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Figure 4 in Morphology of the Podarcis wall lizards (Squamata: Lacertidae) from the Iberian Peninsula and North Africa: patterns of variation in a putative cryptic species complex

Figure 4. Least-squares means for continuous pholidotic traits in the different mitochondrial lineages examined. Vertical bars denote the observed range. Females of each group are always presented first, denoted with a grey vertical bar, and males are in black. See Table 1 for group codes, Material and methods for variable abbreviations, and Figure 1 for the symbols used to represent each lineage. Notice that no data are available for SCGN and SDLN in the PHJS lineage (Table 3).

Figure 3 in Morphology of the Podarcis wall lizards (Squamata: Lacertidae) from the Iberian Peninsula and North Africa: patterns of variation in a putative cryptic species complex

Figure 3. Scatter plots of individual scores (small symbols) and group means (big symbols) of the first three principal components of body shape variation for the mitochondrial lineages examined, considering males (top) and females (bottom) separately. The most highly (+, positively; -, negatively) contributing variables (Table 4) are indicated next to each axis. See Table 1 for group codes and Material and methods for variable abbreviations.

Figure 2 in Morphology of the Podarcis wall lizards (Squamata: Lacertidae) from the Iberian Peninsula and North Africa: patterns of variation in a putative cryptic species complex

Figure 2. Least-squares means for multivariate body size and size-corrected biometric variables in the different mitochondrial lineages examined. Only the characters most relevant for global biometric variation and group discrimination (after principle components analysis and canonical variates analysis, respectively; see Results) are presented. Error bars denote ± standard deviation. Females of each group are always presented first, denoted with a grey vertical bar, and males are in black. See Table 1 for group codes, Material and methods for variable abbreviations, and Figure 1 for symbols used to represent each lineage.

Figure 1 in Morphology of the Podarcis wall lizards (Squamata: Lacertidae) from the Iberian Peninsula and North Africa: patterns of variation in a putative cryptic species complex

Figure 1. Mitochondrial DNA lineages sampled, maximum likelihood tree of phylogenetic relationships between them (A, modified from Kaliontzopoulou et al., 2011), and map of the localities from which the samples analysed morphologically were obtained (B).

opencc-by-nc-4.0Sep 2021View details →

On the effect of morphology and particle-wall interaction on colloidal near-wall dynamics

Related publication: J. A. Rivera-Morán, Y. Liu, S. Monter, C. Hsu, P. Ruckdeschel, M. Retsch, M. K. Lisicki and P. R. Lang. On the effect of morphology and particle-wall interaction on colloidal near-wall dynamics. Soft Matter 2021. DOI: <a href="https://doi.org/10.1039/D1SM01191J">https://doi.org/10.1039/D1SM01191J</a> EUSMI proposal code: E190800323 We investigated the near-wall Brownian dynamics of different types of colloidal particles with a typical size in the 100 nm range using evanescent wave dynamic light scattering (EWDLS). In detail we studied dilute suspensions of silica spheres and shells with a smooth surface and silica particles with controlled surface roughness. While the near wall dynamics of the particle with smooth surface differ only slightly from the theoretical prediction for hard spheres colloids, the rough particles diffuse significantly slower. We analysed the experimental data by comparison with model calculations and suggest that the deviating dynamics of the rough particles are not due to increased hydrodynamic interaction with the wall. Rather, the particle roughness significantly changes their DLVO interaction with the wall, which in turn effects their diffusion.

opennotspecifiedDec 2014View details →

FIGURE 2. Ossicles from, a. dorsal body wall, b. ventral body wall, c. tentacles, d. gonad. Scale 200 in Benthodytes violeta, a new species of a deep-sea holothuroid (Elasipodida: Psychropotidae) from Mar del Plata Canyon (south-western Atlantic Ocean)

FIGURE 2. Ossicles from, a. dorsal body wall, b. ventral body wall, c. tentacles, d. gonad. Scale 200 µm•

opencc-by-4.0Nov 2018View details →

Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall.

We present a molecular modelling and simulation study of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane in interactions with the cell wall.  TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed, binds peptidoglycan largely through electrostatic interactions. Non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides respectively, maintain the position of the cell wall even in the absence of Braun’s lipoprotein. The charged residues that mediate the cell-wall interactions of TolR in our simulations, are conserved across a number of species of Gram-negative bacteria.

opencc-by-4.0Dec 2022View details →

Data for "Coordination of bacterial cell wall and outer membrane biosynthesis"

Raw data used in the paper "Coordination of bacterial cell wall and outer membrane biosynthesis" by Katherine R. Hummels, Samuel P. Berry, Zhaoqi Li, Atsushi Taguchi, Joseph K. Min, Suzanne Walker, Debora S. Marks, and Thomas G. Bernhardt. These data were collected with the aim of understanding how the lipopolysaccharide biosynthetic enzyme LpxC is regulated in diverse gram-negative bacteria, particularly Pseudomonas aeruginosa. The dataset contains the following tarred directories: Experimental data <ul> <li>Microscopy (microscopy.tar.gz)</li> <li>LC-MS/MS (lc-ms_ms.tar.gz)</li> </ul> Covariation analysis <ul> <li>Multiple sequence alignments (alignments.tar.gz)</li> <li>AlphaFold structures (alphafold.tar.gz)</li> <li>EVcomplex models and couplings (evcomplex.tar.gz)</li> <li>Phylogenetic trees (trees.tar.gz)</li> </ul> For more detailed methods and file descriptions, please see README.md. Associated code for analysis can be found at https://github.com/samberry19/evcomplex-interaction-scoring.

