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opencc-by-4.0Dec 2021View details →

Text-fig. 6. Zoophycos showing spreiten structure with a continuously meandering tunnel. Schematic drawing of the specimen from unidentified layer from a block out of the measured profile. Scale in centimetres. in Early Complex Tiering Pattern: Upper Ordovician, Barrandian Area, The Czech Republic

Text-fig. 6. Zoophycos showing spreiten structure with a continuously meandering tunnel. Schematic drawing of the specimen from unidentified layer from a block out of the measured profile. Scale in centimetres.

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Complex cycles of divergence and migration shape lineage structure in the common kingsnake species complex

Aim: The Nearctic is a complex patchwork of habitats and geologic features that form barriers to gene flow resulting in phylogeographic structure and speciation in many lineages. Habitats are rarely stable over geologic time, and the Nearctic has undergone major climatic changes in the past few million years. We use the common kingsnake species complex to study how climate, geography, and history influence lineage formation over a large, complex landscape. Location: Nearctic/North America Taxon: Common kingsnake, Lampropeltis getula, species complex Methods: We analyzed genome-wide sequence data from 51 snakes spanning the majority of the species complex's range. We used population clustering, generalized dissimilarity modeling, and coalescent methods to identify the number of genetic clusters within the L. getula complex, infer the environmental correlates of genetic differentiation, and estimate models of divergence and gene flow among lineages. Results: We identified three major lineages within the L. getula complex and further continuous spatial structure within lineages. The most important ecological correlates of genetic distance in the complex are related to aridity and precipitation, consistent with lineage breaks at the Great Plains/Desert ecotone and the Cochise Filter Barrier. Lineages are estimated to have undergone multiple rounds of isolation and secondary contact, with highly asymmetric migration occurring at present. Main conclusions: Changing climates combined with a large and geologically complex landscape have resulted in a mosaic of discrete and spatially continuous genetic structure. Multiple rounds of isolation and secondary contact as climate fluctuated over the past ~4.4 My have likely driven the evolution of discrete lineages that maintain high levels of gene flow. Continuous structure is strongly shaped by aridity and precipitation, suggesting roles for major precipitation gradients in helping to maintain lineage identity in the face of gene flow when lineages are in geographic contact.

opencc-zeroOct 2022View details →

opencc-by-4.0Jan 2018View details →

X-Ray Structures of Target-Ligand Complexes Containing Compounds with Assay Interference Potential

A total of 2755 crystallographic complexes with ligands containing PAINS-defining substructures were extracted from the Protein Data Bank (PDB). PDB identifiers of these structures are made available together with the the corresponding PDB_PAINS (component identifier, aromatic nonstereo SMILES, PAINS class).

opencc-by-4.0Sep 2010View details →

Figure 1: EDL structure for p-Si-TOWARD THE PHYSICAL BASIS OF COMPLEX SYSTEMS: DIELECTRIC ANALYSIS OF POROUS SILICON NANOCHANNELS IN THE ELECTRICAL DOUBLE LAYER LENGTH RANGE

Figure 1: EDL structure for p-Si (SCL negative charged,²F < ²FR )/aqueous solvent interface. The electrostatic potential and charged atoms in solvent distributions vs the distance z from the wall.

opencc-by-4.0Dec 2014View details →

Figure 3. Structurally complex high rugosity coral-dominated reef habitat. Image shows fixed transect 01 from the start pin looking toward a 180 in Fishes of War in the Pacific National Historic Park

Figure 3. Structurally complex high rugosity coral-dominated reef habitat. Image shows fixed transect 01 from the start pin looking toward a 180° heading in the Asan Beach unit (NPS photo).

opencc-by-4.0Jul 2024View details →

Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)

Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain

opencc-by-sa-4.0Oct 2016View details →

Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform

These scripts demonstrate the use of <a href="https://integrativemodeling.org/">IMP</a>, <a href="https://salilab.org/modeller">MODELLER</a>, and <a href="https://github.com/salilab/pmi">PMI</a> in the modeling of the Nup82 complex using DSS/EDC chemical cross-links and electron microscopy (EM) 2D class averages. First, <a href="https://salilab.org/modeller">MODELLER</a> is used to generate initial structures for the individual components in the Nup82 complex. Then, IMP is used to model these components using DSS/EDC crosslinks and the electron microscopy 2D class averages for the entire Nup82 complex. The modeling protocol will work with a default build of IMP, but for most effective sampling, IMP should be built with <a href="https://integrativemodeling.org/2.5.0/doc/ref/namespaceIMP_1_1mpi.html">MPI</a> so that replica exchange can be used. For more information about how to reproduce this modeling, see the <a href="https://salilab.org/nup82/">Sali lab website</a> or the README file.

opencc-by-sa-4.0Aug 2018View details →

Structural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex

Deregulation of the ubiquitin ligase E6AP is causally linked to the development of human disease, including cervical cancer. In complex with the E6 oncoprotein of human papillomaviruses, E6AP targets the tumor suppressor p53 for degradation, thereby contributing to carcinogenesis. Moreover, E6 acts as a potent activator of E6AP by a yet unknown mechanism. However, structural information explaining how the E6AP-E6-p53 enzyme-substrate complex is assembled, and how E6 stimulates E6AP, is largely missing. We therefore developed and applied different approaches in structural mass spectrometry to show that binding of E6 induces conformational rearrangements in E6AP, which result in the positioning of E6 and p53 in the immediate vicinity of the catalytic centre of E6AP. Our data provides structural and functional insights into the dynamics of the full-length E6AP-E6-p53 enzyme-substrate complex and reveals how E6 can both stimulate the ubiquitin ligase activity of E6AP and facilitate the transfer of ubiquitin from E6AP onto p53.

