Journal: Pathogens

Article Title: Exploration of the Binding Site of Arachidonic Acid in gp63 of Leishmania mexicana and in Orthologous Proteins in Clinically Important Parasites

doi: 10.3390/pathogens13090718

Figure Lengend Snippet: A BLAST search for sequences like L. mexicana gp63 in different parasitic protozoa.

Article Snippet: Entamoeba invadens (ATCC 30994) and Entamoeba dispar (SAW 760) cultures were performed according to ATCC (American Type Culture Collection, Manassas, VA, USA) recommendations and were donated by Dr. Bibiana Chávez Munguía.

Techniques:

Journal: Pathogens

Article Title: Exploration of the Binding Site of Arachidonic Acid in gp63 of Leishmania mexicana and in Orthologous Proteins in Clinically Important Parasites

doi: 10.3390/pathogens13090718

Figure Lengend Snippet: Analysis of RNA-seq data repositories from various parasites including L. mexicana (AMA = intracellular amastigotes; AXA = axenic amastigotes; PRO = promastigotes), T. cruzi , E. histolytica , E. dispar , E. invadens , A. castellanii , and N. fowleri . The figure illustrates the presence of transcripts per million (TPM) of mRNA corresponding to the gp63 protein in L. mexicana and orthologous proteins in the analyzed parasites. The TPM value indicates a relative expression level across the samples. Data for this analysis were from AmoebaDB: http://amoebadb.org/amoeba/ (accessed on 28 September 2023 and TriTrypDB: https://tritrypdb.org (accessed on 28 September 2023). Therefore, to establish a possible functional relationship between orthologous proteins with gp63, a multiple alignment was performed. A shows the alignment of the protein sequences of each parasite. The catalytic site region is indicated on a purple background, and the HExxHAxGF motif, which is conserved across the seven proteins analyzed, can be seen. The sequences of the candidate proteins were examined using the Pfam database to determine the presence of functional domains like the L. mexicana gp63 ( B). The results confirmed that all analyzed sequences share the same domain of the M8 peptidase family. This domain was reported to be present in L. mexicana gp63 . This enzyme is found in eukaryotes, including Leishmania and other protozoan parasites. A domain of the Transcription Factor Immunoglobin (TIG) family, called IPT/TIG, was identified in the E. histolytica protein. This domain is characterized by a fold like that of immunoglobulin and is found in tyrosine kinase receptors such as Met and Ron receptors. In addition, this domain is also present in transcription factors involved in DNA binding ( B).

Article Snippet: Entamoeba invadens (ATCC 30994) and Entamoeba dispar (SAW 760) cultures were performed according to ATCC (American Type Culture Collection, Manassas, VA, USA) recommendations and were donated by Dr. Bibiana Chávez Munguía.

Techniques: RNA Sequencing, Expressing, Functional Assay, Binding Assay

Journal: Pathogens

Article Title: Exploration of the Binding Site of Arachidonic Acid in gp63 of Leishmania mexicana and in Orthologous Proteins in Clinically Important Parasites

doi: 10.3390/pathogens13090718

Figure Lengend Snippet: A phylogenetic tree was constructed for proteins similar to gp63 from L. mexicana . The tree was generated using the complete amino acid sequences of the studied proteins via the neighbor-joining method, employing the phylogenetic inference package (PHYLIP) version 3.5c. The construction utilized the amino acid sequence of gp63 from L. mexicana along with orthologous sequences from various parasites, including L. mexicana (XP_003872886.1), T. cruzi (XP_817808.1), E. histolytica (XP_652632.1), E. dispar (XP_001740726.1), E. invadens (XP_004184102.1), A. castellanii (XP_004337275.1), and N. fowleri (XP_044566011.1).

Article Snippet: Entamoeba invadens (ATCC 30994) and Entamoeba dispar (SAW 760) cultures were performed according to ATCC (American Type Culture Collection, Manassas, VA, USA) recommendations and were donated by Dr. Bibiana Chávez Munguía.

