| 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. |
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| 3. |
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| 4. |
- Nie, Shuai, et al.
(författare)
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Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color
- 2023
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Ingår i: Horticulture Research. - : Oxford University Press. - 2662-6810 .- 2052-7276. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
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| 5. |
- Nie, Shuai, et al.
(författare)
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Progress in phylogenetics, multi-omics and flower coloration studies in Rhododendron
- 2024
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Ingår i: Ornamental Plant Research. - : Maximum Academic Press. - 2769-2094. ; 4
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Forskningsöversikt (refereegranskat)abstract
- The genus Rhododendron exhibits an immense diversity of flower colors and represents one of the largest groups of woody plants, which is of great importance for ornamental plant research. This review summarizes recent progress in deciphering the genetic basis for flower coloration in Rhododendron. We describe advances in phylogenetic reconstruction and genome sequencing of Rhododendron species. The metabolic pathways of flower color are outlined, focusing on key structural and regulatory genes involved in pigment synthesis. Gene duplications and losses associated with color diversification are discussed. In addition, the application of multi-omics approaches and analysis of gene co-expression networks to elucidate complex gene regulatory mechanisms is emphasized. This synthesis of current knowledge provides a foundation for future research on the evolution of flower color diversity within the Rhododendron lineage. Ultimately, these discoveries will support breeding endeavors aimed at harnessing the genetics of flower coloration and developing novel cultivars that exhibit desired floral traits.
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| 6. |
- Wang, Yu-Cheng, et al.
(författare)
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Porous Carbon Membrane-Supported Atomically Dispersed Pyrrole-Type Fe-N-4 as Active Sites for Electrochemical Hydrazine Oxidation Reaction
- 2020
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Ingår i: Small. - : Wiley. - 1613-6810 .- 1613-6829. ; 16:31
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Tidskriftsartikel (refereegranskat)abstract
- The rational design of catalytically active sites in porous materials is essential in electrocatalysis. Herein, atomically dispersed Fe-N-x sites supported by hierarchically porous carbon membranes are designed to electrocatalyze the hydrazine oxidation reaction (HzOR), one of the key techniques in electrochemical nitrogen transformation. The high intrinsic catalytic activity of the Fe-N-x single-atom catalyst together with the uniquely mixed micro-/macroporous membrane support positions such an electrode among the best-known heteroatom-based carbon anodes for hydrazine fuel cells. Combined with advanced characterization techniques, electrochemical probe experiments, and density functional theory calculation, the pyrrole-type Fe-N-4 structure is identified as the real catalytic site in HzOR.
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| 7. |
- Xue, Tian-Tian, et al.
(författare)
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Ignored Biodiversity in Acid Soil Islands in Karst Areas, South China : Impatiens longlinensis (Balsaminaceae), a New Critically Endangered Species
- 2020
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Ingår i: Systematic Botany. - 0363-6445 .- 1548-2324. ; 45:4, s. 891-899
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Tidskriftsartikel (refereegranskat)abstract
- The karst area in South China is notable for its fragile vegetation and unique flora with many narrow endemic species, and is one of the most threatened biodiversity hotspots in the world. However, the biodiversity of acid soil areas scattered in the karst area have previously been underestimated. With a recent increase of new discoveries of plants and animals, the conservation of biodiversity in these acid soil areas has become urgent. This study deals with a new species, Impatiens longlinensis . The new species is similar to I. yui and I. lasiophyton in having pubescence, two lateral sepals, funnelform lower sepal, and linear capsule. But it can be distinguished by having orbicular to obovate dorsal sepals and oblong to elliptic lower and upper lobes of lateral united petals. Moreover, molecular data and micro-morphological evidence also support that the species is new to science. The new species is only known from a valley near the summit of Mt. Jinzhongshan within an area of less than 5 km2. Based on the Red List categories and criteria developed by the International Union for Conservation of Nature, and the threat posed by exploitation for tourism development, we categorize it as Critically Endangered (CR).
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| 8. |
- Yang, Fu-Sheng, et al.
(författare)
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Chromosome-level genome assembly of a parent species of widely cultivated azaleas
- 2020
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea. Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.
