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CX-MS Datasets for "Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex"
<p>This repository contains chemical cross-linking mass spectrometry data of affinity-purified Yeast nuclear pore complexes.</p> <p>Data Files Description:</p> <p>NPC_XL_Identification_Inter_Crosslinked.csv: Inter-protein cross-links identified by pLink 2.</p> <p>NPC_XL_spectra.mgf: MS2 spectra data for the identified cross-links.</p> <p>NPC_XL_proteins.fasta : Protein sequences used for search.</p> <p>Sample Processing:</p> <p>NPCs were immuno-purified from Mlp1 tagged S. cerevisiae strains (Kim et al., 2018). After native elution, 1.0 mM disuccinimidyl suberate (DSS) was added and the sample was incubated at 25ºC for 40 min with shaking (1,200 rpm). The reaction was quenched by adding a final concentration of 50 mM freshly prepared ammonium bicarbonate and incubating for 20 min with shaking (1,200 rpm) at 25ºC. The sample (50 µg) was then concentrated and denatured at 98ºC for 5 min in a solubilization buffer (10% solution of 1-dodecyl-3-methylimidazolium chloride (C12-mim-Cl) in 50 mM ammonium bicarbonate, pH 8.0, 100 mM DTT). After denaturation, the sample was centrifuged at 21,130 g for 10 min and the supernatant was transferred to a 100 kDa MWCO ultrafiltration unit (MRCF0R100, Microcon). The sample was quickly spun at 1,000 g for 2 min and washed twice with 50 mM ammonium bicarbonate. After alkylation (50 mM iodoacetamide), the cross-linked NPC in-filter was digested by trypsin and lysC O/N at 37ºC. After proteolysis, the sample was recovered by centrifugation and peptides were fractionated into 10-12 fractions by using a stage tip self-packed with basic C18 resins (Dr. Masch GmbH). Fractionated samples were pooled prior to LC/MS analysis.</p> <p>Desalted cross-link peptides were dissolved in the sample loading buffer (5% Methanol, 0.2% FA), separated with an automated nanoLC device (nLC1200, Thermo Fisher), and analyzed by an Orbitrap Q Exactive HFX (Pharma mode) mass spectrometer (Thermo Fisher) as previously described (Xiang et al., 2020; Xiang et al., 2021). Briefly, peptides were loaded onto an analytical column (C18, 1.6 μm particle size, 100 Å pore size, 75 μm × 25 cm; IonOpticks) and eluted using a 120-min liquid chromatography gradient. The flow rate was approximately 300 nl/min. The spray voltage was 1.7 kV. The QE HF-X instrument was operated in the data-dependent mode, where the top 10 most abundant ions (mass range 380 – 2,000, charge state 4 - 8) were fragmented by high-energy collisional dissociation (HCD). The target resolution was 120,000 for MS and 15,000 for tandem MS (MS/MS) analyses. The quadrupole isolation window was 1.8 Th; the maximum injection time for MS/MS was set at 200 ms.</p> <p>Data Processing:</p> <p>The raw data were searched with pLink2 (Chen et al., 2019b). An initial MS1 search window of 5 Da was allowed to cover all isotopic peaks of the cross-linked peptides. The data were automatically filtered using a mass accuracy of MS1 ≤ 10 ppm (parts per million) and MS2 ≤ 20 ppm of the theoretical monoisotopic (A0) and other isotopic masses (A+1, A+2, A+3, and A+4) as specified in the software. Other search parameters included cysteine carbamidomethyl as a fixed modification and methionine oxidation as a variable modification. A maximum of two trypsin missed-cleavage sites was allowed. The initial search results were obtained using a default 5% false discovery rate (FDR) expected by the target-decoy search strategy. Spectra were manually verified to improve data quality (Kim et al., 2018; Shi et al., 2014). Cross-linking data were analyzed and plotted with CX-Circos (http://cx-circos.net).</p>
A closer look: High-resolution pore-scale simulations of solute transport and mixing through porous media columns
<p>This dataset contains the results of fluid flow (Navier-Stokes) and solute transport (Advection-Diffusion) simulations within columns of granular media generated by virtual gravitational settling of spherical grains. The experiments comprise three media with different degrees of grain-size variability; a range of grain-Peclet numbers is explored. See the homonymous research paper by Sole-Mari et al. (2022, Water Resources Research) for more information.</p> <p>Grains.zip: Positions and radii of the spherical grains for each value of grain-size variability sigma (Matlab's .mat format).</p> <p>ResultsCoarse.zip: Coarse-scale data presented in the aforementioned WRR paper (Matlab's .mat format).</p> <p>Link to the full micro-scale dataset: (soon available)</p> <p>We thankfully acknowledge the computer resources at MareNostrum and the technical support provided by the Barcelona Supercomputing Center (AECT-2019-3-0014).</p> <p> </p>
