| 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. |
- Zhou, Yongqiang, et al.
(författare)
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How hydrology and anthropogenic activity influence the molecular composition and export of dissolved organic matter : Observations along a large river continuum
- 2021
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Ingår i: Limnology and Oceanography. - : John Wiley & Sons. - 0024-3590 .- 1939-5590. ; 66:5, s. 1730-1742
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Tidskriftsartikel (refereegranskat)abstract
- Large rivers are the main arteries for transportation of carbon to the ocean; yet, how hydrology and anthropogenic disturbances may change the composition and export of dissolved organic matter along large river continuums is largely unknown. The Yangtze River has a watershed area of 1.80 x 10(6) km(2). It originates from the Qinghai-Tibet Plateau and flows 6300 km eastward through the center of China. We collected samples (n = 271) along the river continuum and analyzed weekly samples at the most downstream situated gauging station in 2017-2018 and gathered long-term (2006-2018) water quality data. We found higher gross domestic product, population density, and urban and agricultural land use downstream than upstream of the Three Gorges Dam, coinciding with higher dissolved organic carbon (DOC), UV absorption (a(254)), specific ultraviolet absorbance (SUVA(254)), parallel factor analysis-derived C1-C5, aliphatic compounds, and lower a(250):a(365) and spectral slope (S275-295). Chemical oxygen demand, humic-like C1-C2 and C6, and protein-like C4 and C7 increased, while dissolved oxygen and ammonium decreased with increasing discharge at most of the sites studied, including the intensively monitored downstream site. The annual DOC fluxes were ca. 1.5-1.8 Tg yr(-1), and 12-18% was biodegradable in a 28-d bio-incubation. Our results highlight that urbanization and stormwater periods enhanced the export of both terrestrial organic-rich substances and household effluents from nearshore residential areas. Our study emphasizes the continued need to protect the Yangtze River watershed as increased organic carbon loading or altered composition and bio-lability may change the ecosystem function and carbon cycling.
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| 3. |
- Cai, Jing, et al.
(författare)
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Size-segregated particle number and mass concentrations from different emission sources in urban Beijing
- 2020
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 20:21, s. 12721-12740
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Tidskriftsartikel (refereegranskat)abstract
- Although secondary particulate matter is reported to be the main contributor of PM2.5 during haze in Chinese megacities, primary particle emissions also affect particle concentrations. In order to improve estimates of the contribution of primary sources to the particle number and mass concentrations, we performed source apportionment analyses using both chemical fingerprints and particle size distributions measured at the same site in urban Beijing from April to July 2018. Both methods resolved factors related to primary emissions, including vehicular emissions and cooking emissions, which together make up 76% and 24% of total particle number and organic aerosol (OA) mass, respectively. Similar source types, including particles related to vehicular emissions (1.6 +/- 1.1 mu gm(-3); 2.4 +/- 1.8 x 10(3) cm(-3) and 5.5 +/- 2.8 x 10(3) cm(-3) for two traffic-related components), cooking emissions (2.6 +/- 1.9 mu gm(-3) and 5.5 +/- 3.3 x 10(3) cm(-3)) and secondary aerosols (51 +/- 41 mu gm(-3) and 4.2 +/- 3.0 x 10(3) cm(-3)), were resolved by both methods. Converted mass concentrations from particle size distributions components were comparable with those from chemical fingerprints. Size distribution source apportionment separated vehicular emissions into a component with a mode diameter of 20 nm (traffic-ultrafine) and a component with a mode diameter of 100 nm (traffic-fine). Consistent with similar day- and nighttime diesel vehicle PM2.5 emissions estimated for the Beijing area, traffic-fine particles, hydrocarbon-like OA (HOA, traffic-related factor resulting from source apportionment using chemical fingerprints) and black carbon (BC) showed similar diurnal patterns, with higher concentrations during the night and morning than during the afternoon when the boundary layer is higher. Traffic-ultrafine particles showed the highest concentrations during the rush-hour period, suggesting a prominent role of local gasoline vehicle emissions. In the absence of new particle formation, our re-sults show that vehicular-related emissions (14% and 30% for ultrafine and fine particles, respectively) and cooking-activity-related emissions (32 %) dominate the particle number concentration, while secondary particulate matter (over 80 %) governs PM2.5 mass during the non-heating season in Beijing.
