| 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. |
- Wang, Tingting, et al.
(författare)
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Proteus mirabilis Vesicles Induce Mitochondrial Apoptosis by Regulating miR96-5p/Abca1 to Inhibit Osteoclastogenesis and Bone Loss
- 2022
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Ingår i: Frontiers in Immunology. - Lausanne : Frontiers Media S.A.. - 1664-3224. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Bone loss due to an increased osteoclast activity is common in osteoporosis and rheumatoid arthritis. For the first time, we observed an inhibition of osteoclast formation and bone resorption by outer-membrane vesicles (OMVs) from a Gram-negative, pathogenic bacterium, Proteus mirabilis (P.M). Gene ontogeny and KEGG enrichment analyses of miRNA and mRNA sequencing data demonstrated a significant effect of P.M OMVs on mitochondrial functions and apoptotic pathways. OMVs induced mitochondrial dysfunction through an increased level of intracellular ROS, collapse of mitochondrial membrane potential (ΔΨm), and modulation of Bax, Bcl-2, caspase-3, and cytochrome c expression. In addition, P.M OMVs strongly inhibited miR-96-5p expression, which caused an upregulation of ATP binding cassette subfamily A member 1 (Abca1) in osteoclasts leading to an increased level of mitochondria-dependent apoptosis. Moreover, treatment with P.M but not Escherichia coli OMVs attenuated bone loss in experimental osteoporosis and collagen-induced arthritis. Collectively, we demonstrated osteoprotective functions of OMVs from Proteus mirabilis, which downregulated miR-96-5p causing an increased Abca1 expression and mitochondria-dependent apoptosis. © 2022 Wang, Mo, Ou, Fang, Wu, Wu and Nandakumar.
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| 3. |
- Fang, Qinghua, et al.
(författare)
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Comparative Analysis on Abnormal Methylome of Differentially Expressed Genes and Disease Pathways in the Immune Cells of RA and SLE
- 2021
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Ingår i: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- We identified abnormally methylated, differentially expressed genes (DEGs) and pathogenic mechanisms in different immune cells of RA and SLE by comprehensive bioinformatics analysis. Six microarray data sets of each immune cell (CD19+ B cells, CD4+ T cells and CD14+ monocytes) were integrated to screen DEGs and differentially methylated genes by using R package "limma." Gene ontology annotations and KEGG analysis of aberrant methylome of DEGs were done using DAVID online database. Protein-protein interaction (PPI) network was generated to detect the hub genes and their methylation levels were compared using DiseaseMeth 2.0 database. Aberrantly methylated DEGs in CD19+ B cells (173 and 180), CD4+ T cells (184 and 417) and CD14+ monocytes (193 and 392) of RA and SLE patients were identified. We detected 30 hub genes in different immune cells of RA and SLE and confirmed their expression using FACS sorted immune cells by qPCR. Among them, 12 genes (BPTF, PHC2, JUN, KRAS, PTEN, FGFR2, ALB, SERB-1, SKP2, TUBA1A, IMP3, and SMAD4) of RA and 12 genes (OAS1, RSAD2, OASL, IFIT3, OAS2, IFIH1, CENPE, TOP2A, PBK, KIF11, IFIT1, and ISG15) of SLE are proposed as potential biomarker genes based on receiver operating curve analysis. Our study suggests that MAPK signaling pathway could potentially differentiate the mechanisms affecting T- and B- cells in RA, whereas PI3K pathway may be used for exploring common disease pathways between RA and SLE. Compared to individual data analyses, more dependable and precise filtering of results can be achieved by integrating several relevant data sets.
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| 4. |
- Hu, Tianyu, et al.
(författare)
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Steric hindrance induced low exciton binding energy enables low-driving-force organic solar cells
- 2024
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Ingår i: Aggregate. - 2692-4560 .- 2766-8541. ; In Press
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Tidskriftsartikel (refereegranskat)abstract
- Exciton binding energy (Eb) has been regarded as a critical parameter in charge separation during photovoltaic conversion. Minimizing the Eb of the photovoltaic materials can facilitate the exciton dissociation in low-driving force organic solar cells (OSCs) and thus improve the power conversion efficiency (PCE); nevertheless, diminishing the Eb with deliberate design principles remains a significant challenge. Herein, bulky side chain as steric hindrance structure was inserted into Y-series acceptors to minimize the Eb by modulating the intra- and intermolecular interaction. Theoretical and experimental results indicate that steric hindrance-induced optimal intra- and intermolecular interaction can enhance molecular polarizability, promote electronic orbital overlap between molecules, and facilitate delocalized charge transfer pathways, thereby resulting in a low Eb. The conspicuously reduced Eb obtained in Y-ChC5 with pinpoint steric hindrance modulation can minimize the detrimental effects on exciton dissociation in low-driving-force OSCs, achieving a remarkable PCE of 19.1% with over 95% internal quantum efficiency. Our study provides a new molecular design rationale to reduce the Eb.