Fig.ç3.D isasterina akajimaensis sp. nov., holotype (NSMT E-6758). A, Anal pore and a patch; B, madreporite; C, proximal part of arm, abactinal view; D, oral plate pair and interradial uncalci ed area, some oral spines have been lost (see also Fig. 6 for oral plate pair and interradial uncalci ed area at another interradius); E, proximal part of ambulacral furrow (oral plates seen at the lower-le corner are drawn in Fig. 6); F, inferomarginal spinelets, abactinal view. Abbreviations: als, actinolateral spine; apo, anal pore; fs, furrow spine; imp, inferomarginal plate; ims, inferomarginal spine; ir, interradial; iua, interradial uncalci ed area; md, madreporite; op, oral plate; os, oral spine; r, radial; rp, rigid patch; sas, subambulacral spine. in A New Asterinid Sea Star, Disasterina akajimaensis (Echinodermata: Asteroidea) from the Ryukyu Islands, Japan, with Notes on the Genus Disasterina
Fig.ç3.D isasterina akajimaensis sp. nov., holotype (NSMT E-6758). A, Anal pore and a patch; B, madreporite; C, proximal part of arm, abactinal view; D, oral plate pair and interradial uncalci ed area, some oral spines have been lost (see also Fig. 6 for oral plate pair and interradial uncalci ed area at another interradius); E, proximal part of ambulacral furrow (oral plates seen at the lower-le corner are drawn in Fig. 6); F, inferomarginal spinelets, abactinal view. Abbreviations: als, actinolateral spine; apo, anal pore; fs, furrow spine; imp, inferomarginal plate; ims, inferomarginal spine; ir, interradial; iua, interradial uncalci ed area; md, madreporite; op, oral plate; os, oral spine; r, radial; rp, rigid patch; sas, subambulacral spine.
dataset for paper "Activation energy for pore opening in lipid membranes under an electric field"
<p>Dataset for the paper "Electropermeabilization of hydroperoxidized lipid membranes".</p> <p>Data was generated from Orbit Mini miniaturized bilayer workstation (Nanion Technologies, Munich, Germany), with an inserted microelectrode cavity array (MECA 4) recording chip (Ionera Technologies, Freiburg, Germany).</p> <p>The data files have format .abf, a standard format for electrophysiological data. <br> It can be read by applications such as for instance</p> <p>- Clampex and ClampFit, from the patch-clamp software suite pCLAMP, <br> - Elements Data Analyzer, associated with the elements data reader software from Elements-IC, </p> <p><br> or imported into Python through the package pyABF 2.3.5.</p> <p>import pyabf // abf=pyabf.ABF(path+"/"+f+"/"+abffile) // data = np.vstack((abf.sweepX, abf.data)) </p> <p>Data is organized in five folders named according to target hydroperoxidation degrees:<br> POPC<br> POPC-OOH 25%<br> POPC-OOH 50%<br> POPC-OOH 75%<br> POPC-OOH 100%</p> <p>Inside each of the five above files data is organized by date, and informed with the actual measured hydroperoxidation degree for a given sample. </p>
Text-fig. 9. Wataria kvacekii sp. nov., UF 279-24556. a: Wood ring-porous, earlywood with 2–3 rows of wide pores, vessels solitary and in radial multiples of 2, axial parenchyma scanty vasicentric and some apotracheal diffuse-in-aggregates, TS. b: Series of vessel elements with simple perforations, axial parenchyma strands adjacent to vessels, RLS. c: Alternate intervessel pitting, vessel element end walls horizontal, RLS. d: Vessel-axial parenchyma pitting similar to intervessel pitting, RLS. e, f: Rays with tile cells, storied axial parenchyma, some strands chambered crystalliferous, TLS. g: Detail of ray, TLS. h: Storied imperforate elements. Scale bars: 200 µm in a; 100 µm in b, e; 50 µm in c, d, f, h; 20 µm in g. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa
Text-fig. 9. Wataria kvacekii sp. nov., UF 279-24556. a: Wood ring-porous, earlywood with 2–3 rows of wide pores, vessels solitary and in radial multiples of 2, axial parenchyma scanty vasicentric and some apotracheal diffuse-in-aggregates, TS. b: Series of vessel elements with simple perforations, axial parenchyma strands adjacent to vessels, RLS. c: Alternate intervessel pitting, vessel element end walls horizontal, RLS. d: Vessel-axial parenchyma pitting similar to intervessel pitting, RLS. e, f: Rays with tile cells, storied axial parenchyma, some strands chambered crystalliferous, TLS. g: Detail of ray, TLS. h: Storied imperforate elements. Scale bars: 200 µm in a; 100 µm in b, e; 50 µm in c, d, f, h; 20 µm in g.