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| 9. |
- Gao, Xindi, et al.
(författare)
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Cryptococcal Hsf3 controls intramitochondrial ROS homeostasis by regulating the respiratory process
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Mitochondrial quality control prevents accumulation of intramitochondrial-derived reactive oxygen species (mtROS), thereby protecting cells against DNA damage, genome instability, and programmed cell death. However, underlying mechanisms are incompletely understood, particularly in fungal species. Here, we show that Cryptococcus neoformans heat shock factor 3 (CnHsf3) exhibits an atypical function in regulating mtROS independent of the unfolded protein response. CnHsf3 acts in nuclei and mitochondria, and nuclear- and mitochondrial-targeting signals are required for its organelle-specific functions. It represses the expression of genes involved in the tricarboxylic acid cycle while promoting expression of genes involved in electron transfer chain. In addition, CnHsf3 responds to multiple intramitochondrial stresses; this response is mediated by oxidation of the cysteine residue on its DNA binding domain, which enhances DNA binding. Our results reveal a function of HSF proteins in regulating mtROS homeostasis that is independent of the unfolded protein response.
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| 10. |
- Hu, Lei, et al.
(författare)
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Molecular surface modification of silver chalcogenolate clusters
- 2022
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Ingår i: Dalton Trans.. - : Royal Society of Chemistry (RSC). ; 51, s. 3241-3247
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Tidskriftsartikel (refereegranskat)abstract
- This study presents a molecular surface modification approach to synthesizing a family of silver chalcogenolate clusters (SCCs) containing the same [Ag12S6] core and different surface-bonded organic ligands (DMAc or pyridines; DMAc = dimethylacetamide), with the aim of tuning the luminescence property and increasing the structural stability of the SCCs. The SCCs displayed strong and tuneable luminescence emissions at 77 K (from green to orange to red) as influenced by the peripheral pyridine ligands. In addition, SCC 5 protected by pyridine molecules was stable in ambient air, humid air and even liquid water for a long time (up to 1 week), and it was more structurally stable than SCC 1 bonded with DMAc molecules under the same conditions. The high structural stability of SCC 5 can be explained by the ability of pyridine molecules to form strong coordination bonds with silver atoms. This study offers a new way of designing structurally stable metal nanoclusters with tuneable physicochemical properties.
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| 11. |
- Nie, Shuai, et al.
(författare)
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Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation
- 2022
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from ~ 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.
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| 12. |
- Shangguan, Yidan, et al.
(författare)
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On the Fundamental Diagram for Freeway Traffic: Exploring the Lower Bound of the Fitting Error and Correcting the Generalized Linear Regression Models
- 2023
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Ingår i: MATHEMATICS. - 2227-7390. ; 11:16
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Tidskriftsartikel (refereegranskat)abstract
- In traffic flow, the relationship between speed and density exhibits decreasing monotonicity and continuity, which is characterized by various models such as the Greenshields and Greenberg models. However, some existing models, i.e., the Underwood and Northwestern models, introduce bias by incorrectly utilizing linear regression for parameter calibration. Furthermore, the lower bound of the fitting errors for all these models remains unknown. To address above issues, this study first proves the bias associated with using linear regression in handling the Underwood and Northwestern models and corrects it, resulting in a significantly lower mean squared error (MSE). Second, a quadratic programming model is developed to obtain the lower bound of the MSE for these existing models. The relative gaps between the MSEs of existing models and the lower bound indicate that the existing models still have a lot of potential for improvement.
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| 13. |
- Shi, Yu-Sheng, et al.
