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Text-fig. 27. Scanning electron microscope (SEM) images of stamens and pollen of Valvidistemon globiferus gen. et sp. nov.; Catefica locality, Portugal. a) Stamen in oblique lateral view showing laterally hinged valves, massive connective between the thecae and prominent, globular, apical extension of the connective; b) Stamen in oblique lateral view on the opposite side from (a) showing broken laterally hinged valves and distinct endothecium cells; c) Detail of stamen showing the large, longitudinally aligned cells of the massive connective, broad, poorly defined stamen base, and the laterally hinged valves of one of the thecae; d) Reticulate pollen attached to the inside of the anther wall. Specimen, Catefica 49-S107779 (holotype, a–d). Scale bars = 600 Μm (a, b), 100 Μm (c), 20 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 27. Scanning electron microscope (SEM) images of stamens and pollen of Valvidistemon globiferus gen. et sp. nov.; Catefica locality, Portugal. a) Stamen in oblique lateral view showing laterally hinged valves, massive connective between the thecae and prominent, globular, apical extension of the connective; b) Stamen in oblique lateral view on the opposite side from (a) showing broken laterally hinged valves and distinct endothecium cells; c) Detail of stamen showing the large, longitudinally aligned cells of the massive connective, broad, poorly defined stamen base, and the laterally hinged valves of one of the thecae; d) Reticulate pollen attached to the inside of the anther wall. Specimen, Catefica 49-S107779 (holotype, a–d). Scale bars = 600 Μm (a, b), 100 Μm (c), 20 Μm (d).
Text-fig. 7. Scanning electron microscope (SEM, a–c, e, f) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of fruits and pollen grains of Hedyflora crystallifera; Catefica locality, Portugal. a, b) Lateral view of fruits showing the remains of apical tepals and remains of the hypanthium, which is thicker on the edges of the fruit in (b) (arrows); c) Detail of hypanthium surface between the thickenings on the edges of the fruit showing polygonal cells with a central papilla; d) Transverse section (orthoslice xy0600) of fruit and seed showing the finely crystalliferous endotesta (arrowhead) and sclerified outer tegmen (asterisk); e) Distal view of pollen grain from surface of fruit showing the poorly defined tetrachotomocolpate aperture (daggers indicating the four arms of the aperture) and semi-tectate, reticulate tectum; f) Detail of pollen wall showing narrow muri with indistinctly beaded surface ornamentation of minute verrucae in poorly defined rows and supported by long columellae. Specimens, Catefica 49-S172313 (a), Catefica 49-S153159 (b), Catefica 49-S172324 (c), Catefica 49-S172325 (d), Catefica 50-S170453 (e, f). Scale bars = 300 Μm (a, b), 100 Μm (d), 50 Μm (c), 6 Μm (e), 1.5 Μm (f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 7. Scanning electron microscope (SEM, a–c, e, f) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of fruits and pollen grains of Hedyflora crystallifera; Catefica locality, Portugal. a, b) Lateral view of fruits showing the remains of apical tepals and remains of the hypanthium, which is thicker on the edges of the fruit in (b) (arrows); c) Detail of hypanthium surface between the thickenings on the edges of the fruit showing polygonal cells with a central papilla; d) Transverse section (orthoslice xy0600) of fruit and seed showing the finely crystalliferous endotesta (arrowhead) and sclerified outer tegmen (asterisk); e) Distal view of pollen grain from surface of fruit showing the poorly defined tetrachotomocolpate aperture (daggers indicating the four arms of the aperture) and semi-tectate, reticulate tectum; f) Detail of pollen wall showing narrow muri with indistinctly beaded surface ornamentation of minute verrucae in poorly defined rows and supported by long columellae. Specimens, Catefica 49-S172313 (a), Catefica 49-S153159 (b), Catefica 49-S172324 (c), Catefica 49-S172325 (d), Catefica 50-S170453 (e, f). Scale bars = 300 Μm (a, b), 100 Μm (d), 50 Μm (c), 6 Μm (e), 1.5 Μm (f).
