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Fig. 6 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development

Fig. 6 Phenotype associated with dynein, kinesin, isocitrate dehydrogenase and citrate synthase mRNA subjected to RNAi in female ticks via injection with the corresponding dsRNA. a Dynein dsRNA injection. b Kinesin dsRNA injection. c Isocitrate dehydrogenase dsRNA injection. d Citrate synthase dsRNA injection. e GFP dsRNA injection, control. f No injection, control. Scale-bars: 5 mm

Fig. 7 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development

Fig. 7 Digital micrographs of salivary gland acinar morphological changes in unfed female H. longicornis after RNAi.The time at which the tick bit the host and began sucking blood was recorded as day 0. a–e Dynein dsRNA injection. f–j Kinesin dsRNA injection. k–o Isocitrate dehydrogenase dsRNA injection. p–t Citrate synthase dsRNA injection. u–y GFP dsRNA injection, control. Scale-bars: 25 µm

Fig. 4 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development

Fig. 4 KEGG pathway enrichment analysis of the differentially expressed proteins in 5 different Clusters. Terms with a P-value <0.05 were used to draw the column diagrams. a–e KEGG pathway enrichment for the proteins in Cluster 1 to Cluster 5

Fig. 3 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development

Fig. 3 GO functional annotations for all the differentially expressed proteins. a–c GO annotations of differentially expressed proteins in the salivary glands of partially fed ticks compared with unfed ticks (115:114). d–f GO annotations of differentially expressed proteins in the salivary glands of mated semi-engorged ticks compared with partially fed ticks (116:115). g–i GO annotations of differentially expressed proteins in the salivary glands of engorged ticks compared with mated semi-engorged ticks (117:116). Abbreviations: BP, biological process; CC, cellular component; MF, molecular function; CO, cellular component organization or biogenesis

Fig. 5 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development

Fig. 5 RT-qPCR analyzed the mRNA expression levels of dynein, kinesin, isocitrate dehydrogenase, and citrate synthase during the four feeding stages of salivary gland development

Fig. 2 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development

Fig. 2 Statistics and cluster analysis for the identified proteins and their expression levels in the salivary glands of female H. longicornis. a Venn diagram showing the number of proteins (with CV <20%) identified in the three experiments. b Venn diagram showing the number of proteins with quantitative information. c Cluster analysis according to trends in protein expression in the salivary glands of female ticks

Fig. 1 in Salivary gland proteome analysis of developing adult female HaemaphYSaliS longiCorniS ticks: molecular motor and TCA cycle-related proteins play an important role throughout development

Fig. 1 Workflow for quantitative proteomics analysis of changes in protein expression in the salivary glands of female H. longicornis during the blood-feeding process

opencc-zeroApr 2024View details →

Reinforcing Tunnel Network Exploration in Proteins using Gaussian Accelerated Molecular Dynamics (inputs, outputs, analysis)

<ul> <li>00_LinB-Wt.tar.gz - LinB-Wt: contains raw data that are used for analysis, also conatin folder for GaMD testing.</li> </ul>     1. cMD(Classical MD simulation) analysis files :              1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.         2. Inputs and output files of caver calculations.          3. H-bond raw distance files from all simulations named run1-run5.          4. Distance files used to calculate PCA and cluster analysis.         5. Input files and input structure used to run simulations along with output restart files from each stage of production.             2. GaMD(Gaussian Accelerated MD simulation) analysis files :            1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.         2. Inputs and output files of caver calculations.          3. H-bond raw distance files from all simulations named run1-run5.          4. Distance files used to calculate PCA and cluster analysis.         5. Input files and input structure used to run simulations along with output restart files from each stage of production.     3. GaMD-testing :         1. Input file of GaMD used to run testing and output gamd.log files for multiple run of σOP 1.2 - 1.4 and σOD 2.5.     4. Initial 200ns cMD simulation files used for cluster analysis :         1. Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and 200ns stripped water and ions simulation in Amber *.nc format         2. Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format in rst folder.         3. Ouput files from Simulation for each stage of the minimization, equilibration and production runs in Amber *.out format in out folder. <ul> <li>01_LinB-Open.tar.gz - LinB Open mutant: contains raw data that are used for analysis.</li> </ul>     1. cMD(Classical MD simulation) analysis files :              1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.         2. Inputs and output files of caver calculations.          3. H-bond raw distance files from all simulations named run1-run5.          4. Distance files used to calculate PCA and cluster analysis.         5. Input files and input structure used to run simulations along with output restart files from each stage of production.             2. GaMD(Gaussian Accelerated MD simulation) analysis files :            1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.         2. Inputs and output files of caver calculations.          3. H-bond raw distance files from all simulations named run1-run5.          4. Distance files used to calculate PCA and cluster analysis.         5. Input files and input structure used to run simulations along with output restart files from each stage of production.     3. Initial 200ns cMD simulation files used for cluster analysis :         1. Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and 200ns stripped water and ions simulation in Amber *.nc format         2. Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format in rst folder.         3. Ouput files from Simulation for each stage of the minimization, equilibration and production runs in Amber *.out format in out folder. <ul> <li>02_LinB-Closed.tar.gz - LinB Closed mutant: contains raw data that are used for analysis.</li> </ul>     1. cMD(Classical MD simulation) analysis files :              1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.         2. Inputs and output files of caver calculations.          3. H-bond raw distance files from all simulations named run1-run5.          4. Distance files used to calculate PCA and cluster analysis.         5. Input files and input structure used to run simulations along with output restart files from each stage of production.             2. GaMD(Gaussian Accelerated MD simulation) analysis files :            1. Analysis of catalytic residue’s RMSD, whole protein RMSD and RMSF along with whole protein’s Rg and sasa.         2. Inputs and output files of caver calculations.          3. H-bond raw distance files from all simulations named run1-run5.          4. Distance files used to calculate PCA and cluster analysis.         5. Input files and input structure used to run simulations along with output restart files from each stage of production.     3. Initial 200ns cMD simulation files used for cluster analysis :         1. Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and 200ns stripped water and ions simulation in Amber *.nc format         2. Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format in rst folder.         3. Ouput files from Simulation for each stage of the minimization, equilibration and production runs in Amber *.out format in out folder. <ul> <li>03_TT_analysis.tar.gz - TransportTools: contains config file and all the raw data from all set and subset of reclustered (using in-house python script) caver calculations used for running TT.</li> </ul>     1. Caver input data for comparison between 500ns, 1 us, 2.5 us and 5us between LinB-Wt and it’s mutants.     2. TransportTools log file.     3. Main statistics result of comparative analysis. <ul> <li>04_reweighting.tar.gz: directory contains reweighted .csv files after running in-house reweighting protocol.             1. GaMD log files from each simulation of LinB-Wt and it’s mutants.     2. CSV files from TT result folder.     3. Result *.csv file contained reweighted tunnel properties in folder reweighted_filtered_new.</li> <li>05_caverdock.tar.gz: contains raw data for caverdock calculations uisng 100 best tunnels with four ligands 2-bromoethanol (be), 1,2-dibromoethane (dbe), Bromide ion (br-) and water (h2o).</li> </ul>     1. Top 100 tunnels present in tunnel folder for all three tunnels ST, p1b and p3 with subdirectory containing three variants and four ligand, whichare used for running caverdock.     2. Ligand *.pdbqt file and receptor *.pdbqt are present in each 100 tunnel folder of respective caverdock calculation.     3. Inside each variant and each ligand, there is respective result of migration analysis with energy barrier calculation of respective tunnels *energy_barriers-new.log* and further simplied *.csv files that was used for preparing figure in manuscript.

Figure 6. A in Classical taxonomy, molecular phylogeny and genetic analysis of the genus Exitianus Ball, 1929 (Hemiptera: Cicadellidae: Deltocephalinae) from Egypt

Figure 6. A. Amino acids variations of the COX1 gene generated by WebLogo3 server. B. Multiple amino acids alignments for selected Exitianus isolates generated by MultAlin server.

Figure 2. Exitianus nanus. A in Classical taxonomy, molecular phylogeny and genetic analysis of the genus Exitianus Ball, 1929 (Hemiptera: Cicadellidae: Deltocephalinae) from Egypt

Figure 2. Exitianus nanus. A. Habitus, dorsal view; B. Habitus, female ventral view; C. Habitus, male ventral view; D. Pronotum & scutellum; E. Face; F. Male genitalia (pygofer, subgenital plate, valva, styles and connective, aedeagus).