(författare)
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Limonoids from Citrus : Chemistry, anti-tumor potential, and other bioactivities
- 2020
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Ingår i: Journal of Functional Foods. - : ELSEVIER. - 1756-4646 .- 2214-9414. ; 75
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Tidskriftsartikel (refereegranskat)abstract
- Citrus limonoids are tetranortriterpenoids compounds mainly found in oranges, lemons, grapefruits, and other fruits of Citrus. They are proved to be the leading cause of bitterness in Citrus fruits and are mainly consumed for therapeutic purposes and as food. Numerous studies have focused on Citrus limonoids and intend to develop new chemotherapeutic or complementary medicine in recent years. Citrus limonoids showed various bioactivities such as anti-tumor, antioxidative, anti-inflammatory, anti-neurological diseases, immunomodulatory, anti -insect, anti-bacteria, antiviral activities, etc. This review summarized limonoids from Citrus to date, along with their chemical structures and biological activities with a particular focus on their anti-tumor potential.
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| 14. |
- Wang, Ze-Kun, et al.
(författare)
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Assembly of Discrete Chalcogenolate Clusters into a One-Dimensional Coordination Polymer with Enhanced Photocatalytic Activity and Stability
- 2020
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 59:4, s. 2121-2126
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Tidskriftsartikel (refereegranskat)abstract
- Interlinking discrete supertetrahedral chalcogenolate clusters with conjugated bipyridine linkers form a one-dimensional coordination polymer, [Cd6Ag4(SPh)16(DMF)(H2O)(bpe)]n (1a), displaying a broader visible-light absorption and a narrower band gap than those of the discrete cluster. More importantly, the coordination polymer demonstrates enhanced activity and stability for the photocatalytic degradation of organic dye in water.
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| 15. |
- Wei, Minrui, et al.
(författare)
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Vibronic fine structure in the nitrogen 1s photoelectron spectra of molecules from Franck-Condon simulations: Azines
- 2022
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society (APS). - 2469-9926 .- 2469-9934. ; 106:2
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Tidskriftsartikel (refereegranskat)abstract
- Vibronic coupling plays a pivotal role in molecular spectroscopy. We present a theoretical study on vibrationally resolved x-ray photoelectron spectra (XPS) of seven azines (CxHyNz; pyridine, three diazines, two triazines, and one tetrazine) at the nitrogen 1s edge, to explore the vibronic coupling effects as influenced by consecutive replacement of the CH group with a N atom. Franck-Condon simulations were performed with the Duschinsky rotation effect included, where the electronic structure was calculated by the density functional theory. Validations on pyrimidine show good agreement with the experiment, weak functional dependence, and weak mode mixing effect. We observed an evident blue shift in binding energies with the increasing number of N atoms in this series, together with molecule-dependent vibronic fine structures. These molecules have either C2v or Cs molecular symmetry at the optimized core-ionized geometries. Franck-Condon-active vibrational modes were identified to be low frequency (500–1650 cm−1), totally symmetric (A1 or A′), in-plane ring deformation modes. Core ionization on N∗ always leads to elongation of the N∗−N bond length, accompanied by an increase of the ∠C−N∗−X bond angle (X=C, N). Our study predicts accurate theoretical reference spectra for the azine family and provides useful information on the properties of the core-ionized states as influenced by the structural change of CH↔N replacement.
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| 16. |
- Yao, JT, et al.
(författare)
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Early modulation of macrophage ROS-PPARγ-NF-κB signalling by sonodynamic therapy attenuates neointimal hyperplasia in rabbits
- 2020
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1, s. 11638-
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Tidskriftsartikel (refereegranskat)abstract
- Disruption of re-endothelialization and haemodynamic balance remains a critical side effect of drug-eluting stents (DES) for preventing intimal hyperplasia. Previously, we found that 5-aminolevulinic acid-mediated sonodynamic therapy (ALA-SDT) suppressed macrophage-mediated inflammation in atherosclerotic plaques. However, the effects on intimal hyperplasia and re-endothelialization remain unknown. In this study, 56 rabbits were randomly assigned to control, ultrasound, ALA and ALA-SDT groups, and each group was divided into two subgroups (n = 7) on day 3 after right femoral artery balloon denudation combined with a hypercholesterolemic diet. Histopathological analysis revealed that ALA-SDT enhanced macrophage apoptosis and ameliorated inflammation from day 1. ALA-SDT inhibited neointima formation without affecting re-endothelialization, increased blood perfusion, decreased the content of macrophages, proliferating smooth muscle cells (SMCs) and collagen but increased elastin by day 28. In vitro, ALA-SDT induced macrophage apoptosis and reduced TNF-α, IL-6 and IL-1β via the ROS-PPARγ-NF-κB signalling pathway, which indirectly inhibited human umbilical artery smooth muscle cell (HUASMC) proliferation, migration and IL-6 production. ALA-SDT effectively inhibits intimal hyperplasia without affecting re-endothelialization. Hence, its clinical application combined with bare-metal stent (BMS) implantation presents a potential strategy to decrease bleeding risk caused by prolonged dual-antiplatelet regimen after DES deployment.