Text-fig. 5. Scanning electron microscope images of the seed of Canrightia sp.; Catefica locality, Portugal. a) Seed in ventral view showing the slightly protruding chalaza (ch) at the apex, pointed micropyle (mi) at the base and pitted surface of the endotesta; b) Detail of endotesta surface showing larger pits in longitudinal rows and the finer pits created by crystals in the cells of the endotesta. Specimen, Catefica MM158-P0289 (a, b). Scale bars = 300 Μm (a), 100 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 5. Scanning electron microscope images of the seed of Canrightia sp.; Catefica locality, Portugal. a) Seed in ventral view showing the slightly protruding chalaza (ch) at the apex, pointed micropyle (mi) at the base and pitted surface of the endotesta; b) Detail of endotesta surface showing larger pits in longitudinal rows and the finer pits created by crystals in the cells of the endotesta. Specimen, Catefica MM158-P0289 (a, b). Scale bars = 300 Μm (a), 100 Μm (b).
Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d).
Text-fig. 3. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of fruits of Canrightia foveolata sp. nov.; Catefica locality, Portugal. a) Volume rendering of fruit showing prominent rim around the middle of the fruit with reduced tepals (arrowheads) and partly abraded fruit wall exposing the pitted endotesta surface of one of two seeds (arrow); note two of the vascular bundles (vb) extending from the base of the fruit to the tepals; b) Voltex of fruit showing prominent rim around the fruit (arrowhead) and dense precipitation of crystals in the endothelium cells of one of the two seeds in the fruit; c) Longitudinal section of fruit (orthoslice yz0520) showing the inferred hypanthium rim (arrow head) and two seeds, one with a dense precipitation of crystals; note the prominent endothelium cells (asterisks) of the inner integument and the well-developed fruit wall above the seeds; d) Transverse section through basal part of fruit and seeds close to the micropyle (orthoslice xy0312) showing partly abraded fruit wall with five vascular bundles (vb) and details of the seed coat with endotesta (oi-end) surrounding the tegmen consisting of an outer epidermis (ii-o), middle layer (ii-m) and a distinct inner epidermis (endothelium) consisting of radially elongated cells (asterisk); e) Transverse section (orthoslice xy1680) through apical part of the fruit close to chalaza showing the tips of two seeds; note the endotesta (oi-end) surrounded by thick-walled cells of the exotesta (oi-o); f) Transverse section (orthoslice xy1485) through fruit in the region of the hypanthium rim showing sections through the two seeds close to the chalazal region; note endotesta (oi-end) surrounded by larger cells of exotesta (oi-o) and fruit wall (fr). Specimen, Catefica 49-S174249 (holotype, a–f). Scale bars = 300 Μm (a–c, e, f), 100 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 3. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of fruits of Canrightia foveolata sp. nov.; Catefica locality, Portugal. a) Volume rendering of fruit showing prominent rim around the middle of the fruit with reduced tepals (arrowheads) and partly abraded fruit wall exposing the pitted endotesta surface of one of two seeds (arrow); note two of the vascular bundles (vb) extending from the base of the fruit to the tepals; b) Voltex of fruit showing prominent rim around the fruit (arrowhead) and dense precipitation of crystals in the endothelium cells of one of the two seeds in the fruit; c) Longitudinal section of fruit (orthoslice yz0520) showing the inferred hypanthium rim (arrow head) and two seeds, one with a dense precipitation of crystals; note the prominent endothelium cells (asterisks) of the inner integument and the well-developed fruit wall above the seeds; d) Transverse section through basal part of fruit and seeds close to the micropyle (orthoslice xy0312) showing partly abraded fruit wall with five vascular bundles (vb) and details of the seed coat with endotesta (oi-end) surrounding the tegmen consisting of an outer epidermis (ii-o), middle layer (ii-m) and a distinct inner epidermis (endothelium) consisting of radially elongated cells (asterisk); e) Transverse section (orthoslice xy1680) through apical part of the fruit close to chalaza showing the tips of two seeds; note the endotesta (oi-end) surrounded by thick-walled cells of the exotesta (oi-o); f) Transverse section (orthoslice xy1485) through fruit in the region of the hypanthium rim showing sections through the two seeds close to the chalazal region; note endotesta (oi-end) surrounded by larger cells of exotesta (oi-o) and fruit wall (fr). Specimen, Catefica 49-S174249 (holotype, a–f). Scale bars = 300 Μm (a–c, e, f), 100 Μm (d).
