Journal: BMC Evolutionary Biology

Article Title: Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes

doi: 10.1186/1471-2148-6-27

Figure Lengend Snippet: Distribution of the four genes in the taxa sampled in this study. A hypothetical tree of eukaryotes for which genomes have been fully sampled and published, *; is close to completion, **; or only partially sampled (genome sequence survey or expressed sequence tags), ***; indicating their classification into "super-groups" [29-31], showing the presence or absence of the four genes in the study. Please notice that the gene absences in the genomes that are close to completion are unconfirmed, they may turn into presences upon publication. A and B refer to strongly separated groups in the phylogenetic analyses, as indicated in Figures 2-4 & 6. The priS genes encode the hybrid-cluster proteins, fprA genes encode the A-type flavoproteins, nagB genes encode glucosamine-6-phosphate isomerase proteins and the adhE genes encode the alcohol dehydrogenase E proteins.

Article Snippet: Trichomonas vaginalis (strain G3) nagB and fprA cDNA clones were identified in the ongoing EST project (Hirt, R.P., Embley, T.M., and Harriman, N.), and two priS Naegleria gruberi (strain NEG-M, ATCC 30224) cDNA clones were identified in an ongoing EST project (Sjögren, Å.M., Andersson, J.O., Gill, E., Roger, A.J., unpublished).

Techniques: Sequencing

Journal: BMC Evolutionary Biology

Article Title: Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes

doi: 10.1186/1471-2148-6-27

Figure Lengend Snippet: Protein maximum likelihood trees of the short and long versions of glucosamine-6-phosphate isomerase ( nagB gene) . ML tree based on 229 unambiguously aligned aa positions from the N-terminal part of the alignment of the glucosamine-6-phosphate isomerase protein. The grey boxes A and B indicate strongly separated groups which include eukaryotic sequences. The sequences in the B box (with the exception of the R. baltica 3 sequence) have an approximately 500 aa long conserved C-terminal extension of the protein which is absent from all other sequences in the alignment. The sequences in box B, together with the sequences indicated with asterisks were excluded in a separate analysis shown in , to test the influence of the removal of the long version of the protein and long branches on the relative positions of eukaryotic sequences. The tree is arbitrarily rooted. Details about the phylogenetic analyses are found in the Methods section and . Labelling as in Figure 2.

Article Snippet: Trichomonas vaginalis (strain G3) nagB and fprA cDNA clones were identified in the ongoing EST project (Hirt, R.P., Embley, T.M., and Harriman, N.), and two priS Naegleria gruberi (strain NEG-M, ATCC 30224) cDNA clones were identified in an ongoing EST project (Sjögren, Å.M., Andersson, J.O., Gill, E., Roger, A.J., unpublished).

Techniques: Sequencing

Journal: BMC Evolutionary Biology

Article Title: Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes

doi: 10.1186/1471-2148-6-27

Figure Lengend Snippet: Protein maximum likelihood trees of the long version of glucosamine-6-phosphate isomerase ( nagB gene) . Phylogenetic tree based on 560 unambiguously aligned aa positions from the glucosamine-6-phosphate isomerase sequences that have the long C-terminal extension (box B in Figure 4). In a separate analysis the partial Mastigamoeba balamuthi sequence was included and its position is indicated with an arrow with the bootstrap support value in parenthesis. The tree is arbitrarily rooted. Details about the phylogenetic analyses are found in the Methods section and . Labelling as in Figure 2.

Article Snippet: Trichomonas vaginalis (strain G3) nagB and fprA cDNA clones were identified in the ongoing EST project (Hirt, R.P., Embley, T.M., and Harriman, N.), and two priS Naegleria gruberi (strain NEG-M, ATCC 30224) cDNA clones were identified in an ongoing EST project (Sjögren, Å.M., Andersson, J.O., Gill, E., Roger, A.J., unpublished).

Techniques: Sequencing

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Parameters used for qRT-PCR of Trichomonas vaginalis peptidases.

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques: Concentration Assay

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Three-dimensional model for TvMP50 of Trichomonas vaginalis . ( A ) PIDDT values for the amino acid sequence of the structure modeled using Alphafold. ( B ) Active site, represented by the green marking. ( C ) Identification of amino acids from the enzyme’s active site. ( D ) Electrostatic charge on the surface of the TvMP50 calculated for pH values of 4 to 7. The red-white-blue scale refers to the minimum (−5 kT/e, red) and maximum (5 kT/e, blue) potentials of the surface.

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques: Sequencing

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Three-dimensional model for TvGP63 of Trichomonas vaginalis . ( A ) PIDDT values for the amino acid sequence of the structure modeled using Alphafold. ( B ) Active site, represented by the green marking. ( C ) Identification of amino acids from the enzyme’s active site ( D ) Electrostatic charge on the surface of the TvMP50 calculated for pHs 4 to 7. The red-white-blue scale refers to the minimum (−5 kT/e, red) and maximum (5 kT/e, blue) potentials of the surface.

