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230 results for “structure determination”
FIGURE 12 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 12. Paucumara falcata. Photomicrographs of AChE nerve system structure. (A) whole animal, ventral view; (B) posterior end. Numbers 1–4: four lateral nerve branches given off by the cerebral ganglion. Scale bar: A = 200 µm, B = 100 µm.
FIGURE 10 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 10. Paucumara falcata. Diagrammatic horizontal reconstruction: (A) entire animal; (B) copulatory apparatus, based on examination of several specimens; ventral view.
FIGURE 2 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 2. Nerpa fistulata. Live specimens: (A–B) whole animal, dorsal view; (C) copulatory apparatus, showing penis, oviduct, lateral bursae and gonopore. (D) sperm. Scale bar: A–B = 100 µm, C = 50 µm, D = 10µm
Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing
Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history.
Data from: Is population structure in the European white stork determined by flyway permeability rather than translocation history?
European white stork are long considered to diverge to eastern and western migration pools as a result of independent overwintering flyways. In relatively recent times, the western and northern distribution has been subject to dramatic population declines and country-specific extirpations. A number of independent reintroduction programs were started in the mid 1950s to bring storks back to historical ranges. Founder individuals were sourced opportunistically from the Eastern and Western European distributions and Algeria, leading to significant artificial mixing between eastern and western flyways. Here we use mitochondrial and microsatellite DNA to test the contention that prior to translocation, eastern and western flyways were genetically distinct. The data show a surprising lack of structure at any spatial or temporal scale suggesting that even though birds were moved between flyways, there is evidence of natural mixing prior to the onset of translocation activities. Overall a high retention of genetic diversity, high Nef, and an apparent absence of recent genetic bottleneck associated with early 20th century declines suggest that the species is well equipped to respond to future environmental pressures.
FIGURE 5 in CCDC 696447: Experimental Crystal Structure Determination
FIGURE 5. Accumulation curve of the number of species of Blattaria (Dictyoptera) recorded in Brazil described over time.
FIGURE 3 in CCDC 696447: Experimental Crystal Structure Determination
FIGURE 3. Percentage of the number of types housed in each institution. See Institutional Abbreviations at the beginning.
FIGURE 2 in CCDC 696447: Experimental Crystal Structure Determination
FIGURE 2. Number of species of Blattaria (Dictyoptera) recorded in Brazil described at each decade from 1750, when the first species were described, until present days.
Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population
<p>Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance, and direction, these individual-level decisions further modulate the demography, relatedness, and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a Great Crested Newt (<i>Triturus cristatus</i>) SSP. We collected capture-recapture data of 5564 individuals and genetic data of 950 individuals across a SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes.</p>
Atomic-Resolution Structure of the Protein Encoded by Gene V of fd Bacteriophage in Complex with Viral ssDNA Determined by Magic-Angle Spinning Solid-State NMR
<p>F-specific filamentous phages, elongated particles with circular single-stranded DNA encased in a symmetric protein capsid, undergo an intermediate step, where thousands of homodimers of a non-structural protein, gVp, bind to newly synthesized strands of DNA, preventing further DNA replication and preparing the circular genome in an elongated conformation for assembly of a new virion structure at the membrane. While the structure of the free homodimer is known, the ssDNA-bound conformation has yet to be determined. We report an atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage in the nucleoprotein complex elucidated via Magic-Angle Spinning solid-state NMR. The model presents significant conformational changes with respect to the free form. These modifications facilitate the binding mechanism and possibly promote cooperative binding in the assembly of the gVp-ssDNA complex.</p> <p>The raw NMR data used for structure determination are uploaded as original Bruker directories from topspin version 3.5. Processing details are given in the supporting Information of the manuscript. PDB ID is 8ACZ. BMRB accession number is 51391.</p>
