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opencc-zeroSep 2018View details →

Sub-cellular Fractionation of H. pylori for separating total membrane components from Cytoplasm-periplasm

Alterations:Cell extract was centrifuged at 148000g instead of 140000g, in order to prevent contamination of total membrane in the cytoplasm-periplasm fraction.

opencc-by-4.0Jul 2018View details →

Gas permeation through single-crystal ZIF-8 membranes

Dataset supporting publication: Chen Chen, Aydin Ozcan, A. Ozgur Yazaydin and Bradley P. Ladewig, Gas permeation through single-crystal ZIF-8 membranes, Journal of Membrane Science, <a href="http://Chen Chen, Aydin Ozcan, A. Ozgur Yazaydin and Bradley P. Ladewig, Gas permeation through single-crystal ZIF-8 membranes, Journal of Membrane Science, https://doi.org/10.1016/j.memsci.2019.01.027">https://doi.org/10.1016/j.memsci.2019.01.027</a> Dataset supporting preprint: Chen, Chen; Ozcan, Aydin; Yazaydin, A. Ozgur; Ladewig, Bradley (2019): Gas Permeation Through Single-Crystal ZIF-8 Membranes. ChemRxiv. Preprint. <a href="https://doi.org/10.26434/chemrxiv.7571186.v1">https://doi.org/10.26434/chemrxiv.7571186.v1</a>

openFeb 2019View details →

Exploiting Fluoropolymers Immiscibility to Tune Surface Properties and Mass Transfer in Blend Membranes for Membrane Contactor Applications: dataset

This is the dataset related to the article published in ACS Applied Polymer Materials 2019, 1 (3), pp 326–334 Exploiting Fluoropolymers Immiscibility to Tune Surface Properties and Mass Transfer in Blend Membranes for Membrane Contactor Applications DOI 10.1021/acsapm.8b00105

opencc-by-4.0Apr 2019View details →

Atomistic simulations of the adenosine A2 receptor in membranes with varying levels of SDPE

An adenosine A2 receptor was simulated in membranes consisting of DSPC, cholesterol (20 mol%), and varying levels (0, 4, or 8 mol%) of SDPE with a polyunsaturated chain. Upon increasing SDPE concentration, the concentration of DSPC was correspondingly decreased. The initial structures for these simulations were obtained from the final structures of corresponding coarse-grained simulations, where an SDPE-rich corona formed around the receptor. After fine-graining, the systems were simulated using the CHARMM36 [1] force field for 200 ns using the GROMACS package [2]. These simulations were also repeated in the absence of protein. These systems were set up using the CHARMM-GUI web portal [3]. The corresponding files have the 'NOPROT' suffix, and the simulation parameter file is called md_noprot.mdp. For details on the fine-graining and the simulation protocol, please see the related paper at DOI: 10.1371/journal.pcbi.1007033. The files named PUFA_X.* correspond to simulations with X mol% of SDPE with the protein, whereas the files names PUFA_X_NOPROT.* are the corresponding files in the absence of the protein. For each concentration, a run input file (tpr) and the simulation outputs (xtc, edr, log, gro) are provided. Moreover, the simulations can be extended using the provided cpt files. Moreover, the files required to generate the run input file are also provided. For each system, a topology file (top) and an index file (ndx) are provided. The CHARMM36 force field and the molecule definitions (itp) referenced by the topology are also provided. The used simulation parameters are provided in the md.mdp file. For the fine-graining of SDPE, the mapping file is also provided (sdpe.charmm36.map). [1] DOI: 10.1021/jp101759q [2] DOI: 10.1016/j.softx.2015.06.001 [3] DOI: 10.1021/acs.jctc.5b00935

opencc-by-4.0Apr 2019View details →

Simulations of membrane proteins in a mixture of lipids with varying levels of chain unsaturation

Four structurally distinct membrane proteins were simulated in a mixture of phospholipids. The membranes contained one copy of one of the protein types with equimolar concentrations of DPPC, DOPC, DLiPC, SDPC, and cholesterol. The CHARMM36 force field [1] was employed, and the systems were built using the CHARMM-GUI web portal [2]. The 4-microsecond long simulations were performed using GROMACS [3]. Further details on the setup of the systems as well as on the simulation protocol can be found in the related paper at DOI: 10.1371/journal.pcbi.1007033. The files are named based on the PDB codes of the proteins (1AFO, 2M0B, 3EML, and 3EMN). For each system, the original simulation run input file (tpr) and the corresponding outputs (xtc, edr) are provided. Additionally, the simulations can be extended using the continue point (cpt) file. For each system the files required to generate the run input file are also provided: the topology file (top), index file (ndx), and a common run parameter file (mdp). The CHARMM36 force field can be downloaded from http://mackerell.umaryland.edu/charmm_ff.shtml Notably, the protein definition files (itp) were re-generated. After performing these simulations, the atom ordering of cholesterol in the CHARMM36 force field was changed. The provided gro files, as well as the lipid definition files (itp) correspond to this new atom order. While they can be used to generate a run input file, yet this run input file will not be identical to the one provided. Therefore: 1) for analysis, the provided xtc+tpr files are fine; 2) for extending the simulation, the tpr+cpt files are fine; 3) for new simulations, the tpr file can be generated based on the provided files, yet it cannot be used together with the provided xtc file. [1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/acs.jctc.5b00935 [3] DOI: 10.1016/j.softx.2015.06.001