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques: Sequencing

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Docking pose with lower absolute energy (kcal·mol −1 ) and 3D interaction diagram of the compounds with the amino acids of TvMP50 and TvGP63 from Trichomonas vaginalis . ( A , E ) 1,10-phenanthroline, ( B , F ) phendione, ( C , G ) Ag-phendione, ( D , H ) Cu-phendione.

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques:

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: ( A ) Docking pose with lower absolute energy (kcal·mol −1 ) and ( B ) 3D interaction diagram of the Cu-phendione with the amino acids of TvCP2 from Trichomonas vaginalis .

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques:

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Docking results predicted by AutoDock Vina: binding affinity, interaction type, amino acid residue, and geometric distance (Å) for TvMP50 of Trichomonas vaginalis with test compounds.

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques: Binding Assay, Residue

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Docking results predicted by AutoDock Vina: binding affinity, interaction type, amino acid residue, and geometric distance (Å) for TvGP63 of Trichomonas vaginalis with test compounds.

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques: Binding Assay, Residue

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Docking results predicted by AutoDock Vina: binding affinity, interaction type, amino acid residue, and geometric distance (Å) for TvCP2 of Trichomonas vaginalis with test compounds.

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques: Binding Assay, Residue

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Cu-phendione inhibits proteolytic activity in T. vaginalis . ( A ) Azocasein cleavage rate by parasites treated (12.5 μM) or not with Cu-phendione (CPh), pH 7.0, 37 °C for 90 min. ( B ) Cleavage of Phe-Arg substrate by parasite lysate at pH 5.0, 37 °C for 1 h. Results are expressed as arbitrary fluorescence units (AFU). ( C ) Cleavage of DNP-Pro-Leu-Gly-Met-Trp-Ser-Arg (MMP) substrate by parasite lysate at pH 9.0, 37 °C for 1 h. Results are expressed as arbitrary fluorescence units (AFU). CTL: Untreated control. FNT: 1,10-Phenanthroline. E-64: L-trans -epoxysuccinyl-L-leucylamido(4-guanidino) butane. (*) indicates statistically significant decrease (Student’s t- test; p < 0.05).

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques: Activity Assay, Fluorescence, Control

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Zymogram of the effect of Cu-phendione on T. vaginalis peptidases. Peptidase zymograms with gelatin after 24 h of incubation of ATCC 30236 isolate treated or not with Cu-phendione at MIC (12.5 μM). The region marked by the square was cut out of the zymogram for gel digestion. MW: Molecular weights in SDS-PAGE without gelatin.

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques: Incubation, SDS Page

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Peptidases from Trichomonas vaginalis found in the band demarcated in the zymogram ( Figure S1 ) and identified by mass spectrometry.

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques: Mass Spectrometry, Molecular Weight, Ubiquitin Proteomics

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: Analysis of the mRNA expression of calpain, cathepsin L, cathepsin D, cathepsin B, Gp63, and MP50 relative to the reference gene ( DNATopII ) in T. vaginalis treated with Cu-phendione. Statistically significant differences: (*) p < 0.05; (**) p < 0.005; (****) p < 0.0001.

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques: Expressing

Journal: Pathogens

Article Title: Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis

doi: 10.3390/pathogens12050745

Figure Lengend Snippet: LDH release by the HMVII and VERO cell lineages after contact with Trichomonas vaginalis a .

Article Snippet: The analysis was performed on a G2-XS Q-TOF Xevo mass spectrometer ® and the identification was based on the genome database of T. vaginalis ( T. vaginalis G3, G3; ATCC PRA-98, WGS project AAHC01000000) held on the ProteinLynx Global Server (PLGS) platform version 2.2.5 and Uniprot database ( https://www.uniprot.org/ , accessed on 9 November 2019).

Techniques:

Journal: Microorganisms

Article Title: Diversity and Antimicrobial Resistance in the Streptococcus bovis / Streptococcus equinus Complex (SBSEC) Isolated from Korean Domestic Ruminants

doi: 10.3390/microorganisms9010098

Figure Lengend Snippet: Maximum-likelihood phylogenetic tree based on sodA nucleotide sequences showing the relationships of all Streptococcus isolates reported in this study with seven representative sodA sequences in SBSEC and the outgroup Staphylococcus aureus CIP65.8 T . The blue square boxes denote the presence of four major types (type I, II, III, and IV) of S. equinus isolates obtained in this study. The scale bar represents 0.02 nucleotide substitutions per site. The five representative genomes are emphasized in bold.

Article Snippet: In this study, we selected and sequenced the whole genome of four representative S. equinus isolates (CNU_G3 which grouped in type II; CNU_G6 which clustered with ATCC 33317 T , that was previously reported as S. bovis in type IV; CNU_77-23 which clustered with the type strain of S. equinus (ATCC 9812 T ) in type IV; and CNU_G2 which was not clustered with any other S. equinus strains used in this study) for the following reasons: First, to elucidate their plasticity and diversity in the S. equinus group, and second, to obtain the reference genomes to determine the genetic determinants related to the production of lactic acid and antimicrobial resistances that could be used for further overall screening in the 51 SBSEC isolates.

Techniques: