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Text-fig. 55. Scanning electron microscope (SEM) images of stamen fragments and pollen of Ibrahimia verminculata (a–h) and unnamed pantoporate pollen from pollen clump (i); Torres Vedras locality, Portugal. a) Holotype; stamen fragment that yielded the pollen in (b–f); b–f) Pantoporate pollen grains with vermiculate tectum and regularly spaced microechinate and pores with verrucate aperture membranes; g) Stamen fragment that yielded the pollen in (h); h) Abraded pantoporate pollen with vermiculate tectum and regularly spaced microechinate; i) Pantoporate pollen from coprolite with microreticulate-foveolate tectum and verrucate aperture membranes. Specimens, TV44-S148019 (holotype; a–f), TV44- S136782 (g, h), TV142-S170216 (i). Scale bars 300 Μm (a, g), 15 Μm (b), 6 Μm (d, e, h, i), 1.5 Μm (c, f). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 55. Scanning electron microscope (SEM) images of stamen fragments and pollen of Ibrahimia verminculata (a–h) and unnamed pantoporate pollen from pollen clump (i); Torres Vedras locality, Portugal. a) Holotype; stamen fragment that yielded the pollen in (b–f); b–f) Pantoporate pollen grains with vermiculate tectum and regularly spaced microechinate and pores with verrucate aperture membranes; g) Stamen fragment that yielded the pollen in (h); h) Abraded pantoporate pollen with vermiculate tectum and regularly spaced microechinate; i) Pantoporate pollen from coprolite with microreticulate-foveolate tectum and verrucate aperture membranes. Specimens, TV44-S148019 (holotype; a–f), TV44- S136782 (g, h), TV142-S170216 (i). Scale bars 300 Μm (a, g), 15 Μm (b), 6 Μm (d, e, h, i), 1.5 Μm (c, f).
Text-fig. 52. Scanning electron microscope (SEM) images of tricolpate pollen of Samylinaea punctata gen. et sp. nov from a pollen clump; Torres Vedras locality, Portugal. a) Pollen clump (probable stamen fragment) that yielded the pollen in this Text-figure; b) Polar view of pollen grain showing two colpi, granular aperture membrane, and punctate tectum; c) Orbicule showing very finely granular surface; d) Pollen wall showing short columellae, well-developed punctate tectum and slightly thinner foot layer; e–h) Pollen grains showing punctate tectum and the folds associated with the irregular development of the colpi. Specimen, TV44-S174565 (holotype; a–h). Scale bars 300 Μm (a), 6 Μm (b, e–h), 3 Μm (c, d). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 52. Scanning electron microscope (SEM) images of tricolpate pollen of Samylinaea punctata gen. et sp. nov from a pollen clump; Torres Vedras locality, Portugal. a) Pollen clump (probable stamen fragment) that yielded the pollen in this Text-figure; b) Polar view of pollen grain showing two colpi, granular aperture membrane, and punctate tectum; c) Orbicule showing very finely granular surface; d) Pollen wall showing short columellae, well-developed punctate tectum and slightly thinner foot layer; e–h) Pollen grains showing punctate tectum and the folds associated with the irregular development of the colpi. Specimen, TV44-S174565 (holotype; a–h). Scale bars 300 Μm (a), 6 Μm (b, e–h), 3 Μm (c, d).