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| 4. |
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| 5. |
- Chen, Xiaolong, et al.
(författare)
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Nontrivial resource requirement in the early stage for containment of epidemics
- 2019
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Ingår i: Physical review. E. - 2470-0045 .- 2470-0053. ; 100:3
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Tidskriftsartikel (refereegranskat)abstract
- During epidemic control, containment of the disease is usually achieved through increasing a devoted resource to reduce the infectiousness. However, the impact of this resource expenditure has not been studied quantitatively. For disease spread, the recovery rate can be positively correlated with the average amount of resource devoted to infected individuals. By incorporating this relation we build a novel model and find that insufficient resource leads to an abrupt increase in the infected population size, which is in marked contrast with the continuous phase transitions believed previously. Counterintuitively, this abrupt phase transition is more pronounced in less contagious diseases. Furthermore, we find that even for a single infection source, the public resource needs to be available in a significant amount, which is proportional to the total population size, to ensure epidemic containment. Our findings provide a theoretical foundation for efficient epidemic containment strategies in the early stage.
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| 6. |
- Han, Ning, et al.
(författare)
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Achieving Efficient Electrocatalytic Oxygen Evolution in Acidic Media on Yttrium Ruthenate Pyrochlore through Cobalt Incorporation
- 2023
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Ingår i: Advanced Functional Materials. - : Wiley. - 1616-301X .- 1616-3028. ; 33:20
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Tidskriftsartikel (refereegranskat)abstract
- The development of electrocatalysts for the oxygen evolution reaction (OER) especially in acidic media remains the major challenge that still requires significant advances, both in material design and mechanistic exploration. In this study, the incorporation of cobalt in Y2-xCoxRu2O7−δ results in an ultrahigh OER activity because of the charge redistribution at eg orbitals between Ru and Co atoms. The Y1.75Co0.25Ru2O7−δ electrocatalyst exhibits an extremely small overpotential of 275 mV in 0.5 m H2SO4 at the current density of 10 mA cm−2, which is smaller than that of parent Y2Ru2O7−δ (360 mV) and commercial RuO2 (286 mV) catalysts. The systematic investigation of the composition related to OER activity shows that the Co substitution will also bring other effective changes, such as reducing the bandgap, and creating oxygen vacancies, which result in fast OER charge transfer. Meanwhile, the strengthening of the bond hybridization between the d orbitals of metal (Y and Ru) and the 2p orbitals of O will intrinsically enhance the chemical stability. Finally, theoretical calculations indicate that cobalt substitution reduces the theoretical overpotential both through an adsorbate evolution mechanism and a lattice oxygen-mediated mechanism.
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| 7. |
- Shen, Qian, et al.
(författare)
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The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis
- 2018
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Ingår i: Molecular Plant. - : Cell Press. - 1674-2052 .- 1752-9867. ; 11:6, s. 776-788
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Tidskriftsartikel (refereegranskat)abstract
- Artemisia annua, commonly known as sweet wormwood or Qinghao, is a shrub native to China and has long been used for medicinal purposes. A. annua is now cultivated globally as the only natural source of a potent anti-malarial compound, artemisinin. Here, we report a high-quality draft assembly of the 1.74-gigabase genome of A. annua, which is highly heterozygous, rich in repetitive sequences, and contains 63 226 protein-coding genes, one of the largest numbers among the sequenced plant species. We found that, as one of a few sequenced genomes in the Asteraceae, the A. annua genome contains a large number of genes specific to this large angiosperm clade. Notably, the expansion and functional diversification of genes encoding enzymes involved in terpene biosynthesis are consistent with the evolution of the artemisinin biosynthetic pathway. We further revealed by transcriptome profiling that A. annua has evolved the sophisticated transcriptional regulatory networks underlying artemisinin biosynthesis. Based on comprehensive genomic and transcriptomic analyses we generated transgenic A. annua lines producing high levels of artemisinin, which are now ready for large-scale production and thereby will help meet the challenge of increasing global demand of artemisinin.
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| 8. |
- Zhang, Juqing, et al.