Figure 1. Exitianus capicola. A in Classical taxonomy, molecular phylogeny and genetic analysis of the genus Exitianus Ball, 1929 (Hemiptera: Cicadellidae: Deltocephalinae) from Egypt

Figure 1. Exitianus capicola. A. Habitus, dorsal view; B. Habitus, female ventral view; C. Habitus, male ventral view; D. Pronotum

Figure 3. Exitianus pondus. A in Classical taxonomy, molecular phylogeny and genetic analysis of the genus Exitianus Ball, 1929 (Hemiptera: Cicadellidae: Deltocephalinae) from Egypt

Figure 3. Exitianus pondus. A. Habitus, dorsal view; B. Habitus, female ventral view; C. Habitus, male ventral view; D. Pronotum & scutellum; E. Face; F. Male genitalia (pygofer, subgenital plate, valva, styles and connective, aedeagus); G. Aedeagus, lateral view.

Figure 2 in Assessment of melatonin-alpha adrenergic receptor complexes by molecular docking analysis

Figure 2. Two-dimensional schematic diagrams of the intermolecular interactions in the complexes between ligand melatonin and alpha-2A adrenergic receptor 6kux (A) and 6kuy (B). The ligand melatonin is positioned in the center of the diagrams and its nitrogen, oxygen and carbon atoms are indicated in blue, red and black spheres, respectively, connected to each other by solid blue lines. The amino acids Asp113 and Ser204 of the active binding sites of the receptor proteins are indicated by nitrogen, oxygen and carbon atoms represented as blue, red and black spheres, respectively, connected to each other by solid yellow lines. Hydrogen bonding interactions in the ligand-receptor complexes are represented in green dashed lines with their respective distances in angstroms Å. Hydrophobic contacts are represented in red arcs with spokes radiating towards the ligand atoms they contact, and the contacted atoms are shown with spokes radiating back.

Figure 1 in Assessment of melatonin-alpha adrenergic receptor complexes by molecular docking analysis

Figure 1. Molecular docking interactions of the ligand melatonin (in green) in the active binding sites of the adrenoceptors visualized from UCSF Chimera1.15. Tridimensional structures of the adrenergic receptors 6kux in purple (A) and 6kuy in pink (B).

opencc-by-4.0Dec 2015View details →

Fig. 3. Phylogenetic trees from reported 18S in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data

Fig. 3. Phylogenetic trees from reported 18S rRNA genes of insects according to NJ. A. Based on sequences of full-length. B. Based on second conserved region.

opencc-by-4.0Dec 2015View details →

Fig. 4 in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data

Fig. 4. Phylogenetic trees based on partial sequences from reported cox1 genes of insects according to NJ.

opencc-by-4.0Dec 2015View details →

Fig.1 in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data

Fig.1. PCR result of 18S rRNA of Lymantria dispar. Separated bands (from left to right). 18S1, 18S2, 18S rRNA, DL2000 marker.

Fig. 13 in Identification and Distribution of Wedge Clams (Donacidae: Bivalvia) in Thailand by Geometric Morphometric and Molecular Analysis.

Fig. 13. Phylogenetic analysis based on genetic sequence derived from cytochrome oxidase I (COI) gene of Donax spp. and other related species using the maximum likelihood (ML) method. The bootstrap values were calculated with 1000 replicates.

Fig. 11 in Identification and Distribution of Wedge Clams (Donacidae: Bivalvia) in Thailand by Geometric Morphometric and Molecular Analysis.

Fig. 11. Frequency distribution of Discriminant analysis of two overlapping populations, Donax (Deltachion) bruneirufi (grey) and D. (Deltachion) spinosus (white).

Fig. 12 in Identification and Distribution of Wedge Clams (Donacidae: Bivalvia) in Thailand by Geometric Morphometric and Molecular Analysis.

Fig. 12. Outline overlain, size-normalized average outline of each two species in discriminant analysis; Donax (Latona) solidus (white) and D. (Latona) cuneatus (grey) (A); D. (Latona) solidus (white) and D. (Latona) faba (grey area) (B); D. (Latona) cuneatus (white area) and Donax (Latona) faba (grey area) (C); D. (Deltachion) bruneirufi (white) and D. (Deltachion) spinosus (grey) (D). Arrows highlight distinct position from overlain shape of white area species extend from grey area species.