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| 17. |
- Zheng, Xiaoqi, et al.
(författare)
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Drivers of change in China’s energy-related CO2 emissions
- 2020
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Ingår i: Proceedings of the National Academy of Science of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:1, s. 29-36
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Tidskriftsartikel (refereegranskat)abstract
- CO2 emissions are of global concern because of climate change. China has become the largest CO2 emitter in the world and presently accounts for 30% of global emissions. Here, we analyze the major drivers of energy-related CO2 emissions in China from 1978 when the reform and opening-up policy was launched. We find that 1) there has been a 6-fold increase in energy-related CO2 emissions, which was driven primarily (176%) by economic growth followed by population growth (16%), while the effects of energy intensity (−79%) and carbon intensity (−13%) slowed the growth of carbon emissions over most of this period; 2) energy-related CO2 emissions are positively related to per capita gross domestic product (GDP), population growth rate, carbon intensity, and energy intensity; and 3) a portfolio of command-and-control policies affecting the drivers has altered the total emission trend. However, given the major role of China in global climate change mitigation, significant future reductions in China’s CO2 emissions will require transformation toward low-carbon energy systems.
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| 18. |
- Zhu, Bin, et al.
(författare)
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Evaluation of TMPA satellite precipitation in driving VIC hydrological model over the upper Yangtze river basin
- 2020
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Ingår i: Water. - : MDPI AG. - 2073-4441. ; 12:11
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Tidskriftsartikel (refereegranskat)abstract
- Although the Tropical Rainfall Measurement Mission (TRMM) has come to an end, the evaluation of TRMM satellite precipitation is still of great significance for the improvement of the Global Precipitation Measurement (GPM). In this paper, the hydrological utility of TRMM Multi-satellite Precipitation Analysis (TMPA) 3B42 RTV7/V7 precipitation products was evaluated using the variable infiltration capacity (VIC) hydrological model in the upper Yangtze River basin. The main results show that (1) TMPA 3B42V7 had a reliable performance in precipitation estimation compared with the gauged precipitation on both spatial and temporal scales over the upper Yangtze River basin. Although TMPA 3B42V7 slightly underestimated precipitation, TMPA 3B42RTV7 significantly overestimated precipitation at daily and monthly time scales; (2) the simulated runoff by the VIC hydrological model showed a high correlation with the gauged runoff and lower bias at daily and monthly time scales. The Nash–Sutcliffe coefficient of efficiency (NSCE) value was as high as 0.85, the relative bias (RB) was −6.36% and the correlation coefficient (CC) was 0.93 at the daily scale; (3) the accuracy of the 3B42RTV7-driven runoff simulation had been greatly improved by using the hydrological calibration parameters obtained from 3B42RTV7 compared with that of gauged precipitation. A lower RB (14.38% vs. 66.58%) and a higher CC (0.87 vs. 0.85) and NSCE (0.71 vs. −0.92) can be found at daily time scales when we use satellite data instead of gauged precipitation data to calibrate the VIC model. However, the performance of the 3B42V7-driven runoff simulation did not improve in the same operation accordingly. The cause might be that the 3B42V7 satellite products have been adjusted by gauged precipitation. This study suggests that it might be better to calibrate the parameters using satellite data in hydrological simulations, especially for unadjusted satellite data. This study is not only helpful for understanding the assessment of multi-satellite precipitation products in large-scale and complex areas in the upper reaches of the Yangtze River, but also can provide a reference for the hydrological utility of the satellite precipitation products in other river basins of the world.
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