Fig. 5 in Phenotypic structure of Colombian populations of Anastrepha fraterculus complex (Diptera: Tephritidae)

Fig. 5. Box-plots of the significant linear variables and Kruskal-Wallis analysis of means comparing eggs among populations of the Anastrepha fraterculus Andean morphotype in Colombia. Means topped by the same letter are not significantly different at the 5% significance level.

Fig. 3 in Phenotypic structure of Colombian populations of Anastrepha fraterculus complex (Diptera: Tephritidae)

Fig. 3. Box-plots of the significant linear variables and Kruskal-Wallis analysis of means comparing males among populations of the Anastrepha fraterculus Andean morphotype in Colombia. Means topped by the same letter are not significantly different at the 5% significance level.

Fig. 4 in Phenotypic structure of Colombian populations of Anastrepha fraterculus complex (Diptera: Tephritidae)

Fig. 4. Box-plots of the significant linear variables and Kruskal-Wallis analysis of means comparing larvae among populations of the Anastrepha fraterculus Andean morphotype in Colombia. Means topped by the same letter are not significantly different at the 5% significance level.

Fig. 2 in Phenotypic structure of Colombian populations of Anastrepha fraterculus complex (Diptera: Tephritidae)

Fig. 2. Box-plots of the significant linear variables and Kruskal-Wallis analysis of means comparing females among populations of the Anastrepha fraterculus Andean morphotype in Colombia. Means topped by the same letter are not significantly different at the 5% significance level.

Fig. 1 in Phenotypic structure of Colombian populations of Anastrepha fraterculus complex (Diptera: Tephritidae)

Fig. 1. Geographic distribution of populations of the Anastrepha fraterculus Andean morphotype collected in Colombia. Chp: Cachipay; Dtm: Duitama; Flb: Florida Blanca; Ibg: Ibagué; Lun: La Unión; Pns: Pensilvania; Rnd: Roldanillo; Sby: Sibundoy; Svl: Sevilla.

FIGURE 4 in Visualizing the fluid flow through the complex skeletonized respiratory structures of a blastoid echinoderm

FIGURE 4. Visualization of the flow within the 3D printed model (Re = 0.376, see Table 1). Flow in the folds consists of horizontal bands of distinct red and blue color, indicating no adoral component to flow and no mixing within the folds, consistent with Hypothesis 2 (see text, Figure 2.2). The still used in the print version of this paper is a single frame from the flow pattern observed, showing the steady-state flow pattern after nine minutes of flow. The animation is sped up 16x (for video see palaeo-electronica.org/content/2015/1073-blastoid-hydrospire-fluid-flow).

FIGURE 2. Schematic showing hypothesized flow patterns within the hydrospire folds. 2.1 in Visualizing the fluid flow through the complex skeletonized respiratory structures of a blastoid echinoderm

FIGURE 2. Schematic showing hypothesized flow patterns within the hydrospire folds. 2.1, In Hypothesis 1, the flow has an adoral component representing respiratory leakage. 2.2, In Hypothesis 2, the flow is entirely radial, without leakage. See text for further discussion.

FIGURE 3 in Visualizing the fluid flow through the complex skeletonized respiratory structures of a blastoid echinoderm

FIGURE 3. Digital and physical models use to visualize fluid flow. 3.1, Digital solid model of approximately the lower quarter of a hydrospire of Pentremites rusticus, using Blender (see text). 3.2, 3D-printed rendering of the digital model, shown with inlet headers connected.

FIGURE 1 in Visualizing the fluid flow through the complex skeletonized respiratory structures of a blastoid echinoderm

FIGURE 1. Anatomy of the hydrospires of the blastoid Pentremites rusticus. 1.1, Location of one of the five radially distributed hydrospires within the calyx, showing incurrent hydrospire pores, and excurrent spiracle (inferred direction of water flow indicated by the arrows). 1.2, Oblique view of a section of a hydrospire and associated structures. Modified from Schmidtling and Marshall (2010).

opencc-by-4.0Feb 2014View details →

Fig. 2 in Community structure of termites in a hill dipterocarp forest of Belum- Temengor Forest Complex, Malaysia: emergence of pest species

Fig. 2. The composition of termite assemblages in the natural forest and disturbed forest areas of the Belum–Temengor Forest Complex.

opencc-by-4.0Feb 2014View details →

Fig. 1 in Community structure of termites in a hill dipterocarp forest of Belum- Temengor Forest Complex, Malaysia: emergence of pest species

Fig. 1. Map of Belum–Temengor Forest Complex and location of study sites. Sites: SK = Sungai [=River] Kejar; SM = Sungai Mes; ST = Sungai Telang; SG = Sungai Gadong; SKJBC = Sungai Kejar Base Camp; SKNBC = Sungai Kenarong Base Camp; PB = Pulau [=Island] Bendong; PP = Pulau Pertanian.