Text-fig. 2. Scanning electron microscope (SEM, a, c–f) and synchrotron radiation X-ray tomographic microscopy (SRXTM, b, g) images of the flower of Mugideiriflora portugallica (a, b) and fruits, seeds and pollen of Canrightia resinifera (c–g); Catefica locality, Portugal. a) Oblique, apical view of flower showing multiparted organization with numerous laminar tepals, stamens that are rhomboidal and flattened in transverse section and carpels that are borne on the short conical apex of the receptacle; b) Transverse section (orthoslice xy0800) through basal part of flower showing the elongate bases of the laminar tepals and the flattened rhomboidal bases of the stamens; c) Fruit in lateral view showing irregular surface resulting from the abundant resin bodies in the fruit and hypanthium wall, scars from stamens on the rim of the hypanthium (arrowheads) and the lobed apical stigmatic region (st); d) Broken fruit with one or two seeds missing but showing three pendant, orthotropous seeds with pointed micropylar regions (mi) and a finely pitted crystalliferous endotesta; note the remains of the apical vascular bundles (vb); e) Single seed isolated from a fruit showing two distinct bundles (vb) still attached apically to the chalazal region of the seed, the pointed micropyle (mi) and the finely pitted surface of the crystalliferous endotesta; f) Monocolpate pollen from stigmatic region of fruit showing the long colpus and coarse reticulum; g) Transverse section (orthoslice xy0705) through a fruit showing four seeds all with radially elongated endothelium cells formed from the inner epidermis of the tegmen (asterisks). Specimens, Catefica 150-S174254 (a, b), Catefica 49-S170377 (c), Catefica 49-S170372 (d), Catefica 50-S170401 (e), Catefica 50-S170404 (f), Catefica 50-S174906 (g). Scale bars = 300 Μm (a–e, g), 6 Μm (f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 2. Scanning electron microscope (SEM, a, c–f) and synchrotron radiation X-ray tomographic microscopy (SRXTM, b, g) images of the flower of Mugideiriflora portugallica (a, b) and fruits, seeds and pollen of Canrightia resinifera (c–g); Catefica locality, Portugal. a) Oblique, apical view of flower showing multiparted organization with numerous laminar tepals, stamens that are rhomboidal and flattened in transverse section and carpels that are borne on the short conical apex of the receptacle; b) Transverse section (orthoslice xy0800) through basal part of flower showing the elongate bases of the laminar tepals and the flattened rhomboidal bases of the stamens; c) Fruit in lateral view showing irregular surface resulting from the abundant resin bodies in the fruit and hypanthium wall, scars from stamens on the rim of the hypanthium (arrowheads) and the lobed apical stigmatic region (st); d) Broken fruit with one or two seeds missing but showing three pendant, orthotropous seeds with pointed micropylar regions (mi) and a finely pitted crystalliferous endotesta; note the remains of the apical vascular bundles (vb); e) Single seed isolated from a fruit showing two distinct bundles (vb) still attached apically to the chalazal region of the seed, the pointed micropyle (mi) and the finely pitted surface of the crystalliferous endotesta; f) Monocolpate pollen from stigmatic region of fruit showing the long colpus and coarse reticulum; g) Transverse section (orthoslice xy0705) through a fruit showing four seeds all with radially elongated endothelium cells formed from the inner epidermis of the tegmen (asterisks). Specimens, Catefica 150-S174254 (a, b), Catefica 49-S170377 (c), Catefica 49-S170372 (d), Catefica 50-S170401 (e), Catefica 50-S170404 (f), Catefica 50-S174906 (g). Scale bars = 300 Μm (a–e, g), 6 Μm (f).
Text-fig. 25. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov.; Catefica locality, Portugal. a) Stamen fragment showing two pairs of pollen sacs along the margins of the stamen with a broad connective that separates the thecae, except near the apex where the thecae meet; b) Detail of surface of pollen sacs showing larger cells (arrows), interpreted as ethereal oil cells; c) Pollen in situ from specimen in (a); d) Stamen fragment with apical and basal portion missing and surface slightly abraded and compressed obscuring cellular details; note remains of another stamen attached to the underside of the stamen; e–h) Pollen in situ from specimen in (d) showing long aperture (e) and pollen wall with heterobrochate reticulum (e–h); note narrow muri with flatten and smooth surface and short columellae (h). Specimens, Catefica 49-S115859 (a–c), Catefica 151-S105281 (holotype, d–h). Scale bars = 600 Μm (a, d), 50 Μm (b), 6 Μm (c, e–g), 1.5 Μm (h). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 25. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov.; Catefica locality, Portugal. a) Stamen fragment showing two pairs of pollen sacs along the margins of the stamen with a broad connective that separates the thecae, except near the apex where the thecae meet; b) Detail of surface of pollen sacs showing larger cells (arrows), interpreted as ethereal oil cells; c) Pollen in situ from specimen in (a); d) Stamen fragment with apical and basal portion missing and surface slightly abraded and compressed obscuring cellular details; note remains of another stamen attached to the underside of the stamen; e–h) Pollen in situ from specimen in (d) showing long aperture (e) and pollen wall with heterobrochate reticulum (e–h); note narrow muri with flatten and smooth surface and short columellae (h). Specimens, Catefica 49-S115859 (a–c), Catefica 151-S105281 (holotype, d–h). Scale bars = 600 Μm (a, d), 50 Μm (b), 6 Μm (c, e–g), 1.5 Μm (h).
