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1,084 results for “substrate”
Figure 2 in Spatial distribution and substrate selection by the orb-weaver spider Eustala perfida Mello-Leitão, 1947 (Araneae: Araneidae)
Figure 2. Colour patterns of Eustala perfida and one event of predation of a female by an araneophagic spider (Gelanor sp., Mimetidae). The total body length of adult individuals is approximately 6 mm. Photographs: Y.F. Messas.
Figure 1 in Spatial distribution and substrate selection by the orb-weaver spider Eustala perfida Mello-Leitão, 1947 (Araneae: Araneidae)
Figure 1. (A) Adult female of Eustala perfida camouflaged on a trunk covered by lichen and moss. The arrow indicates spider position; (B) frontal; (C) lateral views of webs of adult female. Photographs: Y.F. Messas.
Figure 3 in Action of the saproxylic scarab larva Cetonia aurataeformis (Coleoptera: Scarabaeoidea: Cetoniidae) on woody substrates
Figure 3. FTIR spectra of litter (L), Betula alba wood (BW) and Quercus pyrenaica wood (QW), normalized with the band about 1028 cm−1.
Figure 2 in Action of the saproxylic scarab larva Cetonia aurataeformis (Coleoptera: Scarabaeoidea: Cetoniidae) on woody substrates
Figure 2. Thermal curves of (A) Betula alba wood (BW) and frass (BF), (B) Quercus pyrenaica wood (QW) and frass (QF), (C) litter (L) and frass (LF). Y-axis shows the mass change in respect to temperature (dm/dt: derivation of mass in respect to temperature).
Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation 2nd part
<p>Microhabitat conditions determine the magnitude and speed of microbial processes but have been challenging to investigate. In this study we used microfluidic devices to determine the effect of the spatial distortion of a pore space on fungal and bacterial growth<i>,</i> interactions, and substrate degradation. The devices contained channels differing in bending angles and order. Sharper angles reduced fungal and bacterial biomass, especially when angles were repeated in the same direction. Substrate degradation was only decreased by angles when fungi and bacteria were grown together. Investigation at the cellular scale suggests that this was caused by fungal habitat modification, which branched in sharp and repeated turns, blocking the dispersal of bacteria and the substrate. Our results demonstrate how the geometry of microstructures can influence microbial activity. This can be transferable to soil pore spaces, where spatial occlusion and microbial feedback on microstructures is thought to explain organic matter stabilization.</p>
FIGURE. Helminthosporium velutinum (HKAS 107064, new host record and a new record from Guizhou Province) a–c. Colony on the substrate. d. Conidiophores. e–g. Conidiophore and conidia. h–l. Conidia. m. Germinating conidium. n, o. Culture on PDA from. n. above o. below after 4 weeks. Scale bars: d = 100 μm, e–g =50 μm, h–m = 20 μm. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. Helminthosporium velutinum (HKAS 107064, new host record and a new record from Guizhou Province) a–c. Colony on the substrate. d. Conidiophores. e–g. Conidiophore and conidia. h–l. Conidia. m. Germinating conidium. n, o. Culture on PDA from. n. above o. below after 4 weeks. Scale bars: d = 100 μm, e–g =50 μm, h–m = 20 μm.
FIGURE. Myrmecridium schulzeri (IFRD500–012) a, b. Colonies on natural substrate. c–e. Conidiophores with conidia. f, g. Conidiogenous cells with conidia. h–l. Conidia. m Germinating conidia on PDA. n, o. Culture on PDA, n. from front, o. from reverse. Scale bars: c–e, h = 20 μm, m = 10 μm, f, g = 5 μm, i–l = 2 μm. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. Myrmecridium schulzeri (IFRD500–012) a, b. Colonies on natural substrate. c–e. Conidiophores with conidia. f, g. Conidiogenous cells with conidia. h–l. Conidia. m Germinating conidia on PDA. n, o. Culture on PDA, n. from front, o. from reverse. Scale bars: c–e, h = 20 μm, m = 10 μm, f, g = 5 μm, i–l = 2 μm.
