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Fig. 5 in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.

Fig. 5 Phylogenetic reconstruction of the 18S rRNA gene tree of the novel Sarcocystis species and other tissue cyst-forming coccidia based on 1465 homologous positions of 40 aligned nucleotide sequences under the minimum evolution (ME) criterion; selected eimeriid coccidia served as outgroup. The new sequences of Sarcocystis sp. from China are highlighted by black symbols. Branch support values are shown for 1000 bootstrap replicates of three independent alignments with a site coverage of 95%. The shaded box highlights the taxa included in the so-called S. zuoi complex

Fig. 6 in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.

Fig. 6 ML analysis of the ITS1 region of Sarcocystis sp., S. zuoi and other species of the Sarcocystidae; members of the Toxoplasmatinae served as outgroup. Bootstrap branch support values are shown in triplicate, indicating results from three independent alignments and analyses.The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 204 homologous positions of 33 nucleotide sequences

Fig. 1 a–f in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.

Fig. 1 a–f Light microscopic and ultrastructural morphology of sarcocysts of Sarcocystis sp. in SD rats 5 months after inoculation with sporocysts isolated from rat snakes in Thailand. a Typical sporocyst from a fecal sample of Coelognathus radiatus; sporocysts from C. flavolineatus were identical in size and appearance; asterisk indicates single sporozoite. b Live sarcocyst, freed from muscle tissue; note the broad, palisade-like villar protrusions that could at times resemble those of Sarcocystis singaporensis with which this species can co-occur; however, the protrusions lack the basal stalks typical for the former species; the arrow highlights the septated compartments in the interior of the sarcocyst, and the inset shows a micrograph of live cystozoites freshly released from a cyst (arrowheads). c Typical structure of a cyst wall protrusion (isolate from C. flavolineatus); the arrows point to the electron-dense, knob-like structures of the primary cyst wall, whereby the knobs could apparently fuse to form an electron-dense borderline in larger protrusions (inset: arrowhead); also note the electron-light, thin layer of ground substance (GS) underneath the protrusions. d Typical cystozoites of the new species, which contained only two rhoptries (arrowheads) among relatively few micronemes (asterisks); additionally, the cystozoites exhibited vesicle-like structures in the anterior third of the cell containing electron-light, reticulate matter (arrow); the inset shows such a vesicle-like compartment at higher magnification, which was apparently not bound by a membrane (white arrow) and often located near micronemes (white asterisk); dense granules were present but rarely observed. e Interior and cyst wall of a mature sarcocyst (isolate from C. radiatus); metrocytes (asterisks) exclusively divided by endodyogeny, producing only two cystozoites (CZ). f Full-length section through a 15-µm-long protrusion of the sarcocyst wall; note that larger protrusions often occurred close to the tips of a cyst and showed a base with folds. AP, apicoplast; MI, mitochondrion; NU, nucleus; PT, villar protrusions

Fig. 4 in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.

Fig. 4 Two separate phylogenies of the 28S rRNA gene (longer and shorter sequence fragments) of the new Sarcocystis sp. sampled in China, newly sequenced S. zuoi from China and novel Sarcocystis isolates from Borneo. Symbols indicate the new sequences of this study, whereby taxa considered conspecific are grouped by shape. GenBank accession numbers are given behind each taxon name. a Maximum likelihood (ML) analysis of an alignment of 29 sequences and 1383 homologous positions. Branch support by bootstrapping (1000 replicate trees) is shown next to the branches, whereby the results of three independent analyses based on independent alignments are shown. The scale bar indicates the number of substitutions per site. All positions with <85% site coverage were eliminated, i.e. fewer than 15% alignment gaps, missing data and ambiguous bases were allowed at any position (partial deletion option). Selected eimeriid coccidia served as outgroup. b ML analysis of a trimmed alignment including five shorter sequences of Sarcocystis sampled in Borneo compared with the samples of Sarcocystis sp. from China; a total of 16 sequences and 366 homologous positions with site coverage of 95% were compared. Sarcocystis pantherophisi served as outgroup. The corresponding natural intermediate hosts are also indicated

Fig. 2 in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.

