| 1. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
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.
|
|
| 2. |
- Kanoni, Stavroula, et al.
(författare)
-
Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
-
Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
-
Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
|
|
| 3. |
- Belopolski, Ilya, et al.
(författare)
-
Observation of a linked-loop quantum state in a topological magnet
- 2022
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 604:7907, s. 647-652
-
Tidskriftsartikel (refereegranskat)abstract
- Quantum phases can be classified by topological invariants, which take on discrete values capturing global information about the quantum state1–13. Over the past decades, these invariants have come to play a central role in describing matter, providing the foundation for understanding superfluids5, magnets6,7, the quantum Hall effect3,8, topological insulators9,10, Weyl semimetals11–13 and other phenomena. Here we report an unusual linking-number (knot theory) invariant associated with loops of electronic band crossings in a mirror-symmetric ferromagnet14–20. Using state-of-the-art spectroscopic methods, we directly observe three intertwined degeneracy loops in the material’s three-torus, T3, bulk Brillouin zone. We find that each loop links each other loop twice. Through systematic spectroscopic investigation of this linked-loop quantum state, we explicitly draw its link diagram and conclude, in analogy with knot theory, that it exhibits the linking number (2, 2, 2), providing a direct determination of the invariant structure from the experimental data. We further predict and observe, on the surface of our samples, Seifert boundary states protected by the bulk linked loops, suggestive of a remarkable Seifert bulk–boundary correspondence. Our observation of a quantum loop link motivates the application of knot theory to the exploration of magnetic and superconducting quantum matter.
|
|
| 4. |
- Chen, Jialin, et al.
(författare)
-
Fos Promotes Early Stage Teno-Lineage Differentiation of Tendon Stem/Progenitor Cells in Tendon
- 2017
-
Ingår i: Stem Cells Translational Medicine. - : John Wiley & Sons. - 2157-6564 .- 2157-6580. ; 6:11, s. 2009-2019
-
Tidskriftsartikel (refereegranskat)abstract
- Stem cells have been widely used in tendon tissue engineering. The lack of refined and controlled differentiation strategy hampers the tendon repair and regeneration. This study aimed to find new effective differentiation factors for stepwise tenogenic differentiation. By microarray screening, the transcript factor Fos was found to be expressed in significantly higher amounts in postnatal Achilles tendon tissue derived from 1 day as compared with 7-days-old rats. It was further confirmed that expression of Fos decreased with time in postnatal rat Achilles tendon, which was accompanied with the decreased expression of multiply tendon markers. The expression of Fos also declined during regular in vitro cell culture, which corresponded to the loss of tendon phenotype. In a cell-sheet and a three-dimensional cell culture model, the expression of Fos was upregulated as compared with in regular cell culture, together with the recovery of tendon phenotype. In addition, significant higher expression of tendon markers was found in Fos-overexpressed tendon stem/progenitor cells (TSPCs), and Fos knock-down gave opposite results. In situ rat tendon repair experiments found more normal tendon-like tissue formed and higher tendon markers expression at 4 weeks postimplantation of Fos-overexpressed TSPCs derived nonscaffold engineering tendon (cell-sheet), as compared with the control group. This study identifies Fos as a new marker and functional driver in the early stage teno-lineage differentiation of tendon, which paves the way for effective stepwise tendon differentiation and future tendon regeneration.
|
|
| 5. |
- Jin, Ying-Hui, et al.
(författare)
-
Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
-
Ingår i: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
-
Tidskriftsartikel (refereegranskat)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
|
|
| 6. |
- Li, Xing-Yu, et al.
(författare)
-
Comparative Study of Dayside Pulsating Auroras Induced by Ultralow-Frequency Waves
- 2023
-
Ingår i: Universe. - : MDPI AG. - 2218-1997. ; 9:6
-
Tidskriftsartikel (refereegranskat)abstract
- Pulsating auroras are usually observed with ultralow-frequency (ULF) waves in the Pc 3-5 band (period 10-600 s). These auroras are thought to result from interactions between energetic electrons and chorus waves, but their relationship with ULF waves remains an open question. In this study, we investigated this question by conducting a comparative study on two ULF wave events with pulsating auroras observed near the magnetic footprints. Conjugate observations from the Magnetospheric Multiscale mission and the Chinese Yellow River Station were used. In both events, lower-band chorus waves were observed, which were suggested to be connected with the auroral pulsations by wavelet analysis. The intensity of these waves oscillates at the period of the ULF waves, but the physics laid behind them differs by events. During the event of 22 January 2019, compressional ULF waves changed the threshold for the whistler anisotropy instability periodically, affecting the emission of chorus waves. In the event on 10 January 2016, poloidal ULF waves modulated the chorus wave generation by regulating electron temperature anisotropy through drift resonance. ULF waves in these events may originate from perturbations in the solar wind. We highlight the role of ULF waves in the solar wind-magnetosphere-ionosphere coupling, which requires further study.
|
|
| 7. |
- Shi, Yu-Sheng, et al.