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| 5. |
- King, Matthew R., et al.
(författare)
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Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient
- 2024
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 187:8, s. 24-1889
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Tidskriftsartikel (refereegranskat)abstract
- Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.
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| 6. |
- Li, Qizhao, et al.
(författare)
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Twisted-Planar-Twisted expanded porphyrinoid dimer as a rudimentary reaction-based methanol indicator
- 2020
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Directly linked porphyrin dimers have attracted considerable attention because of their intriguing electronic features. Most emphasis has been placed on either dimers with large dihedral angles between the constituent planar monomeric subunits or those with overall planarity, referred to as "Planar-Twisted-Planar" and "Planar-Planar-Planar", respectively. Herein, we report a "Twisted-Planar-Twisted" framework, the hexaphyrin dimer D that exists in a trans configuration. Treatment of D with MeOH affords two isomeric dimers, MD1 and MD2, both of which incorporate a methoxy moiety and exist in cis orientations with respect to the tethering linkage. The methanol-promoted conversion is accompanied by a readily discernible color change from green to brown and is not induced to an appreciable level by other alcohols. Dimer D thus acts as a rudimentary, albeit highly selective, reaction-based methanol indicator. This work provides a promising approach for constructing reaction-based chemosensors using porphyrinoid dimers of nonplanar subunits with biased reactivity. Directly linked porphyrin dimers show intriguing electronic features but emphasis has been placed on planar monomeric units. Here, the authors report a Twisted-Planar-Twisted framework which can undergo a cis-trans transformation accompanied by a colour change in presence of methanol, making this framework applicable as a methanol sensor.
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| 7. |
- Li, Yachen, et al.
(författare)
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Intrauterine and early postnatal exposures to submicron particulate matter and childhood allergic rhinitis : A multicity cross-sectional study in China
- 2024
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Ingår i: Environmental Research. - : Elsevier. - 0013-9351 .- 1096-0953. ; 247
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Tidskriftsartikel (refereegranskat)abstract
- Background: Airborne particulate matter pollution has been linked to occurrence of childhood allergic rhinitis (AR). However, the relationships between exposure to particulate matter with an aerodynamic diameter <= 1 µm (PM1) during early life (in utero and first year of life) and the onset of childhood AR remain largely unknown. This study aims to investigate potential associations of in utero and first-year exposures to size-segregated PMs, including PM1, PM1-2.5, PM2.5, PM2.5-10, and PM10, with childhood AR.Methods: We investigated 29286 preschool children aged 3-6 years in 7 Chinese major cities during 2019-2020 as the Phase II of the China Children, Families, Health Study. Machine learning-based space-time models were utilized to estimate early-life residential exposure to PM1, PM2.5, and PM10 at 1 x 1-km resolutions. The concentrations of PM1-2.5 and PM2.5-10 were calculated by subtracting PM1 from PM2.5 and PM2.5 from PM10, respectively. Multiple mixed-effects logistic models were used to assess the odds ratios (ORs) and 95% confidence intervals (CIs) of childhood AR associated with per 10-µg/m3 increase in exposure to particulate air pollution during in utero period and the first year of life.Results: Among the 29286 children surveyed (mean +/- standard deviation, 4.9 +/- 0.9 years), 3652 (12.5%) were reported to be diagnosed with AR. Average PM1 concentrations during in utero period and the first year since birth were 36.3 +/- 8.6 µg/m3 and 33.1 +/- 6.9 µg/m3, respectively. Exposure to PM1 and PM2.5 during pregnancy and the first year of life was associated with an increased risk of AR in children, and the OR estimates were higher for each 10-µg/m3 increase in PM1 than for PM2.5 (e.g., 1.132 [95% CI: 1.022-1.254] vs. 1.079 [95% CI: 1.014-1.149] in pregnancy; 1.151 [95% CI: 1.014-1.306] vs. 1.095 [95% CI: 1.008-1.189] in the first year of life). No associations were observed between AR and both pre- and post-natal exposure to PM1-2.5, indicating that PM1 rather than PM1-2.5 contributed to the association between PM2.5 and childhood AR. In trimester-stratified analysis, childhood AR was only found to be associated with exposure to PM1 (OR = 1.077, 95% CI: 1.027-1.128), PM2.5 (OR = 1.048, 95% CI: 1.018-1.078), and PM10 (OR = 1.032, 95% CI: 1.007-1.058) during the third trimester of pregnancy. Subgroup analysis suggested stronger PM-AR associations among younger (<5 years old) and winter-born children.Conclusions: Prenatal and postnatal exposures to ambient PM1 and PM2.5 were associated with an increased risk of childhood AR, and PM2.5-related hazards could be predominantly attributed to PM1. These findings highlighted public health significance of formulating air quality guideline for ambient PM1 in mitigating children's AR burden caused by particulate air pollution.