Fig. 2 Light microscopic and ultrastructural morphology of sarcocysts from Maxomys whiteheadi in Borneo (a–c) and wild Rattus norvegicus in China (d, e). Note, due to ethanol fixation some ultrastructural details of the samples from Borneo are poorly resolved. a Richardsen's dye-stained 1.0-µm thin section through a mature sarcocyst showing the villar protrusions (PT) of the cyst wall and numerous relatively small cystozoites (CZ). b Same sample as before under the electron microscope; note the thin layer of ground substance underneath the protrusions. c Enlarged part of the interior of the sarcocyst showing cystozoites—although with limited resolution—that possess a pair of rhoptries each, which is characteristic for this Sarcocystis species (black and white arrows; compare with Fig. 1d). d Live sarcocyst isolated from striated muscle tissue of a wild Norway rat in China; the inset shows live cystozoites that were freshly released from a cyst. e Ultrastructure of the same sarcocyst as before; note that the villar protrusions are highly similar to the samples from Borneo and Thailand regarding size and shape (Fig. 1e); again, cystozoites only exhibit one pair of rhoptries (arrows) and relatively few micronemes

Fig. 3 in A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov.

Fig. 3 Graph showing the size of sporocysts (length plotted against diameter, in μm; error bars indicate s.e.) of the Sarcocystis isolates from the colubrid snakes Coelognathus flavolineatus and C. radiatus in Thailand and closely related Sarcocystis. Every isolate/ species is indicated by a different symbol (legend), whereby sporocyst samples with the same shape index (= length/diameter) share the same background shading: white = 1.3; dark = 1.5; Sarcocystis pantherophisi = 1.2. Here, S. pantherophisi is included as reference for the snake host Sarcocystis lineage S2, while all other species belong to lineage S1 (except for S. murinotechis, for which no genetic information is available)

opencc-by-4.0Jun 2024View details →

Dataset for the publication: Impact of unintentionally formed CH2O in oxygenated fuel exhausts on DeNOx-SCR at different NO2/NOx ratios under close to real conditions

The dataset covers the research data of the publication in Catalysis Science & Technology with the title "Impact of unintentionally formed CH2O in oxygenated fuel exhausts on DeNOx-SCR at different NO2/NOx ratios under close to real conditions" (DOI: 10.1039/d2cy01935c).

opencc-by-4.0Jun 2024View details →

Data for: Intrinsically Disordered Proteins form Condensates with Gradually Collapsing Conformations at the Interface

