| 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. |
- Christensen, Kirsten E, et al.
(författare)
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A germanate built from 68126 cavity co-templated by a (H2O)16 water cluster and 2-methylpiperazine
- 2008
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Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 47:41, s. 7868-7871
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Tidskriftsartikel (refereegranskat)abstract
- Totally tubular: A new tubular germanate is cotemplated by 2-methylpiperazine and an (H2O)16 cluster in a hydro(solvo)thermal synthesis. The germanate features a large, highly symmetric 68126 cavity (see picture; yellow sphere) built from 12 Ge7X19 (X=O, OH, F) clusters (GeX6 red, GeX5 yellow, GeX4 green).
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| 3. |
- Dinh, Thanh Theresa, et al.
(författare)
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An NKX-COUP-TFII morphogenetic code directs mucosal endothelial addressin expression
- 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
- Immunoglobulin family and carbohydrate vascular addressins encoded by Madcam1 and St6gal1 control lymphocyte homing into intestinal tissues, regulating immunity and inflammation. The addressins are developmentally programmed to decorate endothelial cells lining gut post-capillary and high endothelial venules (HEV), providing a prototypical example of organ- and segment-specific endothelial specialization. We identify conserved NKX-COUP-TFII composite elements (NCCE) in regulatory regions of Madcam1 and St6gal1 that bind intestinal homeodomain protein NKX2-3 cooperatively with venous nuclear receptor COUP-TFII to activate transcription. The Madcam1 element also integrates repressive signals from arterial/capillary Notch effectors. Pan-endothelial COUP-TFII overexpression induces ectopic addressin expression in NKX2-3+ capillaries, while NKX2-3 deficiency abrogates expression by HEV. Phylogenetically conserved NCCE are enriched in genes involved in neuron migration and morphogenesis of the heart, kidney, pancreas and other organs. Our results define an NKX-COUP-TFII morphogenetic code that targets expression of mucosal vascular addressins.
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| 4. |
- Li, Jian, et al.
(författare)
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Modulated structure determination and ion transport mechanism of oxide-ion conductor CeNbO4+δ
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- CeNbO4+δ, a family of oxygen hyperstoichiometry materials with varying oxygen content (CeNbO4, CeNbO4.08, CeNbO4.25, CeNbO4.33) that shows mixed electronic and oxide ionic conduction, has been known for four decades. However, the oxide ionic transport mechanism has remained unclear due to the unknown atomic structures of CeNbO4.08 and CeNbO4.33. Here, we report the complex (3 + 1)D incommensurately modulated structure of CeNbO4.08, and the supercell structure of CeNbO4.33 from single nanocrystals by using a three-dimensional electron diffraction technique. Two oxide ion migration events are identified in CeNbO4.08 and CeNbO4.25 by molecular dynamics simulations, which was a synergic-cooperation knock-on mechanism involving continuous breaking and reformation of Nb2O9 units. However, the excess oxygen in CeNbO4.33 hardly migrates because of the high concentration and the ordered distribution of the excess oxide ions. The relationship between the structure and oxide ion migration for the whole series of CeNbO4+δ compounds elucidated here provides a direction for the performance optimization of these compounds.
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| 5. |
- Xiang, Menglan, et al.
(författare)
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A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature
- 2020
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Ingår i: Frontiers in Cardiovascular Medicine. - : FRONTIERS MEDIA SA. - 2297-055X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Single-cell transcriptomics promise to revolutionize our understanding of the vasculature. Emerging computational methods applied to high-dimensional single-cell data allow integration of results between samples and species and illuminate the diversity and underlying developmental and architectural organization of cell populations. Here, we illustrate these methods in the analysis of mouse lymph node (LN) lymphatic endothelial cells (LEC) at single-cell resolution. Clustering identifies five well-delineated subsets, including two medullary sinus subsets not previously recognized as distinct. Nearest neighbor alignments in trajectory space position the major subsets in a sequence that recapitulates the known features and suggests novel features of LN lymphatic organization, providing a transcriptional map of the lymphatic endothelial niches and of the transitions between them. Differences in gene expression reveal specialized programs for (1) subcapsular ceiling endothelial interactions with the capsule connective tissue and cells; (2) subcapsular floor regulation of lymph borne cell entry into the LN parenchyma and antigen presentation; and (3) pathogen interactions and (4) LN remodeling in distinct medullary subsets. LEC of the subcapsular sinus floor and medulla, which represent major sites of cell entry and exit from the LN parenchyma respectively, respond robustly to oxazolone inflammation challenge with enriched signaling pathways that converge on both innate and adaptive immune responses. Integration of mouse and human single-cell profiles reveals a conserved cross-species pattern of lymphatic vascular niches and gene expression, as well as specialized human subsets and genes unique to each species. The examples provided demonstrate the power of single-cell analysis in elucidating endothelial cell heterogeneity, vascular organization, and endothelial cell responses. We discuss the findings from the perspective of LEC functions in relation to niche formations in the unique stromal and highly immunological environment of the LN.
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