Text-fig. 5. Paramblypterus vratislaviensis (AGASSIZ, 1833). Scale bars 5 mm. a: drawing of the skull roof in dorsal view, locality Olivětín, NM-M 2213; b, c: photograph and drawing of the left maxila in lateral view, locality Ruprechtice, NM-M 64696; d: right parietal in dorsal view, locality Ruprechtice "Pod Světlinou", P 64741; e: left maxilla in lateral view, locality Ruprechtice "Pod Světlinou", P 64738; f, g: photograph and drawing of the left mandible in medial view, locality Ruprechtice "Pod Světlinou", P 64738. Abbreviations: ap – anterior pit line, Dpt – dermopterotic, Dsph – dermosphenotic, eo – edge overlapped by surrounding bones, Fr – frontal, mp – medial pit line, Na – nasal, Pa – parietal, pp – posterior pit line, Ptr – postrostral, soc – supraorbital canal, socp – pores of the supraorbital canal. in Actinopterygians Of The Broumov Formation (Permian) In The Czech Part Of The Intra-Sudetic Basin (The Czech Republic)
Text-fig. 5. Paramblypterus vratislaviensis (AGASSIZ, 1833). Scale bars 5 mm. a: drawing of the skull roof in dorsal view, locality Olivětín, NM-M 2213; b, c: photograph and drawing of the left maxila in lateral view, locality Ruprechtice, NM-M 64696; d: right parietal in dorsal view, locality Ruprechtice "Pod Světlinou", P 64741; e: left maxilla in lateral view, locality Ruprechtice "Pod Světlinou", P 64738; f, g: photograph and drawing of the left mandible in medial view, locality Ruprechtice "Pod Světlinou", P 64738. Abbreviations: ap – anterior pit line, Dpt – dermopterotic, Dsph – dermosphenotic, eo – edge overlapped by surrounding bones, Fr – frontal, mp – medial pit line, Na – nasal, Pa – parietal, pp – posterior pit line, Ptr – postrostral, soc – supraorbital canal, socp – pores of the supraorbital canal.
Text-fig. 3. Briveichthys chantepieorum gen. et sp. nov. a, b: drawing and photograph of the jaws, jugal, medial gular and first lepidotrichia of the pectoral fin, GMC 126, whitened, scale bar 5 mm. Abbreviations: Aup – autopalatinum, De – dentalosplenial, ff – fringing fulcra, Gm – medial gular, gpl – gular pit line, ioc – infraorbital sensory canal, Ju – jugal, lep – lepidotrichia, mc – pores of the mandibular sensory canal, Mx – maxilla. in New Actinopterygians From The Permian Of The Brive Basin, And The Ichthyofaunas Of The French Massif Central
Text-fig. 3. Briveichthys chantepieorum gen. et sp. nov. a, b: drawing and photograph of the jaws, jugal, medial gular and first lepidotrichia of the pectoral fin, GMC 126, whitened, scale bar 5 mm. Abbreviations: Aup – autopalatinum, De – dentalosplenial, ff – fringing fulcra, Gm – medial gular, gpl – gular pit line, ioc – infraorbital sensory canal, Ju – jugal, lep – lepidotrichia, mc – pores of the mandibular sensory canal, Mx – maxilla.
Text-fig. 4. Briveichthys chantepieorum gen. et sp. nov. a, b: photograph and drawing of the parasphenoid in dorsal view, GMC 15, whitened, scale bars 5 mm; c: maxillary plate in medial view with horizontal lamina along the ventral edge of the bone, segment of the lower jaw with assembly of large slender teeth of the inner row and coronoids with small teeth, GMC 15, whitened, scale bar 5 mm; d: detail of the sculpture on the maxilla and dentalosplenial, GMC 126, whitened, scale bar 5 mm; e: detail of the teeth of the inner and outer row and coronoids on the lower jaw, the frame delineates the area illustrated in (f) at higher magnification, GMC 15, scale bar 2 mm; f: microsculpture formed by elliptical proximo-distally elongated protuberances on the large conical teeth, GMC 15, scale bar 100 µm; g: small fringing fulcra tightly attached to the anterior edge of a lepidotrichium, individual fulcral scales are indicated by arrows, GMC 18, scale bar 2 mm. Abbreviation: bhf – bucco-hypophysial foramen, Cor – coronoids, cp – corpus parasphenoidis, De – dentalosplenial, hl – horizontal lamina, mc – pores of the mandibular sensory canal, Mx – maxilla, paa – processus ascendens anterior, pap – processus ascendens posterior. in New Actinopterygians From The Permian Of The Brive Basin, And The Ichthyofaunas Of The French Massif Central
Text-fig. 4. Briveichthys chantepieorum gen. et sp. nov. a, b: photograph and drawing of the parasphenoid in dorsal view, GMC 15, whitened, scale bars 5 mm; c: maxillary plate in medial view with horizontal lamina along the ventral edge of the bone, segment of the lower jaw with assembly of large slender teeth of the inner row and coronoids with small teeth, GMC 15, whitened, scale bar 5 mm; d: detail of the sculpture on the maxilla and dentalosplenial, GMC 126, whitened, scale bar 5 mm; e: detail of the teeth of the inner and outer row and coronoids on the lower jaw, the frame delineates the area illustrated in (f) at higher magnification, GMC 15, scale bar 2 mm; f: microsculpture formed by elliptical proximo-distally elongated protuberances on the large conical teeth, GMC 15, scale bar 100 µm; g: small fringing fulcra tightly attached to the anterior edge of a lepidotrichium, individual fulcral scales are indicated by arrows, GMC 18, scale bar 2 mm. Abbreviation: bhf – bucco-hypophysial foramen, Cor – coronoids, cp – corpus parasphenoidis, De – dentalosplenial, hl – horizontal lamina, mc – pores of the mandibular sensory canal, Mx – maxilla, paa – processus ascendens anterior, pap – processus ascendens posterior.