<h3>Data for: Intrinsically Disordered Proteins form Condensates with Gradually Collapsing Conformations at the Interface</h3> We ran simulations for four different systems: <ul> <li>WT: A1-LCD WT (N=137), wild-type (WT) sequence of the low-complexity domain (LCD) of the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), with electrostatic interactions, at temperature T=260K</li> <li>WT_noEL_T260: A1-LCD WT (N=137), without electrostatic interactions, at temperature T=260K</li> <li>WT_noEL_T290: A1-LCD WT (N=137), without electrostatic interactions, at temperature T=290K</li> <li>HP: homopolymer consisting of prolines (N=137), at temperature T=550</li> </ul> For every system, we ran five independent simulations over 5µs (1000 frames) and used the last 900 frames (4.5µs) for our analysis. This data repository consists of    (1) folders containing the data for every seperate run (*_i, i=1,2,3,4,5) in simulation units    (2) folders containing the averaged data of all five runs (*_AVG), converted to SI units    (3) a droplet folder, containing the data (square radius of gyration and asphericity) for the whole droplet (for all four systems, all five runs) Units are also clarified in each file's header. The simulation units can be converted to SI units via: <ul> <li>Distance: D = 0.45nm</li> <li>Mass: M = 57.05amu</li> <li>Energy: epsilon = 0.2 kcal/mol</li> </ul>   Details for (1) and (2): Each folder (*_i, i=1,2,3,4,5, and *_AVG) contains the following subfolders and files: Ree: <ul> <li>distribCos2_all.dat: distribution of cos^2(θ_{ee}) of the whole chains, where θ_{ee} is the angle between the polymer's center r_c and the chain’s end-to-end vector Ree [Fig. S3b, Fig. S6b, Fig. S9b, Fig. S12b]</li> <li>distribCos2_segment_i.dat: distribution of cos^2(θ_{ee,s}) of segment seg_i, where θ_{ee,s} is the angle between the segment's center r_{c,s} and the segment’s end-to-end vector R_{ee,s} [Fig. S4d, Fig. S7d, Fig. S10d, Fig. S13d]</li> <li>distribCos2_segments_all.dat: distribution of cos^2(θ_{ee,s}) of all segments seg_i, where θ_{ee,s} is the angle between the segment's center r_{c,s} and the segment’s end-to-end vector R_{ee,s} [Fig. S4d, Fig. S7d, Fig. S10d, Fig. S13d]</li> <li>distribMonomer_all.dat: distribution of the monomers [Fig. 1, Fig. S4c, Fig. S7c, Fig. S10c, Fig. S13c]</li> <li>distribPolymer_all.dat: distribution of the polymers (whole chains, binned via polymer center position) [Fig. 1, Fig. S4c, Fig. S7c, Fig. S10c, Fig. S13c]</li> <li>distribPolymerEndPos.dat: distribution of the polymer end positions (whole chains) [Fig. S4c, Fig. S7c, Fig. S10c, Fig. S13c]</li> <li>distribPolymerEndPos_segment_i.dat: distribution of the polymer segment end positions of seg_i</li> <li>distribPolymerEndPos_segment_all.dat: distribution of the polymer segment end positions of all segments</li> <li>distribPolymerRee2_all.dat: distribution of Ree^2 (whole chains), binned via polymer center position r_c</li> <li>distribPolymerRee_segment_i.dat: distribution of Ree^2 of segment seg_i, binned via segment center position r_{c,s}</li> <li>distribPolymerRee_segments_all.dat: distribution of Ree^2 of all segments, binned via segment center position r_{c,s}</li> <li>distribPolymerSegment_i.dat: distribution of polymer segment seg_i, binned via segment center position r_{c,s}</li> <li>distribPolymerSegments_all: distribution of all polymer segments, binned via segment center position r_{c,s}</li> </ul> Rg: <ul> <li>distribCos2_all.dat: distribution of cos^2(θ) of the whole chains, where θ is the angle