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>
The structure of the thermal landscape determined behavioral and physiological responses to simulated predation risk_data
<p><span>Although predators can deter an animal from regulating its body temperature by basking or shuttling, this response to predation should depend on the spatial distribution of thermal resources.</span><span> </span></p> <p><span><span>By </span><span>simulating predation risk, we showed that movement, thermoregulation, and corticosterone of male lizards (<em>Sceloporus jarrovi</em>) depended on the spatial distribution of shade.</span></span></p> <p><span><span>Simulated risk caused lizards to move less, thermoregulate worse, and circulate more corticosterone than they did without risk. However, a patchier distribution of shade enabled lizards to move more, thermoregulate better, and circulate less corticosterone when exposed to a simulated predator.</span></span></p> <p><span><span>In the absence of simulated risk, lizards in patchier environments moved less, thermoregulated better, and circulated less corticosterone, indicating the distribution of shade also affected the energetic cost of thermoregulation.</span></span></p> <p><span><span>This study provides the first test of a spatial theory of thermoregulation under the perceived risk of predation.</span></span></p>
Fig. 2. X-Ray crystal structures determined for 1,8,9,11,12,14–17,19,20 in Stimulation of insulin secretion by 5-methylcoumarins and its sulfur analogues isolated from Clutia lanceolata Forssk
Fig. 2. X-Ray crystal structures determined for 1,8,9,11,12,14–17,19,20. Atoms are shown as thermal ellipsoids drawn at the 50% probability level.
Fig. 6 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 6. (A) The ORTEP diagram of 8a (Cu Kα). (B) Synthesis of 8a: EDCI, DMAP, CH2Cl2, r. t., 48h, 70.6%.
Fig. 4 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 4. Comparison of the experimental and calculated ECD spectra of 1–7 in MeOH. Spectra were calculated at the B3LYP/6–311++ G(2d,p)//B3LYP/6-31G (d) level.
Fig. 8 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 8. Cytotoxic activities of compounds 1–16 against two hepatocellular carcinoma cell lines. (A) Inhibition ratio of all isolates at 50.0 μM. Sora: sorafenib at 16.0 μM, positive control. (B) Compounds with inhibition ratios> 40% were screened out to treat HepG2 cells in subsequent experiments and cell viability was determined by MTT assays.
Fig. 7 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 7. Influence of different configurations of 23-OCH on the δ (C-23, C24, C25) and δ (H-23, H-24) values of compounds 7–10 (1 H NMR 600 MHz, 13C NMR 3 C H 150 MHz).
Fig. 1. Structure analysis, determined using 15 in Association analysis and molecular tagging of phytochemicals in the endangered medicinal plant licorice (Glycyrrhiza glabra L.)
Fig. 1. Structure analysis, determined using 15 AFLP primer combinations and the STRUCTURE software, of the 170 individual Glycyrrhiza glabra plants sampled in 59 localizations. Sub-populations A and B are represented in green and red color, respectively. Individuals (identified by numbers) are grouped in localizations (identified by L1, L2, etc., and also by the corresponding codes). See Supplementary Table 4 for information on the different localizations. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in UPLC-MS/MS-based molecular networking and NMR structural determination for the untargeted phytochemical characterization of the fruit of Crescentia cujete (Bignoniaceae)
Fig. 2. (A) Molecular network of the molecular family of flavonoid glycosides and phenylethanoid extracted from the MN of the fruit extract of Crescentia cujete. (B) Proposed fragmentation pathway observed in the MS/MS spectrum naringin (33).
Fig. 1 in UPLC-MS/MS-based molecular networking and NMR structural determination for the untargeted phytochemical characterization of the fruit of Crescentia cujete (Bignoniaceae)
Fig. 1. UPLC-MS/MS based molecular networking in negative ionization mode of the fruit extract of Crescentia cujete. AG: alkyl glycosides, BC: benzoyl and cinnamoyl derivatives, FG1-3: flavonoid glucosides, PE: phenylethanoid derivatives, IG1-2: iridoids glycosides. Node text indicates the parent ion, node color shows the chemical group (green: n-alkyl sugars, sky blue: benzoyl derivatives, dark blue: cinnamoyl derivatives, red: flavonoids glycosides, purple: phenylpropanoids derivatives, and gold: iridoid glycosides). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
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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.