Techniques: Construct, Generated, Sequencing

Journal: Pathogens

Article Title: Exploration of the Binding Site of Arachidonic Acid in gp63 of Leishmania mexicana and in Orthologous Proteins in Clinically Important Parasites

doi: 10.3390/pathogens13090718

Figure Lengend Snippet: Predicted functions of gp63 homologues in Trypanosomatids and Amoeba species.

Article Snippet: Entamoeba invadens (ATCC 30994) and Entamoeba dispar (SAW 760) cultures were performed according to ATCC (American Type Culture Collection, Manassas, VA, USA) recommendations and were donated by Dr. Bibiana Chávez Munguía.

Techniques: Activity Assay, Clinical Proteomics, Membrane, Binding Assay

Journal: Pathogens

Article Title: Exploration of the Binding Site of Arachidonic Acid in gp63 of Leishmania mexicana and in Orthologous Proteins in Clinically Important Parasites

doi: 10.3390/pathogens13090718

Figure Lengend Snippet: Comparing the three-dimensional structures of proteins orthologous to L. mexicana gp63. The 3D structures of the analyzed proteins were modeled using the Swiss model. Subsequently, the overlap analysis of these structures was conducted using TopMatch-web. In the visual representation, structurally aligned sequences are highlighted in orange and red to indicate a match, while dissimilar structures are depicted in green or blue. ( A ) Comparative analysis between L. major (PDB ID: LML1) and L. mexicana (XP_003872886.1) is illustrated. ( B ) Comparison between the leishmanolysin (PDB ID: LML1) of L. major and protein XP_817808.1 of T. cruzi is shown. ( C ) Sequences from the genus Entamoeba ( E. histolytica XP_652632.1, E. dispar XP_001740726, and E. invadens XP_004184102.1) are compared with the leishmanolysin (PDB ID: LML1) from L. major . ( D ) Comparative analysis with free-living amoebae, A. castellanii and N. fowleri (XP_004337275.1, XP_044566011.1), respectively, is presented.

Article Snippet: Entamoeba invadens (ATCC 30994) and Entamoeba dispar (SAW 760) cultures were performed according to ATCC (American Type Culture Collection, Manassas, VA, USA) recommendations and were donated by Dr. Bibiana Chávez Munguía.

Techniques: Comparison

Journal: Pathogens

Article Title: Exploration of the Binding Site of Arachidonic Acid in gp63 of Leishmania mexicana and in Orthologous Proteins in Clinically Important Parasites

doi: 10.3390/pathogens13090718

Figure Lengend Snippet: Values of the superposition of the structure’s analysis. (Length) The number of pairs of residues that are structurally equivalent; (QC %) Query cover based on alignment length, expressed in percent; (TC %) Target cover based on alignment length, expressed in percent; (Score) Measure of structural similarity; (RMS) Root-mean-square error of the superposition in Ångströms; and (SI %) Sequence identity of the query and target in the equivalent regions, expressed in percent.

Article Snippet: Entamoeba invadens (ATCC 30994) and Entamoeba dispar (SAW 760) cultures were performed according to ATCC (American Type Culture Collection, Manassas, VA, USA) recommendations and were donated by Dr. Bibiana Chávez Munguía.

Techniques: Sequencing

Journal: Pathogens

Article Title: Exploration of the Binding Site of Arachidonic Acid in gp63 of Leishmania mexicana and in Orthologous Proteins in Clinically Important Parasites

doi: 10.3390/pathogens13090718

Figure Lengend Snippet: Molecular docking between arachidonic acid (AA) and each studied target. ( A ) Displays overlapping structures of L. major with each model obtained by homology modeling. The surface of the ligand is highlighted in purple. ( B ) Provides an expanded view of the catalytic site of L. mexicana , showcasing the superposition of each obtained ligand. The ligands showing affinity for the catalytic site of the molecular docking study are represented as follows: light blue for L. mexicana , light green for T. cruzi , gray for E. histolytica , yellow for E. dispar , blue for E. invadens , red for A. castellanii , and dark green for N. fowleri .