Substrate-Binding Guides Individual Melibiose Permeases MelB to Structurally Soften and to Destabilize Cytoplasmic Middle-Loop C3. Blaimschein et al.: Data sets
<p>Data sets used in the manuscript 'Substrate-Binding Guides Individual Melibiose Permeases MelB to Structurally Soften and to Destabilize Cytoplasmic Middle-Loop C3' by Blaimschein et al.</p> <p>The analysis scripts can be found at https://doi.org/10.5281/zenodo.7268838</p>
DATASET: Nanoporous Au Formation on Au Substrates via High Voltage Electrolysis
<p>This folder contains all the data shown in the figures of the manuscript or SI titled<br> "Nanoporous Au Formation on Au Substrates via High Voltage Electrolysis" (doi:10.26434/chemrxiv-2022-mx2qd).<br> For each figure, a folder is created here where the corresponding data can be found.</p>
Apparent thermal acclimation of soil heterotrophic respiration mainly mediated by substrate availability
<p><span>Multiple lines of existing evidence suggest that increasing CO<sub>2</sub> emission from soils</span> <span>in response to rising temperatures could accelerate global warming. However, in experimental studies, the initial positive response of soil heterotrophic respiration (</span><span>R</span><sub><span>H</span></sub><span>) to</span><span> warming often weakens over time (referred to apparent thermal acclimation). If the</span><span> decreased </span><span>R</span><span>H</span> <span>is driven by</span><span> the thermal adaptation of soil microbial community, the potential for soil carbon (C) losses would be reduced substantially. In the meanwhile, the response could </span><span>equally be caused by substrate depletion, and would then </span><span>reflect the gradual loss of soil C.</span> <span>To address uncertainties regarding the causes of apparent thermal acclimation, we carried out </span><span>sterilization and inoculation</span><span> experiments using the soil samples from an alpine meadow with 6-years of warming and nitrogen (N) addition. We demonstrate</span><span> that substrate depletion, rather than microbial adaptation, determined the response of R<sub>H</sub> to long-term warming. Furthermore, </span><span>N addition appeared to alleviate the apparent acclimation of </span><span>R</span><sub><span>H</span></sub><span> to warming. Our study provides strong empirical support for </span><span>substrate availability being the cause of the </span><span>apparent acclimation of soil </span><span>microbial respiration to temperature. Thus, t</span><span>hese mechanistic insights</span><span> could</span><span> facilitate efforts of biogeochemical modeling to accurately project soil C stocks in the future climate.</span></p>
Species of Acantholichen occurring only in the Neotropics show a high degree of endemism (Dal Forno et al. 2016). Of the seven species now recognized in this genus (Table 2), 71.4% (5) are known only from South America. As with Dictyonema, Acantholichen seem to be specific to substrate type and appears in the Andean small forest occurring on mosses in tree bark inhabiting mostly exposed habitats. Cyphellostereum is also represented by a high number of species restricted to the Neotropics [6 (66.6%)], while one is known only from North America, one from Southeastern United States and Puerto Rico, and another species is known only from Borneo and Fiji (Table 2). It is probably due to their unusual appearance that these lichens are getting confused with free-living cyanobacteria colonies, and that there are still undescribed species in the Neotropics. in Eight new species of lichenized Basidiomycota in the genera Acantholichen, Cyphellostereum and Dictyonema s.str. (Agaricales, Hygrophoraceae) from northern South America
Species of Acantholichen occurring only in the Neotropics show a high degree of endemism (Dal Forno et al. 2016). Of the seven species now recognized in this genus (Table 2), 71.4% (5) are known only from South America. As with Dictyonema, Acantholichen seem to be specific to substrate type and appears in the Andean small forest occurring on mosses in tree bark inhabiting mostly exposed habitats. Cyphellostereum is also represented by a high number of species restricted to the Neotropics [6 (66.6%)], while one is known only from North America, one from Southeastern United States and Puerto Rico, and another species is known only from Borneo and Fiji (Table 2). It is probably due to their unusual appearance that these lichens are getting confused with free-living cyanobacteria colonies, and that there are still undescribed species in the Neotropics.