between the polymer's center r_c and the eigenvector belonging to the largest eigenvalue of the chain’s gyration tensor [Fig. S3b, Fig. S6b, Fig. S9b, Fig. S12b]</li> <li>distribCos2_segment_i.dat: distribution of cos^2(θ_s) of segment seg_i, where θ_s is the angle between r_{c,s} and the eigenvector belonging to the largest eigenvalue of the segment’s gyration tensor [Fig. S4b, Fig. S7b, Fig. S10b, Fig. S13b]</li> <li>distribCos2_segments_all.dat: distribution of cos^2(θ_s) of all segments seg_i, where θ_s is the angle between r_{c,s} and the eigenvector belonging to the largest eigenvalue of the segment’s gyration tensor [Fig. S4b, Fig. S7b, Fig. S10b, Fig. S13b]</li> <li>distribMonomer_all.dat: distribution of the monomers [Fig. 1, Fig. S4c, Fig. S7c, Fig. S10c, Fig. S13c]</li> <li>distribPolymer_all.dat: distribution of the polymers (whole chains, binned via polymer center position) [Fig. 1, Fig. S4c, Fig. S7c, Fig. S10c, Fig. S13c]</li> <li>distribMonomerRg_all.dat: distribution of monomer weighted Rg^2 (whole chains), referred to as R_{g,mono}^2 (following Farag et. al) [Fig. 2, Fig. S3a, Fig. S6a, Fig. S9a, Fig. S12a]</li> <li>distribPolymerRg_all.dat: distribution of Rg^2 (whole chains), binned via polymer center position r_c [Fig. 2, Fig. S3a, Fig. S6a, Fig. S9a, Fig. S12a]</li> <li>distribPolymerRg_segment_i.dat: distribution of Rg^2 of segment seg_i, referred to as R_{g,s}^2, binned via segment center position r_{c,s} [Fig. S4a, Fig. S7a, Fig. S10a, Fig. S13a]</li> <li>distribPolymerSegment_i.dat: distribution of polymer segment seg_i, binned via segment center position r_{c,s}</li> <li>distribPolymerSegments_all: distribution of all segments, binned via segment center position r_{c,s}</li> </ul> resDist: <ul> <li>distribPolymerRee2_base_resDistance_s.dat: distribution of Ree2 of all chain segments of length s=|j-i|, binned according to the segment base position r_i [Fig. 3, Fig. S5, Fig. S8, Fig. S11, Fig. S14]</li> <li>distribPolymerRee2_center_resDistance_s.dat: distribution of Ree2 of all chain segments of length s=|j-i|, binned according to the segment center position r_{c,s} [Fig. 3, Fig. S5, Fig. S8, Fig. S11, Fig. S14]</li> <li>distribPolymerRg2_base_resDistance_s.dat: distribution of Rg2 of all chain segments of length s=|j-i|, binned according to the segment base position r_i [Fig. 3, Fig. S5, Fig. S8, Fig. S11, Fig. S14]</li> </ul> distribPolymerRg2_center_resDistance_s.dat: distribution of Rg2 of all chain segments of length s=|j-i|, binned according to the segment center position r_{c,s} [Fig. 3, Fig. S5, Fig. S8, Fig. S11, Fig. S14]     Details for (3): The folder 'droplet' contains four system folders (HP, WT, WT_noEL_T260, WT_noEL_T290). Each of those folders contains the following files: <ul> <li>runX_cluster_Rg2_Rg2Normal_kappa2.dat: for every run X, one finds the time evolution (in simulation units, with 1e8 timesteps = 1µs) of the square radius of gyration Rg2 of the full droplet, its x-, y- and z-components, its three eigenvalues and the droplet asphericity A (referred to as kappa2 in the header) [Fig.S1c, Fig.S1d]</li> <li>AVG_cluster_Rg2_Rg2Normal_kappa2.dat: average of the parameters from the runX_cluster_Rg2_Rg2Normal_kappa2.dat files, over all five runs, using the last 900 snapshots (4.5µs) of every run [Fig. S1a, Fig. S1b]</li> <li>STD_cluster_Rg2_Rg2Normal_kappa2.dat: standard deviation of the parameters from the runX_cluster_Rg2_Rg2Normal_kappa2.dat files, over all five runs, using the last 900 snapshots (4.5µs) of every run [Fig. S1a, Fig. S1b]</li> </ul>