Text-fig. 51. Scanning electron microscope (SEM) images of tricolpate pollen of Mcdougallia irregularis gen. et sp. nov. from a stamen fragment; Torres Vedras locality, Portugal. a) Holotype; stamen fragment that yielded the pollen in this Text-figure; b) Polar view of tricolpate pollen grain showing the continuous psilate tectum in the apocolpium and the poorly developed discontinuous foveolate-reticulate tectum in the mesocolpial areas, note irregular fold in tectum wall (arrowhead); c) Equatorial view of pollen grain showing the discontinuous tectum in the mesocolpial areas; d) Pollen grains showing variably developed tectum, colpi with a finely granular aperture membrane and the folds (arrowheads) associated with the irregular development of the colpi; e) Orbicule showing faintly striate surface; f) Pollen wall showing very short columellae, thin tectum and thin foot layer. Specimen, TV44-S148215 (holotype). Scale bars 300 Μm (a), 6 Μm (b–d), 3 Μm (e, f). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 51. Scanning electron microscope (SEM) images of tricolpate pollen of Mcdougallia irregularis gen. et sp. nov. from a stamen fragment; Torres Vedras locality, Portugal. a) Holotype; stamen fragment that yielded the pollen in this Text-figure; b) Polar view of tricolpate pollen grain showing the continuous psilate tectum in the apocolpium and the poorly developed discontinuous foveolate-reticulate tectum in the mesocolpial areas, note irregular fold in tectum wall (arrowhead); c) Equatorial view of pollen grain showing the discontinuous tectum in the mesocolpial areas; d) Pollen grains showing variably developed tectum, colpi with a finely granular aperture membrane and the folds (arrowheads) associated with the irregular development of the colpi; e) Orbicule showing faintly striate surface; f) Pollen wall showing very short columellae, thin tectum and thin foot layer. Specimen, TV44-S148215 (holotype). Scale bars 300 Μm (a), 6 Μm (b–d), 3 Μm (e, f).
Text-fig. 30. Scanning electron microscope (SEM) images of monocolpate pollen of Dejaxia brevicolpites gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Holotype; pollen clump (possible single pollen sac) that yielded the pollen in this Textfigure; b, c) Group of almost spherical pollen grains showing the irregularly undulating psilate tectum and abundant orbicules; d–g) Pollen grains showing the short colpi with a granular aperture membrane (d, f) and the irregularly undulating psilate tectum with scattered small perforations; note abundant orbicules (g); h) Pollen grain in proximal view showing the irregularly undulating psilate tectum resulting from the depressions around the perforations in the pollen wall. Specimen, TV44-S137909 (holotype). Scale bars 300 Μm (a), 30 Μm (b), 12 Μm (c), 6 Μm (d–h). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 30. Scanning electron microscope (SEM) images of monocolpate pollen of Dejaxia brevicolpites gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Holotype; pollen clump (possible single pollen sac) that yielded the pollen in this Textfigure; b, c) Group of almost spherical pollen grains showing the irregularly undulating psilate tectum and abundant orbicules; d–g) Pollen grains showing the short colpi with a granular aperture membrane (d, f) and the irregularly undulating psilate tectum with scattered small perforations; note abundant orbicules (g); h) Pollen grain in proximal view showing the irregularly undulating psilate tectum resulting from the depressions around the perforations in the pollen wall. Specimen, TV44-S137909 (holotype). Scale bars 300 Μm (a), 30 Μm (b), 12 Μm (c), 6 Μm (d–h).
Text-fig. 25. Scanning electron microscope (SEM) images of Appomattoxia minuta sp. nov. fruits and associated monocolpate pollen grains; Torres Vedras locality, Portugal. a–c) Lateral view of fruits (a, holotype) covered with hooked hairs showing the apical stigmatic area; d–g) Pollen grains from the fruits in (a) and (b) showing short monocolpate aperture, granular aperture membrane and microechinate tectum. Specimens, TV44-S136786 (holotype; a, d, e), TV44-S136787 (b, f, g), TV43-S105022 (c). Scale bars 300 Μm (a–c), 30 Μm (e), 6 Μm (d, f, g). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 25. Scanning electron microscope (SEM) images of Appomattoxia minuta sp. nov. fruits and associated monocolpate pollen grains; Torres Vedras locality, Portugal. a–c) Lateral view of fruits (a, holotype) covered with hooked hairs showing the apical stigmatic area; d–g) Pollen grains from the fruits in (a) and (b) showing short monocolpate aperture, granular aperture membrane and microechinate tectum. Specimens, TV44-S136786 (holotype; a, d, e), TV44-S136787 (b, f, g), TV43-S105022 (c). Scale bars 300 Μm (a–c), 30 Μm (e), 6 Μm (d, f, g).
