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Fig. 5 in Conoidecyclics A-C from marine macroalga Turbinaria conoides: Newly described natural macrolides with prospective bioactive properties

Fig. 5. (A1-A2) Representative hydrogen binding interactions between conoidecyclic C and the amino acyl residues in the catalytic sites of COX-2; (A3-A4) Representative hydrogen binding interactions between conoidecyclic C and the amino acyl residues in the catalytic sites of 5-LOX; (A5-A6) Representative hydrogen binding interactions between conoidecyclic C and the amino acyl residues in the catalytic sites of PTP-1B; (A7-A8) Representative hydrogen binding interactions between conoidecyclic C and the amino acyl residues in the catalytic sites of ACE as obtained from in silico molecular docking analysis.

Fig. 3 in Conoidecyclics A-C from marine macroalga Turbinaria conoides: Newly described natural macrolides with prospective bioactive properties

Fig. 3. (A1-A2) Representative hydrogen binding interactions between conoidecyclic A and the amino acyl residues in the catalytic sites of COX-2; (A3-A4) Representative hydrogen binding interactions between conoidecyclic A and the amino acyl residues in the catalytic sites of 5-LOX; (A5-A6) Representative hydrogen binding interactions between conoidecyclic A and the amino acyl residues in the catalytic sites of PTP-1B; (A7-A8) Representative hydrogen binding interactions between conoidecyclic A and the amino acyl residues in the catalytic sites of ACE as obtained from in silico molecular docking analysis.

Fig. 1 in Conoidecyclics A-C from marine macroalga Turbinaria conoides: Newly described natural macrolides with prospective bioactive properties

Fig. 1. Structural representations of conoidecyclics A-C purified from the solvent extract of T. conoides. The thallus structure (leaf-like) of T. conoides was illustrated.

Fig. 4 in Conoidecyclics A-C from marine macroalga Turbinaria conoides: Newly described natural macrolides with prospective bioactive properties

Fig. 4. (A1-A2) Representative hydrogen binding interactions between conoidecyclic B and the amino acyl residues in the catalytic sites of COX-2; (A3-A4) Representative hydrogen binding interactions between conoidecyclic B and the amino acyl residues in the catalytic sites of 5-LOX; (A5-A6) Representative hydrogen binding interactions between conoidecyclic B and the amino acyl residues in the catalytic sites of PTP-1B; (A7-A8) Representative hydrogen binding interactions between conoidecyclic B and the amino acyl residues in the catalytic sites of ACE as obtained from in silico molecular docking analysis.

Fig. 6 in Conoidecyclics A-C from marine macroalga Turbinaria conoides: Newly described natural macrolides with prospective bioactive properties

Fig. 6. Kinetic studies of the pharmacologic response with regard to inhibition mode of ACE-I (A–C), PTP-1B (D–F) and 5-LOX (G–I), respectively to the studied conoidecyclics A-C. Representation of Dixon plots for conoidecyclics A-C, for the determination of the inhibition constant Ki. The Ki value was determined from the negative X-axis value at the point of the intersection of the four lines. The data were expressed as the mean reciprocal of initial velocity for triplicates (n = 3) at each substrate concentration. Different concentrations of isolated compounds were used, and the inhibitory potentials were expressed in mM.

opennotspecifiedOct 2021View details →

Fig. 2 in Volatile phenolics: A comprehensive review of the anti-infective properties of an important class of essential oil constituents

Fig. 2. World map showing the publications of the different countries involved in scholarly publication of the anti-infective properties of volatile phenolics (1985–2019) as retrieved from the Scopus database.

opennotspecifiedOct 2021View details →

Fig. 1 in Volatile phenolics: A comprehensive review of the anti-infective properties of an important class of essential oil constituents

Fig. 1. The number of publications retrieved from Scopus database in 35 years dealing with anti-infective properties of VP's (n = 2310 publications).

opencc-by-4.0Aug 2023View details →

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Supplementary code and data for "Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks"