Text-fig. 8. Carpolithes (a–t). a–e: Carpolithes sp. 1. USNM PAL 772366. Scale bar = 1 cm. a: Lateral view of endocarp, note two longitudinal ridges. b: Lateral view of endocarp rotated 90° from (a), note single lateral ridge in center, a, b reflected light, palladium coated. c: Lateral view, Micro-CT scan surface rendering. d: View of rounded end of the endocarp, reflected light, palladium coated. e: View of the opposite (pointed) end of the endocarp, note split; reflected light, palladium coated. f–j: Carpolithes sp. 2. USNM PAL 772367. Scale bar = 5 mm. f: Lateral view, base down; note raphe-like structure (arrow), reflected light, palladium coated. g: Lateral view, the raphe-like structure extending vertically from the base. h: Lateral view, rotated 90° from (g). i: Lateral view, the opposite face to that in (h). j: Basal view, raphe-like structure running from the center to the right of the image. g–j: CT scan surface renderings. k–o: Carpolithes sp. 3 USNM PAL 772368. Scale bar = 5 mm. k: Ventral view of the specimen, note flared apical extension, reflected light, uncoated. l: Dorsal view illustrating the flared apical extension, rotated 180o from (k). m: Lateral view rotated 90° from that in (l). n: Apical view, the apical extension with central pore (arrow) and a clear lineation running down the side to the top of the image. o: Basal view. l–o: Micro-CT scan surface renderings. p–t: Carpolithes sp. 4. USNM PAL 772369. Scale bar = 3 mm. p: Basal view illustrating the concentric rings of radiating possible cells surrounding a central depression. q: Lateral view, base down, note possible cellular pattern. r: Lateral view, rotated 180° from (q), base down; p–r: reflected light, palladium coated. s, t: Basal and lateral views, micro-CT scan surface renderings. in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 8. Carpolithes (a–t). a–e: Carpolithes sp. 1. USNM PAL 772366. Scale bar = 1 cm. a: Lateral view of endocarp, note two longitudinal ridges. b: Lateral view of endocarp rotated 90° from (a), note single lateral ridge in center, a, b reflected light, palladium coated. c: Lateral view, Micro-CT scan surface rendering. d: View of rounded end of the endocarp, reflected light, palladium coated. e: View of the opposite (pointed) end of the endocarp, note split; reflected light, palladium coated. f–j: Carpolithes sp. 2. USNM PAL 772367. Scale bar = 5 mm. f: Lateral view, base down; note raphe-like structure (arrow), reflected light, palladium coated. g: Lateral view, the raphe-like structure extending vertically from the base. h: Lateral view, rotated 90° from (g). i: Lateral view, the opposite face to that in (h). j: Basal view, raphe-like structure running from the center to the right of the image. g–j: CT scan surface renderings. k–o: Carpolithes sp. 3 USNM PAL 772368. Scale bar = 5 mm. k: Ventral view of the specimen, note flared apical extension, reflected light, uncoated. l: Dorsal view illustrating the flared apical extension, rotated 180o from (k). m: Lateral view rotated 90° from that in (l). n: Apical view, the apical extension with central pore (arrow) and a clear lineation running down the side to the top of the image. o: Basal view. l–o: Micro-CT scan surface renderings. p–t: Carpolithes sp. 4. USNM PAL 772369. Scale bar = 3 mm. p: Basal view illustrating the concentric rings of radiating possible cells surrounding a central depression. q: Lateral view, base down, note possible cellular pattern. r: Lateral view, rotated 180° from (q), base down; p–r: reflected light, palladium coated. s, t: Basal and lateral views, micro-CT scan surface renderings.