Text-fig. 22. Scanning electron microscope (SEM) images of fragmentary stamens (a, b) with in situ pollen of Clavatipollenites sp. 1 (c–g); Torres Vedras locality, Portugal. a, b) Fragmentary tetrasporangiate stamens; c–e) Distal view of pollen grains showing large, rounded aperture and the irregular verrucate aperture membrane; f) Proximal view of pollen grains showing dense reticulum; g) Section through the fractured pollen wall showing foot layer, columellae and muri with faint supratectal ornamentation. Specimens, TV44-S105013 (a, c, d), TV44-S105019 (b, e–g). Scale bars 300 Μm (a, b), 6 Μm (c–f), 3 Μm (g). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 22. Scanning electron microscope (SEM) images of fragmentary stamens (a, b) with in situ pollen of Clavatipollenites sp. 1 (c–g); Torres Vedras locality, Portugal. a, b) Fragmentary tetrasporangiate stamens; c–e) Distal view of pollen grains showing large, rounded aperture and the irregular verrucate aperture membrane; f) Proximal view of pollen grains showing dense reticulum; g) Section through the fractured pollen wall showing foot layer, columellae and muri with faint supratectal ornamentation. Specimens, TV44-S105013 (a, c, d), TV44-S105019 (b, e–g). Scale bars 300 Μm (a, b), 6 Μm (c–f), 3 Μm (g).
trajectories for: Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations
<p>Coarse-grained trajectories produced and analysed for publication: </p> <p>----------------------</p> <p>Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations</p> <p>Andreas Haahr Larsen*, Lilya Tata*, Laura John & Mark S.P. Sansom</p> <p>Department of Biochemistry, University of Oxford, Oxford, United Kingdom, OX1 3QU</p> <p>PLOS comp biol (in press) </p> <p>-------------------------</p> <p> </p> <p>** file overview**</p> <p>md_X.xtc: (X=0..14) 15 repeated CG simulations (1500 ns each) of the FYVE domain from EEA1 binding to POPC:POP1 bilayer. The repeats differ in the rotation of the initial frame.<br> </p> <p>final_cg2at_aligned.pdb: initial frame for AT (after CG2AT)</p> <p>prod_cym_cent_repX.xtc (X=1,2,3) 3 repeated AT sims (500 ns each) of the FYVE domain from EEA1 binding to POPC:POP1 bilayer. </p> <p>** scripts for reproduction at GitHub**</p> <p>scripts and files for reproduction are available at: https://github.com/andreashlarsen/Larsen-Tata2021-FYVE</p>
Data for: Exocytosis of the silicified cell wall of diatoms involves extensive membrane disintegration
<p>Diatoms are unicellular algae, characterized by silica cell walls. The silica elements are formed intracellularly in a membrane-bound silica deposition vesicle (SDV), and are exocytosed after completion. How diatoms maintain membrane homeostasis during the exocytosis of these large and rigid silica elements is a long-standing enigma. We studied membrane dynamics during cell wall formation and exocytosis in two model diatom species, using live-cell confocal microscopy, transmission electron microscopy and cryo-electron tomography. Our results show that during the formation of the mineral phase it is in tight association with the SDV membranes, which are forming a precise mold of the delicate geometrical patterns. During exocytosis, the distal SDV membrane and the plasma membrane gradually detach from the mineral and disintegrate in the extracellular space, without any noticeable endocytic retrieval or extracellular repurposing. Within the cell, there is no evidence for the formation of a new plasma membrane, thus the proximal SDV membrane becomes the new barrier between the cell and its environment, and assumes the role of a new plasma membrane. These results provide direct structural observations of diatom silica exocytosis, and point to an extraordinary mechanism in which membrane homeostasis is maintained by discarding, rather than recycling, significant membrane patches.</p>
"Palmitoylation Mediates Membrane Association of Hepatitis E Virus ORF3 Protein and is Required for Infectious Particle Secretion"
<p><strong>Hepatitis E virus (HEV) is a positive-strand RNA virus encoding 3 open reading frames (ORF). HEV ORF3 protein is a small, hitherto poorly characterized protein involved in viral particle secretion and possibly other functions. Here, we show that HEV ORF3 protein forms membrane-associated oligomers. Immunoblot analyses of ORF3 protein expressed in cell-free <em>vs</em>. cellular systems suggested a posttranslational modification. Further analyses revealed that HEV ORF3 protein is palmitoylated at cysteine residues in its N-terminal region, as corroborated by <sup>3</sup>H-palmitate labeling, the investigation of cysteine-to-alanine substitution mutants and treatment with the palmitoylation inhibitor 2-bromopalmitate (2-BP). Abrogation of palmitoylation by site-directed mutagenesis or 2-BP treatment altered the subcellular localization of ORF3 protein, reduced the stability of the protein and strongly impaired the secretion of infectious particles. </strong><strong>Moreover, selective membrane permeabilization coupled with immunofluorescence microscopy revealed that HEV ORF3 protein is entirely exposed to the cytosolic side of the membrane, allowing to propose a model for its membrane topology and interactions required in the viral life cycle. </strong><strong>In conclusion, palmitoylation determines the subcellular localization, membrane topology and function of HEV ORF3 protein in the HEV life cycle. </strong></p>