Figure 3 in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Figure 3. Example of Grad-CAM heatmaps obtained for Podarcis lusitanicus. The upper images show two common patterns observed in male dorsal images (also found, albeit with some differences, in females). The bottom images exhibit the patterns most frequently found in male and female head lateral images (here illustrated in two females).

Figure 2 in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Figure 2. Confusion matrix for male (upper) and female (lower) image classification for the two-class case based on a combination of predictions from six models. Abbreviations used: Pboc, P. bocagei; Plus, P. lusitanicus.

Highly variable (no clear pattern). All portions of the dorsal views were equally used. In head images the area around the eye, the top of the head, the snout and the throat were all used in similar proportions. P. carbonelli Variable for both views. Snout and middle of the dorsum used in dorsal view. Top of the head most frequently (but not strictly) used in lateral view. P. guadarramae Whole body used for dorsal view (but variable); either throat (most common) or ear region used in head lateral views. P. hispanicus Variable. Anterior portion of snout used more frequently than in other species for both dorsal and head lateral views. P. liolepis Highly variable. Whole body used in most dorsal images, area around the eye and throat used in head lateral views, but other patterns common. P. lusitanicus Highly variable. All parts of the dorsum used (but frequently the most posterior part); area around the ear frequently used in head lateral images. P. tunesiacus Highly variable. Dorsal area near the insertion of the posterior limbs used more frequently than in other species; different regions of the head used, often simultaneously. P. Ʋaucheri Highly variable. Different regions of dorsum (from head to the posterior region) used in dorsal images, all portions of the head, but most frequently the throat, used in lateral images. P. Ʋirescens Highly variable. All parts of both images used. Head and anterior part of the dorsum more used than in other species. in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Highly variable (no clear pattern). All portions of the dorsal views were equally used. In head images the area around the eye, the top of the head, the snout and the throat were all used in similar proportions. P. carbonelli Variable for both views. Snout and middle of the dorsum used in dorsal view. Top of the head most frequently (but not strictly) used in lateral view. P. guadarramae Whole body used for dorsal view (but variable); either throat (most common) or ear region used in head lateral views. P. hispanicus Variable. Anterior portion of snout used more frequently than in other species for both dorsal and head lateral views. P. liolepis Highly variable. Whole body used in most dorsal images, area around the eye and throat used in head lateral views, but other patterns common. P. lusitanicus Highly variable. All parts of the dorsum used (but frequently the most posterior part); area around the ear frequently used in head lateral images. P. tunesiacus Highly variable. Dorsal area near the insertion of the posterior limbs used more frequently than in other species; different regions of the head used, often simultaneously. P. Ʋaucheri Highly variable. Different regions of dorsum (from head to the posterior region) used in dorsal images, all portions of the head, but most frequently the throat, used in lateral images. P. Ʋirescens Highly variable. All parts of both images used. Head and anterior part of the dorsum more used than in other species.

Figure 1 in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Figure 1. The two image types analysed in this study (before pre-processing): above, a dorsal view; below, a head lateral image. Both images correspond to the same Podarcis Ʋaucheri s.l. male.