Supplementary code and data for the conference article <blockquote> "Tackling universal properties of minimal trap spaces of boolean networks" Sara Riva, Jean-Marie Lagniez, Gustavo Magaña López, and Loïc Paulevé Proceedings of CMSB 2023, LCNS, Springer.<a href="https://doi.org/10.1007/978-3-031-42697-1_11"> https://doi.org/10.1007/978-3-031-42697-1_11</a> </blockquote> Requirements <ul> <li> Python at least 3.9 </li> <li> <a href="https://github.com/bnediction/bonesis">bonesis</a> (v0.5.6) - <a href="https://doi.org/10.5281/zenodo.7984628">https://doi.org/10.5281/zenodo.7984628</a> With pip: <ul> <li><code>pip install bonesis==0.5.6</code></li> </ul> With conda: <ul> <li><code>conda install -c potassco -c colomoto bonesis=0.5.6</code></li> </ul> </li> <li> for the synthesis: <a href="https://github.com/sybila/biodivine-aeon-py/">AEON.py</a> With pip: <ul> <li><a href="https://rustup.rs">https://rustup.rs</a></li> <li><code>pip install biodivine-aeon</code></li> </ul> With conda <ul> <li><code>conda install -c daemontus biodivine_aeon</code></li> </ul> </li> </ul>   Usage <ul> <li> to execute the CEGAR approach for marker-reprogramming problem:</li> </ul> <pre><code>python reprogramming_cegar.py instances/Moon22/L3_2013_Grieco_et_al/transition_formula.bnet '{"p":1}' 3 </code></pre> The first parameter is the .bnet file, the second one is the marker (in JSON), and the third is the maximum number k of components in a perturbation. To fix the marker, it is also possible to use a special node (ex: p) in the bnet file and require a marker '{"p":1}'. In the Moon22 dataset, information about uncontrollable components are available, one can use <code>--exclude '["Apoptosis","Growth_Arrest","Proliferation"]'</code>. If the marker is given as a component, it must be involed in the uncontrollable list. Moreover, the markers of the Moon22 dataset are contained in the bnet files in a special component <code>p</code>. Concerning the Trappist dataset, the possible markers are contained in files .markers, the user can choose between them. The dataset synthetic_bns contains random generated BNs. Also in this case, different possible markers are contained in files .markers. <ul> <li>to execute the Complementary approach for marker-reprogramming problem:</li> </ul> <pre><code>python reprogramming_complementary.py instances/Moon22/L3_2013_Grieco_et_al/transition_formula.bnet '{"p":1}' 3 </code></pre> Again, uncontrollable components can be specified. <ul> <li>to execute the Enumeration & Filtering approach for marker-reprogramming problem:</li> </ul> <pre><code>python reprogramming_trapspaces_naive.py instances/Moon22/L3_2013_Grieco_et_al/transition_formula.bnet '{"p":1}' 3 </code></pre> Again, uncontrollable components can be specified. <ul> <li>to execute the CEGAR approach for a synthesis problem:</li> </ul> <pre><code>python synthesis.py instances/Moon22/L3_2013_Grieco_et_al/transition_formula.aeon '{"p":1}' </code></pre> The first parameter is the prior knowledge graph in an .aeon file and the second one is the marker (in JSON). Another option is <code>--maxclause</code> which allow one to specify the maximum integer number of clauses authorised in local functions (by default is 128). The option <code>--no-canonic</code> leads to specify the criteria for the refinement of the under-approximation (3 for TS(y)|=M ; 1 for \exists y s.t. TS(y)!=TS(x) or 0 to obtain just a different candidate solution).

Fig. 6 in Structural and functional features of a class VI chitinase from cashew (Anacardium occidentale L.) with antifungal properties

Fig. 6. Morphological alterations induced in Lasiodiplodia theobromae hyphae by Anacardium occidentale chitinase. SEM images of untreated mycelium(A-B), mycelium treated with 500 μg AoChi (C–I) and mycelium treated with 5 μg Carbendazim (J–M) are shown. The assays to evaluate the morphological alterations in L. theobromae grown in vitro in the presence of AoChi and acquisition of SEM images were performed as described in the Methods section. SEM images from fungus grown in the presence of water (A–B) or Carbendazim (J–M) were included for comparison.

Fig. 7 in Structural and functional features of a class VI chitinase from cashew (Anacardium occidentale L.) with antifungal properties

Fig. 7. Three-dimensional molecular model of AoChi and its interaction with a chitin oligomer. (A) Cartoon representation of the three-dimensional molecular model of AoChi, which was generated by homology modeling. Side chains of putative catalytic residues are shown as sticks. Disulfide bonds are colored orange. (B) Detailed view of a chito-oligosaccharide (yellow) docked in the substrate-binding cleft of AoChi. Side chains of AoChi residues that probably interact with the docked ligand through hydrogen bonds (represented as yellow dotted lines) are shown as sticks (cyan). N and O atoms are colored blue and red, respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Structural and functional features of a class VI chitinase from cashew (Anacardium occidentale L.) with antifungal properties

Fig. 5. Effects of temperature (A), pH (B), metal ions (C) and chemical reagents (D) on the hydrolytic activity (A–D) and stability (A–B) of AoChi. Enzymatic assays were performed using the purified recombinant protein (200 μg/mL) and colloidal chitin as substrate, as described in the Methods section. In panels C and D, means that are significantly different (P <0.05; Bonferroni's multiple comparisons test) when compared to control are indicated by asterisks.

Fig. 4 in Structural and functional features of a class VI chitinase from cashew (Anacardium occidentale L.) with antifungal properties

Fig. 4. Polyacrylamide gel electrophoresis (SDS-PAGE) of the purified recombinant chitinase from Anacardium occidentale, a member of class VI that has chitinolytic activity. (A) The recombinant chitinase (lane 1; 35 μg) was reduced with β-mercaptoethanol and subjected to denaturing gel electrophoresis (15% polyacrylamide), as described in the Methods section. Lane M: protein markers. (B) Representative fragmentation mass spectrum (LC-MS/MS) of a tryptic peptide, obtained from in gel-digestion of the 45 kDa protein band, that matched a segment of 17 residues of the primary structure of the recombinant product. (C) Colorimetric enzymatic assay, showing the ability of the recombinant cashew chitinase to degrade colloidal chitin. (D) Plot of initial reaction velocities vs substrate concentration. The enzymatic assays (panels C and D) were performed at pH 6.0 and 40 ◦C, and using colloidal chitin as substrate, as described in the Methods section.