opencc-by-4.0Apr 2019View details →

Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core

Membranes consisting of 260 DAPC and 28 (10 mol%) cholesterol molecules were simulated at various temperatures of 285, 298, 310, 320, and 333 K. Notably, one cholesterol molecule was restrained to the membrane core. The CHARMM36 force field [1] was used and the membranes were generated using CHARMM-GUI [2]. For simulations without a restrained cholesterol, see the other upload at DOI: The simulations were run for 2 microseconds using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations). The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data: <ul> <li>Topology files (top) and molecular definitions (itp)</li> <li>Index files (ndx)</li> <li>A common run parameter file (mdp)</li> <li>A run input file (tpr)</li> <li>Trajectory file (xtc) written every 100 ps</li> <li>Energy file (edr)</li> <li>Log file (log)</li> <li>Final structure file (gro)</li> <li>Continue point file (cpt)</li> </ul> The files are named LLLL_AA_CHOLXX_CORE_TTT.FFF, where <ul> <li>LLLL is the type of phospholipid</li> <li>AA stands for all atom (Coarse-grained data in a separate upload)</li> <li>CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)</li> <li>TTT is the temperature</li> <li>FFF is the tile type (see above)</li> </ul> Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section. [1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/acs.jctc.5b00935 [3] DOI: 10.1016/j.softx.2015.06.001

Extended Data Figure 9 in A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

Extended Data Figure 9 | Scanning electron microscopy images of melanosomes and melanosome impressions preserved in Yi qi holotype (STM 31-2). a–m, Note the high morphological diversity of the preserved melanosomes in the feathers, which include: densely distributed, small round phaeomelanosomes and sparsely distributed, medium-sized oval eumelanosomes in the feathers near the skull (a); medium-sized elongate elliptical eumelanosomes in the feathers near the skull (b, c), neck (d, e), humerus (f, g), and ulna (h, i, j); and large oval and elliptical eumelanosomes in the feathers near the tibiotarsus (k, l). The subspherical phaeomelanosomes in the sheet-like soft tissue (m) appear to be less densely distributed than the melanosomes in the feathers.

Extended Data Figure 7 in A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

Extended Data Figure 7 | Aerodynamic apparatuses in Yi and other tetrapods. a–c, Wing of Yi, Bat Model (a), Maniraptoran Model (b), and Frog Model (c); d, bat wing; e, pigeon wing; f, pterosaur wing; g, giant Japanese flying squirrel wing. Yellow colour indicates styliform element in a, b, c, d, f, and g.

Figure 3 in A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

Figure 3 | Simplified coelurosaurian phylogeny showing the recovered position of Yi. The skeletal silhouette and two possible alternative planform reconstructions of Yi highlight the proportionally long and robust forelimbs and large leg feathers that Yi shares with other basal paravian theropods, indicating the presence of aerial capability, and the inferred membranous wings, a feature unique among known paravians but seen in most other gliding or flying tetrapods. Various uncertainties, such as how the styliform element is oriented and whether membranous tissue is present lateral to the trunk as in most volant tetrapods, imply that a variety of reconstructions of the aerodynamic apparatus of Yi are currently plausible (see Supplementary Information for additional possible reconstructions).

Extended Data Figure 6 in A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

Extended Data Figure 6 | Elemental compositions of the styliform element and comparison samples based on EDS analyses. EDS spectra derived from: a, right manual phalanx II-1; b, right styliform element; c, feathers associated with right tibia; and d, sedimentary matrix.

Figure 2 in A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

Figure 2 | Soft tissues preserved in Yi qi holotype (STM 31-2). a–e, Feathers above the skull (a), along the humerus (b) and along the tibiotarsus (c); isolated basally converging (d) and brush-like (e) feathers; f, sheet-like soft tissue associated with the right forelimb (yellow arrows point to patches of sheet-like soft tissue); g, comparison of sheet-like soft tissue (above digit II) and individual feathers (below digit II).