Dataset of "Hysteresis, Rectification and Relaxation Times of Nanofluidic Pores for Neuromorphic Circuit Applications"
<p>This dataset supports the article published<em> </em>in Advanced Physics Research:</p> <p>"Hysteresis, Rectification and Relaxation Times of Nanofluidic Pores for Neuromorphic Circuit Applications"</p> <p> </p> <p>Raw data for the article "Hysteresis, Rectification and Relaxation Times of Nanofluidic Pores for Neuromorphic Circuit Applications". For further details see the readme.txt file.</p>
Рис. 2. Mukhina elegans (Mukhina, 1981) (самка): А — трофико-сенсорный отΔеΛ теΛа; Б — поΛовая система; В — переΔний конец теΛа; Г — хвост; À — фрагмент кутикуΛы с боковым поΛем бп — боковое поΛе, да — ΔробиΛьный аппарат, в — вуΛьва, зм — заΔняя матка, кб — карΔиаΛьный буΛьбус, кск — кΛетки среΔней кишки, нк — нервное коΛьцо, пм — переΔняя матка, р — ректум, рт — ренетта, с — сперма, ск — среΔняя кишка, сп — семяприемник, ф — фазмиΔы, хс — хейΛостома, эп — экскреторная пора, я — яичник Fig. 2. Mukhina elegans (Mukhina, 1981) (female): A — trophic-sensory part of the body; B — the reproductive system; C — the front end of the body; G — the tail; D — fragment of the cuticle with a side field бп — side field, да — crushing apparatus, в — vulva, зм — posterior uterus, кб — cardial bulb, кск — cells of the mid-intestine, нк — nerve ring, пм — anterior uterus, р — rectum, рт — renetta с — sperm, ск — mid-intestin, сп — seminal receptacle, ф — phasmids, хс — cheilostoma, эп — excretory pore, я — ovary in A New Species Sp. Nov. (Nematoda, Cephalobidae) From Primorsky Region (Russia)
Рис. 2. Mukhina elegans (Mukhina, 1981) (самка): А — трофико-сенсорный отΔеΛ теΛа; Б — поΛовая система; В — переΔний конец теΛа; Г — хвост; À — фрагмент кутикуΛы с боковым поΛем бп — боковое поΛе, да — ΔробиΛьный аппарат, в — вуΛьва, зм — заΔняя матка, кб — карΔиаΛьный буΛьбус, кск — кΛетки среΔней кишки, нк — нервное коΛьцо, пм — переΔняя матка, р — ректум, рт — ренетта, с — сперма, ск — среΔняя кишка, сп — семяприемник, ф — фазмиΔы, хс — хейΛостома, эп — экскреторная пора, я — яичник Fig. 2. Mukhina elegans (Mukhina, 1981) (female): A — trophic-sensory part of the body; B — the reproductive system; C — the front end of the body; G — the tail; D — fragment of the cuticle with a side field бп — side field, да — crushing apparatus, в — vulva, зм — posterior uterus, кб — cardial bulb, кск — cells of the mid-intestine, нк — nerve ring, пм — anterior uterus, р — rectum, рт — renetta с — sperm, ск — mid-intestin, сп — seminal receptacle, ф — phasmids, хс — cheilostoma, эп — excretory pore, я — ovary
Рис. 1. Mukhina orientalis sp. nov. (самка): А — трофико-сенсорный отΔеΛ теΛа; Б — генитаΛьнокауΔаΛьный отΔеΛ теΛа; В — трофико-сенсорный отΔеΛ теΛа второй самки; Г — переΔний конец теΛа; À — хвост второй самки бп — боковое поΛе, да — ΔробиΛьный аппарат, в — вуΛьва, зм — заΔняя матка, кб — карΔиаΛьный буΛьбус, нк — нервное коΛьцо, пм — переΔняя матка, р — ректум, рт — ренетта, ск — среΔняя кишка, скλ — скΛероции кутикуΛы, сп — семяприемник, ф — фазмиΔы, хс — хейΛостома, эп — экскреторная пора, я — яичник Fig. 1. Mukhina orientalis sp. nov. (female): A — trophic-sensory part of the body; Б — genitalcaudal part of the body; В — trophic-sensory part of the body of the second female; Г — front end of the body; À — tail of the second female бп — side field, да — crushing apparatus, в — vulva, зм — posterior uterus, кб — cardial bulb, нк — nerve ring, пм — anterior uterus, р — rectum, ск — mid-intestine, скλ — sclerotic cuticle, сп — seminal receptacle, ф — phasmids, хс — cheilostoma, эп — excretory pore, я — ovary in A New Species Sp. Nov. (Nematoda, Cephalobidae) From Primorsky Region (Russia)