Data set accompanying the paper "Effective cell membrane tension is independent of polyacrylamide substrate stiffness"
<p>This data set contains the data presented in the publication "Effective cell membrane tension is independent of polyacrylamide substrate stiffness". It consists of optical tweezers data and traction force microscopy data of 3T3 fibroblasts and Xenopus retinal ganglion cells on several different substrates.</p>
Ultra-stable self-standing Au nanowires/TiO2 nanoporous membrane system for high-performance photoelectrochemical water splitting cells - Dataset
<p>Dataset of results presented in <em><strong>Mater. Horiz.</strong></em>, 2022,<strong>9</strong>, 2797-2808: Ultra-stable self-standing Au nanowires/TiO<sub>2</sub> nanoporous membrane system for high-performance photoelectrochemical water splitting cells.</p> <p>E. W. would like to acknowledge Alexander von Humboldt Foundation, Bonn, Germany, for funding the postdoctoral fellowship, and the Polish National Agency For Academic Exchange, Polish Returns Programme (Project no. BPN/PPO/ 2021/1/00002), and the National Science Centre, Poland (Project no. 2022/01/1/ST5/00019) for financial support of the project. G. S. would like to acknowledge the National Science Centre, Poland (Project no. 2016/23/B/ST5/00790). The authors thank C. Erdmann for performing the transmission electron microscopy measurements.</p>
Data from: Membrane phase separation drives responsive assembly of receptor signaling domains
<p>Plasma membrane heterogeneity has been tied to a litany of cellular functions and is often explained by analogy to membrane phase separation, yet models based on phase separation alone fall short of describing the rich organization available within cell membranes. We present comprehensive experimental evidence motivating an updated model of plasma membrane heterogeneity in which membrane domains assemble in response to protein scaffolds. Quantitative super-resolution nanoscopy measurements in live B lymphocytes detect membrane domains that emerge upon clustering B cell receptors (BCR). These domains enrich and retain membrane proteins based on their preference for the liquid-ordered phase. Unlike phase separated membranes that consist of binary phases with defined compositions, membrane composition at BCR clusters is modulated through the protein constituents in clusters or the composition of the membrane overall. This tunable domain structure is detected through the variable sorting of membrane probes and impacts the magnitude of BCR activation.</p>
Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f).
Text-fig. 38. Scanning electron microscope (SEM) images of "Stamen with tricolpate pollen sp. 2"; Catefica locality, Portugal. a) Stamen fragment showing the elongate, tetrasporangiate anther but with the base and apex poorly preserved; b, d, e) Pollen grains from stamen fragment in equatorial (b, e) and polar (d) views showing the long colpi with coarsely verrucate aperture membranes and semitectate-microreticulate pollen wall; note small, spherical orbicules scattered on the surface of the tectum (arrows); c) Detail of pollen wall showing smooth muri with very faint transverse striations and a granular to columellate infratectal layer. Specimen, Catefica 153-S105614 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, d, e), 1 Μm (c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 38. Scanning electron microscope (SEM) images of "Stamen with tricolpate pollen sp. 2"; Catefica locality, Portugal. a) Stamen fragment showing the elongate, tetrasporangiate anther but with the base and apex poorly preserved; b, d, e) Pollen grains from stamen fragment in equatorial (b, e) and polar (d) views showing the long colpi with coarsely verrucate aperture membranes and semitectate-microreticulate pollen wall; note small, spherical orbicules scattered on the surface of the tectum (arrows); c) Detail of pollen wall showing smooth muri with very faint transverse striations and a granular to columellate infratectal layer. Specimen, Catefica 153-S105614 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, d, e), 1 Μm (c).