Figure 1 in A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

Figure 1 | Yi qi holotype (STM 31-2). a, b, Photograph (a) and line drawing (b) of specimen; c, skull and mandible in lateral view; d, premaxillary tooth in lateral view; e, left manus; f, styliform elements (the distally unexposed left styliform element articulates with the wrist, and the orientation of the right styliform element implies a similar relationship to the carpus even though its proximal part is missing). Light and dark grey shading indicates feathers and membranous tissues, respectively. an, angular; cv, cervical vertebrae; d, dentary; dr, dorsal ribs; emf, external mandibular fenestra; en, external naris; f, frontal; lf, left femur; lh, left humerus; lmd2–4, left manual digits 2–4; lmt, left metatarsals; lr, left radius; ls, left scapula; lse, left styliform element; lu, left ulna; mb, mandible; mcII–IV, metacarpals II–IV; n, nasal; or, orbit; p, parietal; phII1 to IV4, phalanges II-1 to IV-4; pma, premaxilla; rmd2–4, right manual digits 2–4; rf, right femur; rfi, right fibula; rh, right humerus; rmc, right metacarpals; rmt, right metatarsals; rr, right radius; rse, right styliform element; rt, right tibiotarsus; ru, right ulna; sk, skull. Scale bar, 2 cm.

cranial feathers; 6, proximal part of neck feathers; 7, distal part of humeral feathers; 8, distal part of humeral feathers; 9 and 10, membranous soft tissue near digit II; 11, membranous soft tissue near digit IV; 12, middle part of tibial feathers. in A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

cranial feathers; 6, proximal part of neck feathers; 7, distal part of humeral feathers; 8, distal part of humeral feathers; 9 and 10, membranous soft tissue near digit II; 11, membranous soft tissue near digit IV; 12, middle part of tibial feathers.

elliptical eumelanosomes in the feathers near the skull (b, c), neck (d, e), humerus (f, g), and ulna (h, i, j); and large oval and elliptical eumelanosomes in the feathers near the tibiotarsus (k, l). The subspherical phaeomelanosomes in the sheet-like soft tissue (m) appear to be less densely distributed than the melanosomes in the feathers. in A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

elliptical eumelanosomes in the feathers near the skull (b, c), neck (d, e), humerus (f, g), and ulna (h, i, j); and large oval and elliptical eumelanosomes in the feathers near the tibiotarsus (k, l). The subspherical phaeomelanosomes in the sheet-like soft tissue (m) appear to be less densely distributed than the melanosomes in the feathers.

Extended Data Figure 4 in A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

Extended Data Figure 4 | Volumetric model generated from superimposed CT slices. Because there is little density contrast between the fossil and the matrix, the outline of the fossil is somewhat vague.

Extended Data Fig. 8 in A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs

Extended Data Fig. 8 | Compiled super-tree of the sampled Mesozoic coelurosaurians used in morphometric analyses. Complete tree for the coelurosaurians used in generating the PPCA morphospaces shown in Fig. 3b, c.

the area between the left femur and left manual digits. Arrows denote the positions of the samples. Scale bars, 2 µm. in A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs

the area between the left femur and left manual digits. Arrows denote the positions of the samples. Scale bars, 2 µm.

lil, left ilium;; lti, left tibia; pd, pedal digits; and ub, unidentified bony element. The white box indicates the position from which the sample was taken for histological analysis. Scale bars, 10 mm (a, c, d), 20 mm (b). in A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs

lil, left ilium;; lti, left tibia; pd, pedal digits; and ub, unidentified bony element. The white box indicates the position from which the sample was taken for histological analysis. Scale bars, 10 mm (a, c, d), 20 mm (b).

Extended Data Fig. 6 in A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs

Extended Data Fig. 6 | Scanning electron microscopy photographs of the soft tissues that are preserved in Ambopteryx. a–d, Feather samples associated with the neck. e–f, Samples of membranous tissues taken from the area between the left femur and left manual digits. Arrows denote the positions of the samples. Scale bars, 2 µm.

Extended Data Fig. 1 in A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs

Extended Data Fig. 1 | Additional photographs of Ambopteryx, IVPP V24192. a, Counter slab. b, Skeletal reconstruction based on preserved bones. c, Skull. d, Gastroliths and the unidentified bony stomach content. Abbreviations as in Fig. 1, except for: fe, feather associated with the neck; lil, left ilium;; lti, left tibia; pd, pedal digits; and ub, unidentified bony element. The white box indicates the position from which the sample was taken for histological analysis. Scale bars, 10 mm (a, c, d), 20 mm (b).