Рис. 1. Mukhina orientalis sp. nov. (самка): А — трофико-сенсорный отΔеΛ теΛа; Б — генитаΛьнокауΔаΛьный отΔеΛ теΛа; В — трофико-сенсорный отΔеΛ теΛа второй самки; Г — переΔний конец теΛа; À — хвост второй самки бп — боковое поΛе, да — ΔробиΛьный аппарат, в — вуΛьва, зм — заΔняя матка, кб — карΔиаΛьный буΛьбус, нк — нервное коΛьцо, пм — переΔняя матка, р — ректум, рт — ренетта, ск — среΔняя кишка, скλ — скΛероции кутикуΛы, сп — семяприемник, ф — фазмиΔы, хс — хейΛостома, эп — экскреторная пора, я — яичник Fig. 1. Mukhina orientalis sp. nov. (female): A — trophic-sensory part of the body; Б — genitalcaudal part of the body; В — trophic-sensory part of the body of the second female; Г — front end of the body; À — tail of the second female бп — side field, да — crushing apparatus, в — vulva, зм — posterior uterus, кб — cardial bulb, нк — nerve ring, пм — anterior uterus, р — rectum, ск — mid-intestine, скλ — sclerotic cuticle, сп — seminal receptacle, ф — phasmids, хс — cheilostoma, эп — excretory pore, я — ovary
РИС. 7. НедостаточнаЯ промывка раковин глохидиев после очиЩениЯ в Щелочи (5% КОН). А, С. «Замыленность» пор наружной поверхности створок (Cristaria tuberculata, оЗ. Ханка, Приморский кр.). B. Остаток Щелочи, выпавШий кристаллами на поверхности личинки (Unio dembeae, р. Дуко, ЭфиопиЯ). D. Капли раствора Щелочи (укаЗаны стрелками) на поверхности Шипов крючка (Nodularia douglasiae, р. Гион, о-в Хонсю, ЯпониЯ). МасШтаб 5 мкм (А, С), 2 мкм (B, D). Микроскоп Zeiss MERLIN, напыление углеродом (А, В), хромом (С, D). FIG. 7. Insufficient rinsing of glochidia after cleaning in alkali (5% KOH). A, C. «Blurredness» of the exterior valve pores (Cristaria tuberculata, Khanka Lake, Primorsky Krai). B. Precipitation of alkali crystals on the exterior glochidia surface (Unio dembeae, Duko River, Ethiopia). D. Drops of alkali (indicated by arrows) on the hook spines (Nodularia douglasiae, Gion River, Honshu Island, Japan). Scale bars 5 μm (A, C), 2 μm (B, D). Zeiss MERLIN microscope, sputter coating with carbon (A, B) and chromium (C, D). in Методика подготовки раковин глохидиев (Bivalvia, Unionidae) длЯ работы на сканируюЩем Электронном микроскопе
РИС. 7. НедостаточнаЯ промывка раковин глохидиев после очиЩениЯ в Щелочи (5% КОН). А, С. «Замыленность» пор наружной поверхности створок (Cristaria tuberculata, оЗ. Ханка, Приморский кр.). B. Остаток Щелочи, выпавШий кристаллами на поверхности личинки (Unio dembeae, р. Дуко, ЭфиопиЯ). D. Капли раствора Щелочи (укаЗаны стрелками) на поверхности Шипов крючка (Nodularia douglasiae, р. Гион, о-в Хонсю, ЯпониЯ). МасШтаб 5 мкм (А, С), 2 мкм (B, D). Микроскоп Zeiss MERLIN, напыление углеродом (А, В), хромом (С, D). FIG. 7. Insufficient rinsing of glochidia after cleaning in alkali (5% KOH). A, C. «Blurredness» of the exterior valve pores (Cristaria tuberculata, Khanka Lake, Primorsky Krai). B. Precipitation of alkali crystals on the exterior glochidia surface (Unio dembeae, Duko River, Ethiopia). D. Drops of alkali (indicated by arrows) on the hook spines (Nodularia douglasiae, Gion River, Honshu Island, Japan). Scale bars 5 μm (A, C), 2 μm (B, D). Zeiss MERLIN microscope, sputter coating with carbon (A, B) and chromium (C, D).