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| 8. |
- Lin, Dongxu, et al.
(författare)
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Vapor Deposited Pure alpha-FAPbI(3) Perovskite Solar Cell via Moisture-Induced Phase Transition Strategy
- 2022
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Ingår i: Advanced Functional Materials. - : WILEY-V C H VERLAG GMBH. - 1616-301X .- 1616-3028. ; 32:48
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Tidskriftsartikel (refereegranskat)abstract
- To fabricate stable neat FAPbI(3) perovskite with a pure alpha-phase (pure alpha-FAPbI(3)) is important in the field of photovoltaic commercialization because of its better bandgap than its alloying counterpart with cesium (Cs) or methylammonium (MA) cations. In this work, the first vapor deposited pure alpha-FAPbI(3) thin film solar cell with a power conversion efficiency (PCE) over 20% is achieved by regulating the phase transition process. It is found that under high humidity conditions, a fast phase transition between high-purity alpha- and delta-phase FAPbI(3) can be realized. Moreover, theoretical calculations interestingly reveal a phase transition shortcut induced by the abnormal volume contraction that is ascribed to the formation of double hydrogen bonds at a certain H2O concentration. Therefore, a high-humidity post-treatment strategy is proposed to fabricate alpha-FAPbI(3) solar cells with a champion PCE of 20.19% (0.1 cm(2)) and 18.91% (1 cm(2)), which is currently the highest recorded value in vapor deposited pure alpha-FAPbI(3) perovskite solar cells. This study helps to redefine the effect of a water molecule on FAPbI(3) solar cells. In addition, the demonstrated scaling-up possibility provides another perspective for fabricating uniform high-performance pure alpha-FAPbI(3) perovskite solar cells.
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| 9. |
- Shi, Chen, et al.
(författare)
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Comprehensive Landscape of Heparin Therapy for COVID-19
- 2021
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Ingår i: Carbohydrate Polymers. - OXFORD ENGLAND : Elsevier. - 0144-8617 .- 1879-1344. ; 254
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Forskningsöversikt (refereegranskat)abstract
- The pandemic coronavirus disease 2019 (COVID-19), caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is rapidly spreading globally. Clinical observations found that systemic symptoms caused by SARS-CoV-2 infection are attenuated when using the anticoagulant agent heparin, indicating that heparin may play other roles in managing COVID-19, in addition to prevention of pulmonary thrombosis. Several biochemical studies show strong binding of heparin and heparin-like molecules to the Spike protein, which resulted in inhibition of viral infection to cells. The clinical observations and in vitro studies argue for a potential multiple-targeting effects of heparin. However, adverse effects of heparin administration and some of the challenges using heparin therapy for SARS-CoV-2 infection need to be considered. This review discusses the pharmacological mechanisms of heparin regarding its anticoagulant, anti-inflammatory and direct antiviral activities, providing current evidence concerning the effectiveness and safety of heparin therapy for this major public health emergency.
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| 10. |
- Shi, Tingting, et al.
(författare)
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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees
- 2024
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Ingår i: Molecular Plant. - : Elsevier. - 1674-2052 .- 1752-9867. ; 17:5, s. 725-746
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.
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