(författare)
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Super-enhancers conserved within placental mammals maintain stem cell pluripotency
- 2022
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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 (PNAS). - 0027-8424 .- 1091-6490. ; 119:40
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Tidskriftsartikel (refereegranskat)abstract
- Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive. Here, we performed comprehensive comparative epigenomic and transcription factor binding analyses among pigs, humans, and mice to identify pluripotency-associated SEs. Like typical enhancers, SEs displayed rapid evolu-tion in mammals. We showed that BRD4 is an essential and conserved activator for mammalian pluripotency-associated SEs. Comparative motif enrichment analysis revealed 30 shared transcription factor binding motifs among the three species. The majority of transcriptional factors that bind to identified motifs are known regulators associated with pluripotency. Further, we discovered three pluripotency-associated SEs (SE-SOX2, SE-PIM1, and SE-FGFR1) that displayed remarkable conservation in pla-cental mammals and were sufficient to drive reporter gene expression in a pluripotency-dependent manner. Disruption of these conserved SEs through the CRISPR-Cas9 approach severely impaired stem cell pluripotency. Our study provides insights into the understanding of conserved regulatory mechanisms underlying the maintenance of plu-ripotency as well as species-specific modulation of the pluripotency-associated regula-tory networks in mammals.
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| 9. |
- Zhang, Wei, et al.
(författare)
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Balancing Adsorption, Catalysis, and Desorption in Cathode Catalyst For Li–S Batteries
- 2023
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Ingår i: Advanced Energy Materials. - 1614-6832 .- 1614-6840. ; 13:43
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Tidskriftsartikel (refereegranskat)abstract
- The complicated electrochemical catalytic conversion process of polysulfides in metal–sulfur batteries involves three steps: adsorption, catalysis, and desorption process. Even as huge efforts are made for the understanding of the separate steps (especially for the adsorption and catalysis process), research focusing on the entire process is still scarce. Herein, a series of cobalt phosphides (CoP, CoP2, and CoP3) is employed with identical hollow morphology as model electrocatalysts to investigate the significance of the desorption process and discuss the balancing among the adsorption, catalysis, and desorption of lithium polysulfides (LiPSs). The experimental data demonstrate that, compared to CoP and CoP3, CoP2 exhibits moderate adsorption of LiPSs, which enhances the reduction kinetics of S8 to Li2S and regulates the desorption of short-chain LiPSs. Theoretical calculations further confirm that CoP2 with moderate adsorption of LiPSs exhibits better redox kinetics of LiPSs compared to CoP and CoP3. Moderate adsorption enables the CoP2-based sulfur cathode to deliver excellent stability with 86% capacity retention (2.6 and 2.0 times higher than CoP and CoP3, respectively) over 1000 cycles at 1 C. All these results indicate that in the adsorption-catalysis-desorption chain for LiPSs, all steps need to be considered rather than just focusing on one step of the process.
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| 10. |
- Zhu, Zhenshuo, et al.
(författare)
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Histone demethylase complexes KDM3A and KDM3B cooperate with OCT4/SOX2 to define a pluripotency gene regulatory network
- 2021
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Ingår i: The FASEB Journal. - : John Wiley & Sons. - 0892-6638 .- 1530-6860. ; 35:6
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Tidskriftsartikel (refereegranskat)abstract
- The pluripotency gene regulatory network of porcine induced pluripotent stem cells(piPSCs), especially in epigenetics, remains elusive. To determine the biological function of epigenetics, we cultured piPSCs in different culture conditions. We found that activation of pluripotent gene- and pluripotency-related pathways requires the erasure of H3K9 methylation modification which was further influenced by mouse embryonic fibroblast (MEF) served feeder. By dissecting the dynamic change of H3K9 methylation during loss of pluripotency, we demonstrated that the H3K9 demethylases KDM3A and KDM3B regulated global H3K9me2/me3 level and that their co-depletion led to the collapse of the pluripotency gene regulatory network. Immunoprecipitation-mass spectrometry (IP-MS) provided evidence that KDM3A and KDM3B formed a complex to perform H3K9 demethylation. The genome-wide regulation analysis revealed that OCT4 (O) and SOX2 (S), the core pluripotency transcriptional activators, maintained the pluripotent state of piPSCs depending on the H3K9 hypomethylation. Further investigation revealed that O/S cooperating with histone demethylase complex containing KDM3A and KDM3B promoted pluripotency genes expression to maintain the pluripotent state of piPSCs. Together, these data offer a unique insight into the epigenetic pluripotency network of piPSCs.
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