Text-fig. 19. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a–c) of Aristospermum huberi and scanning electron microscope (SEM, d, e) images of Choffaticarpus compactus; Catefica locality, Portugal. a) Volume rendering of strongly flattened, triangular seed with pointed micropylar region; note thin-walled cells of outer integument preserved along the margins of the seed and pitted surface of the crystalliferous inner cells of outer integument where the outer cells are abraded and the narrow, lateral funicle/raphe; b) Volume rendering of seed showing surface of inner integument (endotesta) with cells showing clear imprints of crystals (arrows); c) Longitudinal section (orthoslice yz0241) of seed showing crystalliferous cells of endotesta (white arrows) and the two fiber layers of the tegmen that are perpendicular to each other (inner integument, ii-f, black arrows); d) Fragment of multiparted, apocarpous fruiting structure showing several helically-arranged, laterally flattened, fruitlets; e) Fruitlet in lateral view showing the prominent ventral face with its lateral groove, short attachment scar, and sunken regions of the fruit wall that indicate the probable presence of oil cells. Specimens, Catefica 49-S266049 (a–c), Catefica 49-S172558 (d), Catefica 49-S118675 (e). Scale bars = 300 Μm (a, c–e), 100 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 19. Synchrotron radiation X-ray tomographic microscopy (SRXTM, a–c) of Aristospermum huberi and scanning electron microscope (SEM, d, e) images of Choffaticarpus compactus; Catefica locality, Portugal. a) Volume rendering of strongly flattened, triangular seed with pointed micropylar region; note thin-walled cells of outer integument preserved along the margins of the seed and pitted surface of the crystalliferous inner cells of outer integument where the outer cells are abraded and the narrow, lateral funicle/raphe; b) Volume rendering of seed showing surface of inner integument (endotesta) with cells showing clear imprints of crystals (arrows); c) Longitudinal section (orthoslice yz0241) of seed showing crystalliferous cells of endotesta (white arrows) and the two fiber layers of the tegmen that are perpendicular to each other (inner integument, ii-f, black arrows); d) Fragment of multiparted, apocarpous fruiting structure showing several helically-arranged, laterally flattened, fruitlets; e) Fruitlet in lateral view showing the prominent ventral face with its lateral groove, short attachment scar, and sunken regions of the fruit wall that indicate the probable presence of oil cells. Specimens, Catefica 49-S266049 (a–c), Catefica 49-S172558 (d), Catefica 49-S118675 (e). Scale bars = 300 Μm (a, c–e), 100 Μm (b).
