure to fine particle (PM2.5) induces DNA methylation changes implicated in inflammation and oxidative stress. We conducted a crossover trial to determine whether B-vitamin supplementation averts such changes. Ten healthy adults blindly received a 2-h, controlled-exposure experiment to sham under placebo, PM2.5 (250 μg/m(3)) under placebo, and PM2.5 (250 μg/m(3)) under B-vitamin supplementation (2.5 mg/d folic acid, 50 mg/d vitamin B6, and 1 mg/d vitamin B12), respectively. We profiled epigenome-wide methylation before and after each experiment using the Infinium HumanMethylation450 BeadChip in peripheral CD4(+) T-helper cells. PM2.5 induced methylation changes in genes involved in mitochondrial oxidative energy metabolism. B-vitamin supplementation prevented these changes. Likewise, PM2.5 depleted 11.1% [95% confidence interval (CI), 0.4%, 21.7%; P = 0.04] of mitochondrial DNA content compared with sham, and B-vitamin supplementation attenuated the PM2.5 effect by 102% (Pinteraction = 0.01). Our study indicates that individual-level prevention may be used to complement regulations and control potential mechanistic pathways underlying the adverse PM2.5 effects, with possible significant public health benefit in areas with frequent PM2.5 peaks.
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