Text-fig. 11. Scanning electron microscope (SEM) images of isolated "Stamen fragment with Clavatipollenites-type pollen sp. 2"; Catefica locality, Portugal. a) Fragment of tetrasporangiate stamen with pollen in situ; b) Detail from stamen fragment showing distal and proximal surfaces of in situ pollen grains; c) Pollen grain in distal view showing short colpus with irregular margin and aperture membrane covered by irregular verrucae; d) Detail of pollen wall showing tiny spherical orbicules; e) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 50-S170389 (a–e). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (c), 3 Μm (d), 1.5 Μm (e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 11. Scanning electron microscope (SEM) images of isolated "Stamen fragment with Clavatipollenites-type pollen sp. 2"; Catefica locality, Portugal. a) Fragment of tetrasporangiate stamen with pollen in situ; b) Detail from stamen fragment showing distal and proximal surfaces of in situ pollen grains; c) Pollen grain in distal view showing short colpus with irregular margin and aperture membrane covered by irregular verrucae; d) Detail of pollen wall showing tiny spherical orbicules; e) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 50-S170389 (a–e). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (c), 3 Μm (d), 1.5 Μm (e).
Text-fig. 13. Scanning electron microscope (SEM) images of "Staminate inflorescence fragment with Clavatipollenites-type pollen sp. 4"; Catefica locality, Portugal. a) Fragment of stamen whorl from staminate inflorescence showing several closely packed, almost sessile stamens that lack a well-developed filament; b, c) Distal and proximal views of pollen grains showing poorly defined aperture with verrucate aperture membrane; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 49-S107782 (a–d). Scale bars = 600 Μm (a), 6 Μm (b, c), 1.5 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 13. Scanning electron microscope (SEM) images of "Staminate inflorescence fragment with Clavatipollenites-type pollen sp. 4"; Catefica locality, Portugal. a) Fragment of stamen whorl from staminate inflorescence showing several closely packed, almost sessile stamens that lack a well-developed filament; b, c) Distal and proximal views of pollen grains showing poorly defined aperture with verrucate aperture membrane; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 49-S107782 (a–d). Scale bars = 600 Μm (a), 6 Μm (b, c), 1.5 Μm (d).
Text-fig. 10. Scanning electron microscope (SEM) images of isolated "Stamen fragment with Clavatipollenites-type pollen sp. 1"; Catefica locality, Portugal. a) Fragment of tetrasporangiate stamen with pollen in situ; b) Detail from stamen fragment showing distal and proximal surfaces of in situ pollen grains and tiny orbicules on the inner surface of the anther wall (arrows); c) Pollen grains in distal view showing short colpi with irregular margins and aperture membrane with irregular verrucae; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 50-S170387 (a–d). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (c), 1.5 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 10. Scanning electron microscope (SEM) images of isolated "Stamen fragment with Clavatipollenites-type pollen sp. 1"; Catefica locality, Portugal. a) Fragment of tetrasporangiate stamen with pollen in situ; b) Detail from stamen fragment showing distal and proximal surfaces of in situ pollen grains and tiny orbicules on the inner surface of the anther wall (arrows); c) Pollen grains in distal view showing short colpi with irregular margins and aperture membrane with irregular verrucae; d) Detail of pollen wall showing the semitectate-reticulate tectum and long, scattered columellae supporting the narrow muri with finely verrucate supratectal ornamentation. Specimen, Catefica 50-S170387 (a–d). Scale bars = 600 Μm (a), 20 Μm (b), 6 Μm (c), 1.5 Μm (d).
Pure POPC Membrane with 1000mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 115 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC Membrane with 450mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 51 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC Membrane with 650mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 76 CaCl2, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p>The initial structures have been obtained from CHARMM-GUI.</p> <p> </p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.