Fig. 3 in Structural and functional features of a class VI chitinase from cashew (Anacardium occidentale L.) with antifungal properties

Fig. 3. Alignment of the amino acid sequence of the CatD of AoChi with known three-dimensional structures of GH19 chitinases from plants. The CatD sequence of AoChi was aligned to GH19 structures from: Carica papaya (PDB ID: 3CQL), Vigna unguiculata subsp. sesquipedalis (PDB ID: 4TX7), Secale cereale (PDB ID: 4DWX), Hordeum vulgare (PDB ID: 2BAA), Oryza sativa subsp. japonica (PDB ID: 2DKV), Canavalia ensiformis (PDB ID: 1DXJ), Brassica juncea (PDB ID: 2Z37), Cryptomeria japonica (PDB ID: 5H7T) and Picea abies (PDB ID: 3HBD). Sites containing residues involved in catalysis (triangles) and substrate-binding (hash marks) are indicated. Disulfide bonds, as observed in the three-dimensional model of AoChi (Fig. 7), are indicated by orange lines. Loop regions (I–V), as assigned by Taira et al. (Taira et al., 2011), are boxed. Loop VI (this work), which is present only in AoChi and other class VI chitinases, is also boxed. Alignment columns are colored according to the ALSCRIPT Calcons convention, as implemented in ALINE (Bond and Schüttelkopf, 2009), using a predefined color scheme, which reflects the conservation of amino acid properties in each column (dark blue: identical residues; white: dissimilar residues). (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 Structural and functional features of a class VI chitinase from cashew (Anacardium occidentale L.) with antifungal properties

Fig. 2. Maximum likelihood (ML) tree showing the phylogenetic relationship of Anacardium occidentale chitinase with representative plant chitinases from classes I, II, IV, VI and VII. The evolutionary history of the sequences was inferred by using the ML method and Whelan and Goldman + Freq. model (Whelan and Goldman, 2001). The tree with the highest log likelihood (12837.58) is shown. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 1.5328)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 3.91% sites). The percentage of trees in which the associated sequences clustered together, as determined by the bootstrap test (100 replicates), is shown next to the branches. This analysis involved 62 amino acid sequences, and the final dataset contained a total of 371 positions (Table S2 and Fig. S7). Evolutionary analyses were conducted in MEGA X (Kumar et al., 2018).

Fig. 1 in Structural and functional features of a class VI chitinase from cashew (Anacardium occidentale L.) with antifungal properties

Fig. 1. Domain architecture of Anacardium occidentale chitinase (AoChi). (A) Graphical representation of AoChi domains (SP: signal peptide; GH19 CatD: GH19 catalytic domain). The catalytic residues of AoChi, Lys(K)128, Glu(E)150 and Tyr(Y)183, are highlighted. (B) Alignment of a stretch of 61 residues from the primary structure of AoChi (from His124 to Trp184), which contains the 3 catalytic residues, with corresponding segments from homologous proteins belonging to plant species from different families and orders (Table S5). Alignment columns are colored according to the ALSCRIPT Calcons convention, as implemented in ALINE (Bond and Schüttelkopf, 2009), using a predefined color scheme, which reflects the conservation of amino acid properties in each column (dark red: identical residues; white: dissimilar residues). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 7 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins

Fig. 7. Antibacterial effects of a series of purified McDef1 concentration against S. aureus (A), E. coli (B), S. pullorum (C) and A. hydrophila (D). 1: 30 μg/ml, 2: 40 μg/ ml, 3: 50 μg/ml, 4: 60 μg/ml, 5: 80 μg/ml, 6: 100 μg/ml, 7: Negative control, empty vector expression supernatant; 8: Positive control, for A̢B̢C: 0.2 mg/mL Ampicillin, for D: 0.5 mg/mL Kanamycin.

Fig. 6 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins

Fig. 6. Antibacterial effects of recombinant yeasts with McDef1 or McDef2 fermentation supernatant on S. aureus (A), S. pullorum (B), E. coli (C) and A. hydrophila (D). 1: Fermentation supernatant of the recombinant McDef1; 2: Fermentation supernatant of the recombinant McDef2; 3: Negative control, empty vector expression supernatant; 4: Positive control, A̢B̢C: 0.2 mg/mL Ampicillin; D: 0.5 mg/mL Kanamycin.

Fig. 4 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins

Fig. 4. Multiple sequence alignments of the mature peptides of McLTP1 homologs from different plants with ClustalW2. The target proteins McLTP1 of this study are highlighted with yellow fluorescent background. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins

Fig. 2. Multiple sequence alignments of the McDef1 (A) and McDef2-5 (B) homologs from different plants with ClustalW2. The conserved domains α-core and γ-core are marked under the homologous sequences respectively. The target proteins McDef1 in (A) and McDef2-5 in (B) of this study are highlighted with yellow fluorescent background. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)