Text-fig. 2. Zamites pateri J.KVAČEK sp. nov.; Pecínov locality, holotype, No. NM-F 5185. a: Abaxial cuticle showing costal and intercostal zones, SEM micro-photograph, scale bar 100 µm. b: Abaxial cuticle, detail of syndetocheilic stoma, SEM microphotograph, scale bar 10 µm. c: Abaxial cuticle showing transversely oriented stomata, SEM micro-photograph, scale bar 50 µm. d: Abaxial cuticle, detail of syndetocheilic stoma showing ledges of guard cells, SEM micro-photograph, scale bar 10 µm. e: Abaxial cuticle showing costal ordinary cells seen from inside, SEM micro-photograph, scale bar 50 µm. f: External side of abaxial cuticle showing stoma sunken in a stomatal pit surrounded by papillae, SEM micro-photograph, scale bar 10 µm. g: External side of abaxial cuticle showing papillae, SEM micro-photograph, scale bar 100 µm. h: External side of abaxial cuticle showing detail of fused papillae, SEM micro-photograph, scale bar 10 µm. in New Species Of Zamites From The Cenomanian Of The Bohemian Cretaceous Basin
Text-fig. 2. Zamites pateri J.KVAČEK sp. nov.; Pecínov locality, holotype, No. NM-F 5185. a: Abaxial cuticle showing costal and intercostal zones, SEM micro-photograph, scale bar 100 µm. b: Abaxial cuticle, detail of syndetocheilic stoma, SEM microphotograph, scale bar 10 µm. c: Abaxial cuticle showing transversely oriented stomata, SEM micro-photograph, scale bar 50 µm. d: Abaxial cuticle, detail of syndetocheilic stoma showing ledges of guard cells, SEM micro-photograph, scale bar 10 µm. e: Abaxial cuticle showing costal ordinary cells seen from inside, SEM micro-photograph, scale bar 50 µm. f: External side of abaxial cuticle showing stoma sunken in a stomatal pit surrounded by papillae, SEM micro-photograph, scale bar 10 µm. g: External side of abaxial cuticle showing papillae, SEM micro-photograph, scale bar 100 µm. h: External side of abaxial cuticle showing detail of fused papillae, SEM micro-photograph, scale bar 10 µm.
Text-fig. 2. Light micrographs of Pinus spp. cuticles prepared with the modified, gentle bleaching procedure. a: Cuticle 1, Pinus sp. 1. Nearly the entire width of the leaf has been preserved. Five parallel rows of stomata are visible. b: Cuticle 1, close-up of (a). Two guard cells are visible around each stoma. c: Cuticle 1, close-up of eight stomata. Two guard cells and eight subsidiary cells are visible around each stoma. d: Cuticle 2, Pinus sp. 2. Some folding of the cuticle occurred during preparation, but many parallel rows of stomata on both sides of a thin, central midvein are evident. e: Cuticle 2, close-up of (d). Pairs of guard cells surround each stoma. f: Cuticle 2, close-up of (e). Subsidiary and epithelial cells can be observed around the stomata. in A Modified, Step-By-Step Procedure For The Gentle Bleaching Of Delicate Fossil Leaf Cuticles
Text-fig. 2. Light micrographs of Pinus spp. cuticles prepared with the modified, gentle bleaching procedure. a: Cuticle 1, Pinus sp. 1. Nearly the entire width of the leaf has been preserved. Five parallel rows of stomata are visible. b: Cuticle 1, close-up of (a). Two guard cells are visible around each stoma. c: Cuticle 1, close-up of eight stomata. Two guard cells and eight subsidiary cells are visible around each stoma. d: Cuticle 2, Pinus sp. 2. Some folding of the cuticle occurred during preparation, but many parallel rows of stomata on both sides of a thin, central midvein are evident. e: Cuticle 2, close-up of (d). Pairs of guard cells surround each stoma. f: Cuticle 2, close-up of (e). Subsidiary and epithelial cells can be observed around the stomata.
Data: Fate of intravenously administered umbilical cord mesenchymal stromal cells and interactions with the host's immune system
<p>This data set includes all the raw data collected for the following article: "Fate of intravenously administered umbilical cord mesenchymal stromal cells and interactions with the host's immune system".</p>
Data for: Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes
<p><span>Proper differentiation of sperm from germline stem cells, essential for production of the next generation, requires dramatic changes in gene expression that drive remodeling of almost all cellular components, from chromatin to organelles to cell shape itself. Here we provide a single nucleus and single cell RNA-seq resource covering all of spermatogenesis in <em>Drosophila</em> starting from in-depth analysis of adult testis single nucleus RNA-seq (snRNA-seq) data from the Fly Cell Atlas (FCA) study (Li et al., 2022). With over 44,000 nuclei and 6,000 cells analyzed, the data provide identification of rare cell types, mapping of intermediate steps in differentiation, and the potential to identify new factors impacting fertility or controlling differentiation of germline and supporting somatic cells. We justify assignment of key germline and somatic cell types using combinations of known markers, <em>in situ</em> hybridization, and analysis of extant protein traps. Comparison of single cell and single nucleus datasets proved particularly revealing of dynamic developmental transitions in germline differentiation. To complement the web-based portals for data analysis hosted by the FCA, we provide datasets compatible with commonly used software such as Seurat and Monocle. The foundation provided here will enable communities studying spermatogenesis to interrogate the datasets to identify candidate genes to test for function <em>in vivo</em>.</span></p>