Article Snippet: Entamoeba invadens (ATCC 30994) and Entamoeba dispar (SAW 760) cultures were performed according to ATCC (American Type Culture Collection, Manassas, VA, USA) recommendations and were donated by Dr. Bibiana Chávez Munguía.

Techniques:

Journal: Pathogens

Article Title: Exploration of the Binding Site of Arachidonic Acid in gp63 of Leishmania mexicana and in Orthologous Proteins in Clinically Important Parasites

doi: 10.3390/pathogens13090718

Figure Lengend Snippet: ( A ) Multiple sequence alignments of proteins like the L. mexicana gp63 protein (XP_003872886.1) alongside counterparts from T. cruzi (XP_817808.1), E. histolytica (XP_652632.1), E. dispar (XP_001740726.1), E. invadens (XP_004184102.1), A. castellanii (XP_004337275.1), and N. fowleri (XP_044566011.1). The alignment, generated using Uniprot online platform, highlights highly conserved or identical residues in red. The green shading indicates identical residues, while light brown and yellow denotes moderately and low conserved residues, respectively. Red letters within blue boxes represent regions within 10 Å of the zinc atom, while the purple background highlights the catalytic site. ( B ) Conserved domains in proteins homologous to gp63. All examined proteins contain the leishmanolysin domain, belonging to the M8 peptidase family, spanning specific regions: 46–570 in L. mexicana , 58–510 in T. cruzi , 27–490 in E. histolytica , 28–490 in E. dispar , 32–423 in E. invadens , 103–406 in A. castellanii , and 222–632 in N. fowleri .

Article Snippet: Entamoeba invadens (ATCC 30994) and Entamoeba dispar (SAW 760) cultures were performed according to ATCC (American Type Culture Collection, Manassas, VA, USA) recommendations and were donated by Dr. Bibiana Chávez Munguía.

Techniques: Sequencing, Generated

Journal: Pathogens

Article Title: Exploration of the Binding Site of Arachidonic Acid in gp63 of Leishmania mexicana and in Orthologous Proteins in Clinically Important Parasites

doi: 10.3390/pathogens13090718

Figure Lengend Snippet: Binding energies and molecular interactions of AA with parasite targets. Catalytic site residues are highlighted in blue for glutamate and in red for histidine. Residues shown in black represent amino acids that interacted with AA within a 5 Å radius.

Article Snippet: Entamoeba invadens (ATCC 30994) and Entamoeba dispar (SAW 760) cultures were performed according to ATCC (American Type Culture Collection, Manassas, VA, USA) recommendations and were donated by Dr. Bibiana Chávez Munguía.

Techniques: Binding Assay

Journal: Pathogens

Article Title: Exploration of the Binding Site of Arachidonic Acid in gp63 of Leishmania mexicana and in Orthologous Proteins in Clinically Important Parasites

doi: 10.3390/pathogens13090718

Figure Lengend Snippet: E. histolytica , E. dispar , and E. invadens exhibit COX-like activity. ( A ) COX activity detection in the genus Entamoeba involved using a commercial kit and exogenous AA in soluble fractions (50 µg protein/25 µL). ( B – D ) Presence of COX-type activity during the encystment process: n ( Ba ), cyst presence was confirmed by calcofluor staining, with cyst purity validated through DIC microscopy analysis ( Bb ). This sample represents the 48-hour encystment process. COX-type activity determination during encystment utilized the commercial kit and exogenous AA, with trophozoite and cyst extracts’ soluble fractions tested using exogenous AA at a final concentration of 20 µM ( C ). In ( Da ), gp63 presence in 48-hour-induced cysts was observed using anti- Leishmania major gp63 monoclonal antibody (CEDARLANE Laboratories Limited, Cat. No. CLP005A, Burlington, Ontario, CA), with the reaction developed through incubation with anti-mouse IgG coupled to FITC. Sample purity was analyzed through DIC microscopy ( Db ). Three independent biological replicates were conducted in triplicate p ≤ 0.01 **, p ≤ 0.001 ***.