(författare)
-
Limonoids from Citrus : Chemistry, anti-tumor potential, and other bioactivities
- 2020
-
Ingår i: Journal of Functional Foods. - : ELSEVIER. - 1756-4646 .- 2214-9414. ; 75
-
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.
|
|
| 8. |
- Song, Jiao-Jiao, et al.
(författare)
-
The 4f-Hybridization Strength in CemMnIn3m+2n Heavy-Fermion Compounds Studied by Angle-Resolved Photoemission Spectroscopy
- 2021
-
Ingår i: Chinese Physics Letters. - : IOP Publishing. - 0256-307X .- 1741-3540. ; 38:10
-
Tidskriftsartikel (refereegranskat)abstract
- We systemically investigate the nature of Ce 4f electrons in structurally layered heavy-fermion compounds CemMnIn3m+2n (with M = Co, Rh, Jr, and Pt, m = 1, 2, n = 0-2), at low temperature using on-resonance angle-resolved photoemission spectroscopy. Three heavy quasiparticle bands f(0), f(7/2)(1) and f(5/2)(1), are observed in all compounds, whereas their intensities and energy locations vary greatly with materials. The strong f(0) states imply that the localized electron behavior dominates the Ce 4f states. The Ce 4f electrons are partially hybridized with the conduction electrons, making them have the dual nature of localization and itinerancy. Our quantitative comparison reveals that the f(5/2)(1)-f (0) intensity ratio is more suitable to reflect the 4f-state hybridization strength.
|
|
| 9. |
- Yuan, Ya Hua, et al.
(författare)
-
Angle-resolved photoemission spectroscopy view on the nature of Ce 4f electrons in the antiferromagnetic Kondo lattice CePd5Al2
- 2021
-
Ingår i: Physical Review B. - : American Physical Society (APS). - 2469-9969 .- 2469-9950. ; 103:12
-
Tidskriftsartikel (refereegranskat)abstract
- We report an angle-resolved photoemission spectroscopy study of the antiferromagnetic Kondo lattice CePd5Al2, focusing on the quasi-two-dimensional k-space nature of its Fermi surface and, tuning photon energy to the Ce 4d-4f on-resonance transition, the hybridization of the Ce 4f state. A strong shoulder feature on the f0 peak was detected, suggesting hybridization between conduction and f bands. On-resonance spectra revealed narrow, yet hybridized quasiparticle bands with sharp peaks and ∼ 9 meV energy dispersion near the Fermi energy EF. The observed dispersive hybridized f band can be well described by a hybridization-band picture based on the periodic Anderson model (PAM). Hence, the 4f electrons in CePd5Al2 display a dual nature, with both localized and itinerant features, but with dominantly localized character.
|
|
| 10. |
- Zhang, Xiao-Jie, et al.
(författare)
-
Auto-suppression of Tet dioxygenases protects the mouse oocyte genome from oxidative demethylation
- 2024
-
Ingår i: Nature Structural & Molecular Biology. - : NATURE PORTFOLIO. - 1545-9993 .- 1545-9985. ; 31:1
-
Tidskriftsartikel (refereegranskat)abstract
- DNA cytosine methylation plays a vital role in repressing retrotransposons, and such derepression is linked with developmental failure, tumorigenesis and aging. DNA methylation patterns are formed by precisely regulated actions of DNA methylation writers (DNA methyltransferases) and erasers (TET, ten-eleven translocation dioxygenases). However, the mechanisms underlying target-specific oxidation of 5mC by TET dioxygenases remain largely unexplored. Here we show that a large low-complexity domain (LCD), located in the catalytic part of Tet enzymes, negatively regulates the dioxygenase activity. Recombinant Tet3 lacking LCD is shown to be hyperactive in converting 5mC into oxidized species in vitro. Endogenous expression of the hyperactive Tet3 mutant in mouse oocytes results in genome-wide 5mC oxidation. Notably, the occurrence of aberrant 5mC oxidation correlates with a consequent loss of the repressive histone mark H3K9me3 at ERVK retrotransposons. The erosion of both 5mC and H3K9me3 causes ERVK derepression along with upregulation of their neighboring genes, potentially leading to the impairment of oocyte development. These findings suggest that Tet dioxygenases use an intrinsic auto-regulatory mechanism to tightly regulate their enzymatic activity, thus achieving spatiotemporal specificity of methylome reprogramming, and highlight the importance of methylome integrity for development. Here the authors show that TET dioxygenases, the erasers of DNA methylation, use a self-limiting mechanism via their LCD domain to ensure adaptable methylome status and protect the genome from excessive oxidative methylation.
|
|