In silico analysis of the structural dynamics and substrate recognition determinants of the human mitochondrial carnitine/acylcarnitine SLC25A20 transporter
<p>Structural models and MD trajectories analyzed in the original article "In silico analysis of the structural dynamics and substrate recognition determinants of the human mitochondrial carnitine/acylcarnitine SLC25A20 transporter". Topologies and trajectories were stripped of the water molecules.</p> <p>- "alphafold2" contains the c-state and m-state models obtained with alphafold2 and colabfold_advanced, respectively;</p> <p>- "slc25a20_cstate" contains the parameter/topology file (slc25a20_cstate_nowat.parm7), the MD simulations of the c-model of the slc25a20 apo protein (prod1_nowat_skip10.nc, prod2_nowat_skip10.nc), and the representative structure used to analyzed the transmembrane helices (cstate1.pdb);</p> <p>- "slc25a20_mstate" contains the parameter/topology file (slc25a20_mstate_nowat.parm7), the MD simulations of the m-state model of the slc25a20 apo protein (prod1_nowat_skip10.nc, prod2_nowat_skip10.nc), and the representative structure used to analyzed the transmembrane helices (cstate2.pdb);</p> <p>- "slc25a20_car" contains the parameter/topology file (slc25a20_carn_nowat.parm7, slc25a20_carn2_nowat.parm7), the MD simulations of the slc25a20-carnitine complex (prod1_nowat_skip2.nc, prod2_nowat_skip2.nc), and a representative structure (snapshot_slc25a20-car.pdb);</p> <p>- "slc25a20_pcar" contains the parameter/topology file (slc25a20_pcarn_nowat.parm7, slc25a20_pcarn2_nowat.parm7), the MD simulations of the slc25a20-propionylcarnitine complex (prod1_nowat_skip2.nc, prod2_nowat_skip2.nc), and a representative structure (snapshot_slc25a20-pcar.pdb).</p> <p>If you include these data in your manuscript, please cite: Pasquadibisceglie A, Quadrotta V and Polticelli F "In silico analysis of the structural dynamics and substrate recognition determinants of the human mitochondrial carnitine/acylcarnitine SLC25A20 transporter"</p>
Insights into substrate transport and water permeation in the mycobacterial transporter MmpL3
<p>These are all input and final structures for a set of simulations investigating the protein MmpL3. All topology, parameter, and NAMD configuration files for running the molecular dynamics simulations are also included. Recommended software to use is Visual Molecular Dynamics (VMD).</p>
Input data for "Characterisation of the mechanism of Bile Salt Hydrolase substrate specificity by experimental and computational analyses"
<p>Topologies, coordinates, input and analysis scripts for Amber20 simulations performed in "Characterisation of the mechanism of Bile Salt Hydrolase substrate specificity by experimental and computational analyses", Structure, 2023</p>
Test of different substrates to Ulva spp spore recruitment
<table> <tbody> <tr> <td> <p><strong>We tested different plastic materials and depths for fixing the spores of the filamentous macroalgae Ulva spp that occurs in the farm's ponds. The objective was to select the best material for the structures and the best cultivation depth. Six different treatments were tested: PVC panel close to the surface, PVC panel 1.2 cm from the surface, PVC panel 3 cm from the surface, PVC panel coated with plastic bag 1.2 cm from the surface, half a PVC pipe, and half a PET bottle. Each treatment had 4 repetitions. The structures were maintained in the supply channel for 30 days. During the test the temperature, salinity, pH, dissolved oxygen (DO), and transparency were monitored, and taken weekly photographic of macroalgae. The harvested macroalgae were weighed to obtain the total mass produced and to calculate the total productivity.</strong></p> </td> </tr> </tbody> </table>
Data and code for "Migration and division in cell monolayers on substrates with topological defects"
<p>Raw data for experiment (experiment.zip) and basic simulation code (simulation.zip) for the paper "Migration and division in cell monolayers on substrates with topological defects"</p>
Fig. 3 in 21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata
Fig. 3. Size exclusion chromatography (SEC) and indication of relative 21MaT activity investigation pools III (A) and IV (B) of the ammonium sulfate precipitation.
Fig. 4 in 21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata
Fig. 4. Docking of modeled AtPMaT1 (ribbon diagram) with an overlay of the potential pregnane substrates (Sub) (shown in grey). The catalytic histidine (His) and the cosubstrate (CoS) are also shown.
Fig. 1 in 21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata
Fig. 1. Postulated biosynthetic pathway of cardenolide formation in Digitalis. The malonylation step [8] is marked by a rectangle. 1 Putative side chain cleaving enzyme (SCCE), 2 NAD:3β-hydroxysteroid dehydrogenase (3βHSD), 3 Δ4,5-3-ketosteroid-isomerase (3KSI), 4 progesterone-5β-reductase (P5βR), 5 NAD:3β-hydroxysteroid dehydrogenase (3βHSD), 6 putative pregnane 14β-hydroxylase, 7 putative pregnane 21β-hydroxylase, 8 malonyl coenzyme A:21- hydroxypregnane 21-O-malonyltransferase (21MaT).
Fig. 6 in 21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata
Fig. 6. Docking of homology modeled malonyltransferases with 3-O-acetylketol (displayed in grey) showing the distances between the catalytic histidine (His), the hydroxy group to be malonylated (Sub) and the malonyl residue presented by the co-substrate (CoA). A AtPMaT1 B AtPMaT2 C DlMaT1.
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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)
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DANDI Archive for NWB datasets
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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.