РИС. 5. ЗагрЯЗнение готовых обраЗцов длЯ СЭМ при длительном хранении в негерметичных условиЯх (A–C) либо при хранении проШедШих процедуру мацерированиЯ беЗ последуюЩего обеЗЗараживаниЯ (D, E). A–С. Бактерии на поверхности глохидиев (Nodularia douglasiae, р. ИлистаЯ, бассейн оЗ. Ханка, Приморский кр.). А. ВнеШний вид глохидиЯ, основное ЗагрЯЗнение на створке в верхней части фото. В. Крючок глохидиЯ, основное ЗагрЯЗнение в левой части фото. С. Створка, вид иЗнутри. D. Единичные бактерии на створке глохидиЯ, вид иЗнутри (Kunashiria japonica, оЗ. Утиное, о-в Зелёный, Курильские о-ва). E. Гифы гриба на створке глохидиЯ, вид на наружную пору (Beringiana beringiana, оЗ. АЗабачье, Камчатка). МасШтаб 50 мкм (А, C), 10 мкм (В, D), 1 мкм (Е). Микроскопы Zeiss MERLIN (А, B, C, E), Zeiss EVO 40 (D), напыление хромом (А–С), Золотом (D), углеродом (Е). FIG. 5. Contamination of the SEM ready-made samples during long-term storage under unsealed conditions (A–C) or during storage the samples that have passed the maceration procedure without subsequent disinfection (D, E). A–C. Bacteria on the glochidia surface (Nodularia douglasiae, Ilistaya River, Khanka Lake basin, Primorsky Krai). A. Glochidium with the main pollution on the valve in the upper part of the photo. B. Hook with the main pollution on the left side of the photo. C. Interior valve. D. Bacteria on the interior valve (Kunashiria japonica, Utinoe Lake, Zeliony Island, Kuril Islands). E. Fungal hyphae on the pore of exterior valve (Beringiana beringiana, Azabachye Lake, Kamchatka). Scale bars 50 μm (A, C), 10 μm (B, D), 1 μm (E). Zeiss MERLIN (A, B, C, E) and Zeiss EVO 40 (D) microscopes, sputter coating with chromium (A–C), gold (D), and carbon (E). in Методика подготовки раковин глохидиев (Bivalvia, Unionidae) длЯ работы на сканируюЩем Электронном микроскопе
РИС. 5. ЗагрЯЗнение готовых обраЗцов длЯ СЭМ при длительном хранении в негерметичных условиЯх (A–C) либо при хранении проШедШих процедуру мацерированиЯ беЗ последуюЩего обеЗЗараживаниЯ (D, E). A–С. Бактерии на поверхности глохидиев (Nodularia douglasiae, р. ИлистаЯ, бассейн оЗ. Ханка, Приморский кр.). А. ВнеШний вид глохидиЯ, основное ЗагрЯЗнение на створке в верхней части фото. В. Крючок глохидиЯ, основное ЗагрЯЗнение в левой части фото. С. Створка, вид иЗнутри. D. Единичные бактерии на створке глохидиЯ, вид иЗнутри (Kunashiria japonica, оЗ. Утиное, о-в Зелёный, Курильские о-ва). E. Гифы гриба на створке глохидиЯ, вид на наружную пору (Beringiana beringiana, оЗ. АЗабачье, Камчатка). МасШтаб 50 мкм (А, C), 10 мкм (В, D), 1 мкм (Е). Микроскопы Zeiss MERLIN (А, B, C, E), Zeiss EVO 40 (D), напыление хромом (А–С), Золотом (D), углеродом (Е). FIG. 5. Contamination of the SEM ready-made samples during long-term storage under unsealed conditions (A–C) or during storage the samples that have passed the maceration procedure without subsequent disinfection (D, E). A–C. Bacteria on the glochidia surface (Nodularia douglasiae, Ilistaya River, Khanka Lake basin, Primorsky Krai). A. Glochidium with the main pollution on the valve in the upper part of the photo. B. Hook with the main pollution on the left side of the photo. C. Interior valve. D. Bacteria on the interior valve (Kunashiria japonica, Utinoe Lake, Zeliony Island, Kuril Islands). E. Fungal hyphae on the pore of exterior valve (Beringiana beringiana, Azabachye Lake, Kamchatka). Scale bars 50 μm (A, C), 10 μm (B, D), 1 μm (E). Zeiss MERLIN (A, B, C, E) and Zeiss EVO 40 (D) microscopes, sputter coating with chromium (A–C), gold (D), and carbon (E).
Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex ("pore water" added over membrane re-entrant loop)
<p>Simulation originally starting with "pore water" above the membrane re-entrant loop.</p> <p>Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE_POPG_DAG_CL bilayer using CHARMM-GUI, and the "generate pore water" feature was used to initially fill the area above the membrane re-entrant loop with water (as opposed to lipids initially being placed in this vicinity). The system was equilibrated and and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation. </p> <p><br>Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.</p>
SI Figure 4: SEM images of either unwashed (left) or washed (right) E. antarcticus nematodes. A. Unwashed head region with arrows pointing to attached material and possible fungal hyphae. B. Washed head region with arrows pointing to the remaining attached material. C. Unwashed annules with arrows pointing to commonly attached foreign material. D. Washed annules with arrows pointing to remaining attached material. E. Unwashed somatic pore with arrows pointing to the common organic material. F. Washed vulva with an arrow pointing to remaining attached organic material. G. Unwashed cuticle with arrows showing a possible biofilm. H. Washed cuticle showing single attached cells indicated with arrows. I. Unwashed cuticle showing an off-axis line of attached material. J. Washed cuticle showing a similar off-axis line of material (as indicated with arrow) but reduced in quantity compared to the unwashed. in External and internal microbiomes of Antarctic nematodes are distinct, but more similar to each other than the surrounding environment
SI Figure 4: SEM images of either unwashed (left) or washed (right) E. antarcticus nematodes. A. Unwashed head region with arrows pointing to attached material and possible fungal hyphae. B. Washed head region with arrows pointing to the remaining attached material. C. Unwashed annules with arrows pointing to commonly attached foreign material. D. Washed annules with arrows pointing to remaining attached material. E. Unwashed somatic pore with arrows pointing to the common organic material. F. Washed vulva with an arrow pointing to remaining attached organic material. G. Unwashed cuticle with arrows showing a possible biofilm. H. Washed cuticle showing single attached cells indicated with arrows. I. Unwashed cuticle showing an off-axis line of attached material. J. Washed cuticle showing a similar off-axis line of material (as indicated with arrow) but reduced in quantity compared to the unwashed.
Fig. 17 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 17. Cytherid ostracod Minyocythere tuberculata (Luppold, 2012) from Borehole Rodewald WA12, 404.5 m, NW Germany, Lower Bajocian. A. SMF Xe 23754, female left valve in external (A1) and internal (A4) views, micro sieve-type pore canals (StPC-m) (A2), macro sieve-type normal pore canals (StPC-M) A3), hinge, posterior (A5) and anterior (A6) parts. B. SMF Xe 23755, female right valve in external view.
Fig. 10 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 10. Cytherid ostracod Minyocythere sp. cf. M. macroporosa sp. nov. from Borehole Rodewald WA12, 404.5 m (A), 386 m (B–E), 404.5 m (F, G), NW Germany, Witchellia laeviuscula Zone (Braun Jura γ upper), Lower Bajocian. A. SMF Xe 23725, male left valve in external view (A1), antero-dorsal area (A2), macro sieve-type normal pore canals (StPC-M) (A3), and micro sieve-type normal pore canals (StPC-m) (A4). B. SMF Xe 23726, female left valve in external view. C. SMF Xe 23727, female carapace in right (C1) and dorsal (C2) views. D. SMF Xe 23728, female right valve in external view. E. SMF Xe 23729, male carapace in dorsal view. F. SMF Xe 23730, fragment of female right valve in internal view. G. SMF Xe 23731, male left valve, internal view (G1), hinge (G2).
Fig. 16 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 16. Normal pore canals (NPC) on juvenile left valves (A, stage A-2; B, stage A-3; C, stage A-4) in cytherid ostracod Minyocythere maculosa (Bate, 1963) from Borehole Rodewald WA6, 390 m, NW Germany, Lower Bajocian (Braun Jura γ). A. SMF Xe 23751, general view (A1), micro sieve-type pore canals (StPC-m) on the outer side of the valve (A2), macro sieve-type normal pore canals (StPC-M) on the outer side of the valve (A3, A4), StPC-M on the inner side of the valve (A5), and simple NPC on the outer side of the valve (A6). B. SMF Xe 23752, general view (B1), StPC-m on the outer side of the valve (B2), StPC-M on the inner side of the valve (B3). C. SMF Xe 23753, general view (C1), StPC-m on the outer side of the valve (C2), StPC-M on the outer side of the valve (C3).
Fig. 3 in Sieve-type normal pore canals in Jurassic ostracods: A review with description of a new genus
Fig. 3. Sieve-type normal pore canals (StPC) in Aphelocythere and Camptocythere spp. A. Aphelocythere perforata Plumhoff, 1963, from Borehole Wesendorf 51a, 1031–1035 m, NW Germany, Upper Aalenian. SMF Xe 5608 (Plumhoff Collection), carapace in external right view (A1), macro StPC (StPC-M) (A2–A4). B, C. Camptocythere praecox Triebel, 1950 from Borehole Hambühren WA 2, 341 m, NW Germany, Leioceras opalinum Zone, Lower Aalenian (Braun Jura α). B. Paratype, SMF Xe 1448, male right valve in external view (B1), mid-anterior area behind marginal rim, ornamentation and pores (large and small) (B2), StPC-M with a peripheral large pore (B3), micro StPC (StPC-m) (B4). C. Paratype, SMF Xe 1448, male right valve in internal view (C1), hinge (C2), StPC-m (C3). D. Camptocythere media Triebel, 1950 from Borehole Altencelle 1014, 212/16 m, NW Germany, Upper Aalenian (Braun Jura β). Paratype, SMF Xe 1513, female left valve in external view (D1), detail, antero-dorsal area, ornamentation and pores (large and small) (D2), round StPC-M (D3), elongate StPC-M (D4), StPC-m (D5).
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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