Highly variable. Mid-portion of the dorsum used frequently (although other areas as well). Tip of the snout used often, but area around the ear and throat are also relevant. P. carbonelli Variable. In the dorsal view, the tip of the snout is frequently used. In the head lateral view, the tip of the snout is also com- monly used, as well as the most posterior region of the head. P. guadarramae Variable. Mid portion of the dorsum and tip of the snout are the regions used more frequently in dorsal and head lateral views, respectively. P. hispanicus Variable. The head and most anterior part of the dorsum are frequently used in the dorsal view. Snout and/or top of posterior region of head used. P. liolepis Variable. Different parts of the dorsum are used, whereas the tip of the snout is used in most head lateral images. P. lusitanicus Anterior dorsum, in the dorsal view, and both snout and posterior side of the head (in head lateral views) frequently used. P. tunesiacus Variable. Tip of the snout and posterior part of the trunk more used than in other species; snout and top head region behind the eye used with some frequency. P. Ʋaucheri Highly variable. All parts of the dorsum used in dorsal images, various parts of the head (but frequently snout and throat combined) used in head lateral images. P. Ʋirescens Highly variable. All portions of the dorsum used in dorsal images, region around and behind the ear more used than in other species for head lateral images. in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Highly variable. Mid-portion of the dorsum used frequently (although other areas as well). Tip of the snout used often, but area around the ear and throat are also relevant. P. carbonelli Variable. In the dorsal view, the tip of the snout is frequently used. In the head lateral view, the tip of the snout is also com- monly used, as well as the most posterior region of the head. P. guadarramae Variable. Mid portion of the dorsum and tip of the snout are the regions used more frequently in dorsal and head lateral views, respectively. P. hispanicus Variable. The head and most anterior part of the dorsum are frequently used in the dorsal view. Snout and/or top of posterior region of head used. P. liolepis Variable. Different parts of the dorsum are used, whereas the tip of the snout is used in most head lateral images. P. lusitanicus Anterior dorsum, in the dorsal view, and both snout and posterior side of the head (in head lateral views) frequently used. P. tunesiacus Variable. Tip of the snout and posterior part of the trunk more used than in other species; snout and top head region behind the eye used with some frequency. P. Ʋaucheri Highly variable. All parts of the dorsum used in dorsal images, various parts of the head (but frequently snout and throat combined) used in head lateral images. P. Ʋirescens Highly variable. All portions of the dorsum used in dorsal images, region around and behind the ear more used than in other species for head lateral images.

Figure 4 in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Figure 4. Confusion matrix for male (upper) and female (lower) image classification for the nine-class experiment based on a combination of predictions from six models. Abbreviations used: Pboc, P. bocagei; Pcar, P. carbonelli; Phis, P. hispanicus; Plio, P. liolepis; Plus, P. lusitanicus; Pvsl, P. Ʋaucheri s.l.; Pvss, P. Ʋaucheri s.s.; Pvir, P. Ʋirescens.

opennotspecifiedMay 2023View details →

FIGURES 1–10 in A new record of Vaucheria incurva (Vaucheriaceae, Xanthophyceae), an extremely rare species, with taxonomic remarks on other Vaucheriae having disintegrated gametangial walls

FIGURES 1–10. Morphology of Vaucheria incurva from new locality: 1–3—general view of proliferating fruiting branches, note multiple proliferations on Figs. 2, 3; 4—detail of fruiting branch with antheridium and oogonium, which are not separated clearly from gametangial pedicels; antheridium is in focus; 5—antheridial pedicel bearing empty antheridium; 6, 7—oogonial pedicels bearing oospores weakly fixed with remnants of oogonial walls; 8–10—mature oospores liberated from oogonial walls. Symbols: a—antheridium, ap—antheridial pedicel, ea—emptied antheridium, fb—fruiting branch, og—oogonium, op—oogonial pedicel, os—oospore, ow—oogonial wall, p—proliferation. Scale bars: 1–3—100 µm, 4–10—30 µm.

Fig. 6 in Undescribed phloroglucinol derivatives with antiviral activities from Dryopteris atrata (Wall. Ex Kunze) Ching

Fig. 6. Antivirus activity of compound 7 against HSV-1 by using a fluorescence assay. Compound 7 was added at 20 μM at different times post-infection (1, 2, 4, 6, 8, 12, and 20 h), and acyclovir was used as the positive control. Data were expressed as mean ± SD from three independent experiments (***p <0.001 compared with the viral control group).

opennotspecifiedJul 2021View details →

Fig. 4 in Acylphloroglucinol derivatives with ATP citrate lyase inhibitory activities from Syzygium oblatum Wall.

Fig. 4. (A) The predicted binding mode of 1 with ACLY and the ligand is shown as yellow sticks. (B) A two-dimensional plot showing the interactions between 1 and the surrounding amino acids. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

opennotspecifiedFeb 2020View details →

Fig. 3 in The role of cell wall phenolics during the early remodelling of cellulosedeficient maize cells

Fig. 3. Representative HPLC-PAD elution profile of phenolic compounds after alkali hydrolysis of protoplasmic fraction from non-habituated (NH, A, C) and DCBhabituated (H, B, D) suspension-cultured cells corresponding at their early logarithmic (A, B) and late logarithmic (C, D) growth phase. Peaks were detected at 300 nm. 50 μl of sample was injected without dilution. Key to peak identity as Fig. 2.

opennotspecifiedFeb 2020View details →

Fig. 4 in The role of cell wall phenolics during the early remodelling of cellulosedeficient maize cells

Fig. 4. Structural models of the primary cell wall of non-habituated (A, B) and DCB-habituated (C, D) maize suspension-cultured cells at their early-logarithmic (A, C) and late-logarithmic (B, D) growth phases. The model shows the molecular interactions between cellulose, arabinoxylans and hydroxycinnamic acids (phenolic compounds). Based on Gómez and McQueen-Mason (2018). Dehydrodiferulates can also be ether-linked to lignin.