Dataset related to: Empagliflozin protects glomerular endothelial cell architecture in experimental diabetes through the VEGF-A/caveolin-1/PV-1 signaling pathway
<p>The files contain all the dataset included in the manuscript divided by figures.</p> <p>Abstract<br> In addition to having blood glucose-lowering effects, inhibitors of sodium glucose cotransporter 2 (SGLT2) afford renoprotection in diabetes. We sought to investigate which components of the glomerular filtration barrier could be involved in the antiproteinuric and renoprotective effects of SGLT2 inhibition in diabetes. BTBR (black and tan, brachyuric) <em>ob/ob</em> mice that develop a type 2 diabetic nephropathy received a standard diet with or without empagliflozin for 10 weeks, starting at 8 weeks of age, when animals had developed albuminuria. Empagliflozin caused marked decreases in blood glucose levels and albuminuria but did not correct glomerular hyperfiltration. The protective effect of empagliflozin against albuminuria was not due to a reduction in podocyte damage as empagliflozin did not affect the larger podocyte filtration slit pore size nor the defective expression of nephrin and nestin. Empagliflozin<br> did not reduce the thickening of the glomerular basement membrane. In BTBR <em>ob/ob</em> mice, the most profound abnormality seen using electron microscopy was in the endothelial aspect of the glomerular capillary, with significant loss of endothelial fenestrations. Remarkably, empagliflozin ameliorated the subverted microvascular endothelial ultrastructure. Caveolae and bridging diaphragms between adjacent endothelial fenestrae were seen in diabetic mice and associated with increased expression of caveolin-1 and the appearance of PV-1. These endothelial abnormalities were limited by the SGLT2 inhibitor. Although no expression of SGLT2 was found in glomerular endothelial cells, SGLT2 was expressed in the podocytes of diabetic mice. VEGF-A, which is a known stimulus for endothelial caveolin-1 and PV-1, was increased in podocytes of BTBR <em>ob/ob</em> mice and normalized by SGLT2 inhibitor treatment.<br> Thus, empagliflozin’s protective effect on the glomerular endothelium of diabetic mice could be due to a limitation of the paracrine signaling of podocyte-derived VEGF-A that resulted in a reduction of the abnormal endothelial caveolin-1 and PV-1, with the consequent preservation of glomerular endothelial function and permeability.</p>
Layer-by-Layer siRNA Particle Assemblies for Localized Delivery of siRNA to Epithelial Cells through Surface-Mediated Particle Uptake
<p>Localized delivery of small interfering RNA (siRNA) is a promising approach for spatial control of cell responses at biomaterial interfaces. Layer-by-layer (LbL) assembly of siRNA with cationic polyelectrolytes has been used in film and nanoparticle vectors for transfection. Herein, we combine the ability of particles to efficiently deliver siRNA with the ability of film polyelectrolyte multilayers to act locally. LbL particles were prepared with alternating layers of poly(l-arginine) and siRNA and capped with hyaluronic acid. Negatively charged LbL particles were subsequently assembled on the poly(l-lysine)-functionalized substrate to form a LbL particle-decorated surface. Cells grown in contact with the particle-decorated surface were able to survive, internalize particles, and undergo gene silencing. This work shows that particle-decorated surfaces can be engineered by using electrostatic interactions and used to deliver therapeutic payloads for cell-instructive biointerfaces.</p>
Dual-modality imaging of immunofluorescence and imaging mass cytometry for high-resolution whole slide imaging with accurate single-cell segmentation
<p>Imaging mass cytometry (IMC) is a powerful multiplexed tissue imaging technology that allows simultaneous detection of more than 30 makers on a single slide. It has been increasingly used for single-cell based spatial phenotyping in a wide range of samples. However, it only acquires a small, rectangle field of view (FOV) with a low image resolution that hinders downstream analysis. Here, we reported a highly practical dual-modality imaging method that combines high-resolution immunofluorescence (IF) and high-dementional IMC on the same tissue slide. Our computational pipeline uses the whole slide image (WSI) of IF as spatial reference, integrates small FOV IMC into a WSI of IMC. The high-resolution IF images enable accurate single-cell segmentation to extract robust high-dimensional IMC features for downstream analysis. We applied this method in esophageal adenocarcinoma of different stages, identified the single-cell pathology landscape via reconstruction of WSI IMC images and demonstrated the advantage of the dual-modality imaging strategy.</p>