Fig. 7 in Skull of a dromaeosaurid dinosaur Shri devi from the Upper Cretaceous of the Gobi Desert suggests convergence to the North American forms

Fig. 7. Comparison of silhouettes of the velociraptorine skulls from different sites of the Upper Cretaceous of the Gobi Desert. A. Shri devi Turner, Montanari, and Norell, 2021, ZPAL MgD-I/97. B, D, E. Velociraptor mongoliensis Osborn, 1924. B. AMNH FARB 6515. D. MPC-D 100/25. E. MPC-D 100/54. C. Velociraptor sp. MPC-D 100/982. F. "Velociraptor" osmolskae Godefroit, Currie, Li, Shang, and Dong, 2008, IMM 99NM-BYM-3/3. G. Linheraptor exquisitus Xu, Choinere, Pittman, Tan, Xiao, Li, Tan, Clark, Norell, Hone, and Sullivan, 2010, IVPP V16923. H. Tsaagan mangas Norell, Clark, Turner, Makovicky, Barsbold, and Rowe, 2006, MPC-D 100/1015. Known elements from any side of the specimen are in grey. Lines present some of the features distinguishing S. devi from other velociraptorines: the maximum height of the antorbital fenestra and its perpendicular projection showing elongation of the fenestra (red lines), the position of the last maxillary alveoli (blue), the anteriormost projection of the quadratojugal (green), and the position of the ventral margin of the external mandibular fenestra (purple).

Fig. 6 in Skull of a dromaeosaurid dinosaur Shri devi from the Upper Cretaceous of the Gobi Desert suggests convergence to the North American forms

Fig. 6. Phylogenetic relationships of Shri devi Turner, Montanari, and Norell, 2021, among the dromaeosaurid dinosaurs. Values of the antorbital fenestra elongation (measured as the ratio of the posterior margin height to the longitudinal length) and elongation of the maxilla (measured as the ratio of the maxilla length to its height; data after Powers et al. 2022) are mapped on the 50% majority rule consensus trees generated from the modified data matrices of Powers et al. 2022 (A), and Napoli et al. 2021 (B). White rectangles represent the missing data.

Fig. 9 in Skull of a dromaeosaurid dinosaur Shri devi from the Upper Cretaceous of the Gobi Desert suggests convergence to the North American forms

Fig. 9. Artistic post-mortem reconstruction of the Shri devi Turner, Montanari, and Norell, 2021, individual represented by a specimen ZPAL MgD-I/97 before its final burial. Artwork by Jakub Zalewski (CC BY-NC-ND-3.0).

Fig. 5 in Skull of a dromaeosaurid dinosaur Shri devi from the Upper Cretaceous of the Gobi Desert suggests convergence to the North American forms

Fig. 5. Results of the PCA for the linear measurements of maxilla (A) and pes (B) for the velociraptorines from the Upper Cretaceous of the Gobi Desert. Blue dots represent specimens from the Djadokhta strata, orange from the Baruungoyot strata, green from Ukhaa Tolgod, and black and grey from Bayan Mandahu.

Fig. 3 in Skull of a dromaeosaurid dinosaur Shri devi from the Upper Cretaceous of the Gobi Desert suggests convergence to the North American forms

Fig. 3. Dromaeosaurid dinosaur Shri devi Turner, Montanari, and Norell, 2021 (ZPAL MgD-I/97) from the Upper Cretaceous, Khulsan, Ömnögovi, Gobi Desert, Mongolia. Photographs (A1, A2, A4, A5) and 3D model (A3, A6, A7) obtained from the CT scan of the left side of the skull in dorsal (A1), medial (A2, A3), anterior (A6), and lateral (A7) views. Elements of the left palate in dorsal (A4) and ventral (A5) views. Right maxilla in the lateral (A8, A9) and anterior (A10) views, with the margin of the antorbital fenestra indicated by dashed lines, and the close up of the fifth (A11) and the second (A12) preserved tooth in labial views showing very weakly developed denticles on the mesial carina. Right mandible in the lateral (A13, A14) and medial (A15, A16) views. B. Explanatory drawings of the skull in left (B1) and right (B2) lateral views with the preserved bones (in grey).