RNA-seq - Definitive endoderm differentiation of human pluripotent stem cells in G1 phase
<p>Backup copy of the processed RNA-seq data at http://ngs.sanger.ac.uk/production/endoderm/</p>
Imaging data-set of mitochondrial Zink Finger localisation in mammalian cells
<p>This repository contains all raw and saved images for experiments with mitochondrial ZincFingers or mtZincFinger-Fluorophores conducted by Timo Rey during 2021 and 2022 at the MRC Mitochondrial Biology Unit without curation (unfiltered).<br> A more detailed description with a selection of representative images and proposed conclusions will follow eventually</p> <p>File-titles should be explicable of cell line and over-expressed plasmid constructs and/or antibodies used. Please refer to the accompanying excel sheet as well as all available plasmid maps for further detail and do not hesitate to enquire by contacting Timo Rey via e-mail, if further clarifications are needed. All images were acquired on an LSM880 Confocal Microscope, except for those on June 2, 2022, which were acquired on an Andro DragonFly Spinning Disk.</p> <p>Have a look and draw your own conclusions!</p>
Acceptable loss: Fitness consequences of salinity-induced cell death in a halotolerant microalga
<p>Environmentally induced reductions in fitness components (survival, fecundity) are generally considered as passive, maladaptive responses to stress. However, there is also mounting evidence for active, programmed forms of environmentally induced cell death in unicellular organisms. While conceptual work has questioned how such programmed cell death (PCD) might be maintained by natural selection, few experimental studies have investigated how PCD influences genetic differences in longer-term fitness across environments. Here, we tracked the population dynamics of two closely related strains of the halotolerant microalga <em>Dunaliella salina</em>, following transfers across salinities. We showed that after a salinity rise, only one of these strains displayed a massive population decline (-69% in one hour), largely attenuated by exposure to a PCD inhibitor. However, this decline was followed by a rapid demographic rebound, characterized by faster growth than the non-declining strain, such that sharper decline was correlated with faster subsequent growth across experiments and conditions. Strikingly, the decline was more pronounced in conditions more favourable to growth (more light, more nutrients, less competition), further suggesting that it was not simply passive. We explored several hypotheses that could explain this decline-rebound pattern, which suggests that <span>successive stresses could select for </span>higher environmentally induced death in this system<span>.</span></p>
Data used in the paper (Two-point optical manipulation reveals mechanosensitive remodeling of cell-cell contacts in vivo)
<p>Data used in the paper (Two-point optical manipulation reveals mechanosensitive remodeling of cell-cell contacts in vivo)</p>
Germinal Center and Cultured B cell expression libraries
<p>Comparison of gene expression profiles between in vitro mitogen-activated spleen B lymphocytes and FACS-sorted Germinal Center B lymphocytes isolated from intestinal PeyerPatches of C57BL/6 mice. In order to explore gene expression signatures that may be orchestrating somatic hypermutation (SHM, also known as affinity maturation) during antigen-induced B lymphocyte differentiation in Germinal Centers (GC), we profiled whole transcriptome gene expression of ex vivo, commensal microflora-activated GC B-cells that exhibit efficient SHM, with in vitro activated B-cell blasts, which fail to undergo SHM. In In particular, we examine our hypothesis that differential expression or the DNA endonucleases apex1 and apex2 regulate SHM. Using Templated Oligo Sequencing (TempO-Seq®) in conjunction with conventional intracellular FACS staining and B lymphocyte cell sorting, we compare gene expression profiles of in vitro mitogen-activated (LPS and anti-IgD-dextran), short-term (48h) cultured B cell blasts with Germinal Center B-cells isolated from intestinal Peyer Patches (PP, identified by surface staining B220+, CD95+, GL7+), compared to each other and to naive PP B-cells (B220+, CD95-, GL7-). We find that unique, distinct transcriptional signatures dominate the DNA repair processes in GC B-cells or in vitro B-cell blast, shedding light on genomic processes that orchestrate efficient affinity maturation of B-cells during GC differentiation. We use Templated Oligo Sequencing (TempO-Seq), a RNA motif-specific short tandem Oligo DNA hybridization technique to quantitatively measure whole transcriptome mRNA in conjunction with conventional surface membrane, fixable live/dead discriminator dye, and intracytoplasmic fluorescence antibody staining followed by FACS to isolate B cell populations of interest.</p>
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