Fig. 4 in Skull of a dromaeosaurid dinosaur Shri devi from the Upper Cretaceous of the Gobi Desert suggests convergence to the North American forms

Fig. 4. Dromaeosaurid dinosaur Shri devi Turner, Montanari, and Norell, 2021 (ZPAL MgD-I/97) from the Upper Cretaceous, Khulsan, Ömnögovi, Gobi Desert, Mongolia. A. Left metatarsus in anterior (A1, A2) and posterior (A3, A4) views, and phalanges of digit IV (A5), digit III (A6), digit II (A7), and digit I (A8) in medial views, metatarsal I in anterior view (A8). Ungual III-4 is presented as a 3D model obtained from the CT scan. B. Plot presenting the elongation of II-3 in relation to the length of metatarsal II in dromaeosaurid dinosaurs. Blue dots represent specimens from the Djadokhta strata, orange from the Baruungoyot strata, black from Bayan Mandahu, and white from North America.

Fig. 8 in Skull of a dromaeosaurid dinosaur Shri devi from the Upper Cretaceous of the Gobi Desert suggests convergence to the North American forms

Fig. 8. Reconstruction of the dromaeosaurid dinosaur Shri devi Turner, Montanari, and Norell, 2021, based on ZPAL MgD-I/97 and MPC-D 100/980. A. Skull; missing elements reconstructed on the base of Velociraptor mongoliensis Osborn, 1924 (MPC-D 100/25 and MPC-D 100/54). B. Whole body silhouette with known remains of the holotype and referred material. Silhouette based on V. mongoliensis drawn by J.A. Headden (Wikimedia Commons CC-BY-3.0).

Fig. 2 in Skull of a dromaeosaurid dinosaur Shri devi from the Upper Cretaceous of the Gobi Desert suggests convergence to the North American forms

Fig. 2. Dromaeosaurid dinosaur Shri devi Turner, Montanari, and Norell, 2021 (ZPAL MgD-I/97) from the Upper Cretaceous, Khulsan, Ömnögovi, Gobi Desert, Mongolia. Specimen prior to the preparation work (A1), and the 3D model of the skeleton, based on the CT and surface scanner data, with elements arranged as originally found (A2).

Figure 7 in Morphology, feeding and behaviour of British Magelona (Annelida: Magelonidae), with discussions on the form and function of abdominal lateral pouches

Figure 7. Various palp positions observed for Magelona mirabilis from in situ experiments. Third picture depicts debris collecting on and in between the palps.

Figure 3 in Morphology, feeding and behaviour of British Magelona (Annelida: Magelonidae), with discussions on the form and function of abdominal lateral pouches

Figure 3. Experimental set-up: A, aquarium tank and cooling system; B, Magelona johnstoni Berwick-upon-Tweed (NMW.Z. 2013.037.0001): live animal in capillary tube. Photo: A.S.Y. Mackie.

Figure 10 in Morphology, feeding and behaviour of British Magelona (Annelida: Magelonidae), with discussions on the form and function of abdominal lateral pouches

Figure 10. Abdominal posteriorly opening pouches from several specimens of Magelona johnstoni: A–B, initiation of new pouches represented by small 'holes' (lateral view) (A: NMW.Z.2013.037.0008e; B: NMW.Z.2013.037.0010d); C, first pouch (~6 chaetigers) from pygidium (lateral view) (NMW.Z.2013.037.0011d); D, first pouch from a regenerating tail (ventral/posterior view) (NMW.Z.2013.037.0008c); E, third pouch (~10 chaetigers) from pygidium (posterior view) (NMW.Z.2013.037.0011d); F, posteriorly opening pouch of an abdominal fragment (lateral posterior view) (NMW.Z.1998.028). Photos: K. Mortimer.

Figure 2 in Morphology, feeding and behaviour of British Magelona (Annelida: Magelonidae), with discussions on the form and function of abdominal lateral pouches

Figure 2. Magelona mirabilis Berwick-upon-Tweed (NMW.Z. 2013.037.0020): A, whole animal; B, anterior (ventral view); C, palp; D, prostomium (ventral view, showing mouth); E, posterior. All MgCl -relaxed. Photos: A.S.Y. Mackie.