Article Snippet: Entamoeba invadens (ATCC 30994) and Entamoeba dispar (SAW 760) cultures were performed according to ATCC (American Type Culture Collection, Manassas, VA, USA) recommendations and were donated by Dr. Bibiana Chávez Munguía.

Techniques: Activity Assay, Staining, Microscopy, Concentration Assay, Incubation

Journal: Cell Reports Medicine

Article Title: Bone transport induces the release of factors with multi-tissue regenerative potential for diabetic wound healing in rats and patients

doi: 10.1016/j.xcrm.2024.101588

Figure Lengend Snippet:

Article Snippet: Rabbit monoclonal anti-PGP9.5 , Cell Signaling Technology , 33575; RRID: AB_3099461.

Techniques: Recombinant, cDNA Synthesis, Expressing, Software, Imaging

Journal: BMC Plant Biology

Article Title: Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium

doi: 10.1186/s12870-024-04818-x

Figure Lengend Snippet: Inventory of Methylobacterium strains examined for glyphosate sensitivity

Article Snippet: Freeze-dried cultures of Methylobacterium spp . were obtained from four microbe collections: the Belgian Coordinated Collections of Microorganisms (BCCM/LMG), the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) [“German Collection of Microorganisms and Cell Cultures”], the Japan Collection of Microorganisms (JCM), and the National Institute of Technology and Evaluation’s (NITE) Biological Resource Center (NBRC).

Techniques: Isolation

Journal: BMC Plant Biology

Article Title: Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium

doi: 10.1186/s12870-024-04818-x

Figure Lengend Snippet: Average ( n = 3) zone of inhibition of each tested strain of Methylobacterium spp. (Table ) against maximum and minimum concentrations glyphosate (380 µg and 95 µg, respectively) in the WeatherMax ® [left] and the Transorb ® [right] products tested

Article Snippet: Freeze-dried cultures of Methylobacterium spp . were obtained from four microbe collections: the Belgian Coordinated Collections of Microorganisms (BCCM/LMG), the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) [“German Collection of Microorganisms and Cell Cultures”], the Japan Collection of Microorganisms (JCM), and the National Institute of Technology and Evaluation’s (NITE) Biological Resource Center (NBRC).

Techniques: Inhibition

Journal: BMC Plant Biology

Article Title: Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium

doi: 10.1186/s12870-024-04818-x

Figure Lengend Snippet: Representative photograph illustrating zone of inhibition of Methylobacterium gnaphali (NBRC 107716) to four concentrations of Transorb ® [left] and WeatherMax ® [right]

Article Snippet: Freeze-dried cultures of Methylobacterium spp . were obtained from four microbe collections: the Belgian Coordinated Collections of Microorganisms (BCCM/LMG), the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) [“German Collection of Microorganisms and Cell Cultures”], the Japan Collection of Microorganisms (JCM), and the National Institute of Technology and Evaluation’s (NITE) Biological Resource Center (NBRC).

Techniques: Inhibition

Journal: BMC Plant Biology

Article Title: Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium

doi: 10.1186/s12870-024-04818-x

Figure Lengend Snippet: Cell viability test ( n = 1) of each strain of Methylobacterium spp. against two concentrations of the Transorb ® (Tsorb) and WeatherMax ® (WMax) product formulations. Negative control involved nutrient-rich trypic soy broth (TSB) with no addition of commercial products

Article Snippet: Freeze-dried cultures of Methylobacterium spp . were obtained from four microbe collections: the Belgian Coordinated Collections of Microorganisms (BCCM/LMG), the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) [“German Collection of Microorganisms and Cell Cultures”], the Japan Collection of Microorganisms (JCM), and the National Institute of Technology and Evaluation’s (NITE) Biological Resource Center (NBRC).

Techniques: Negative Control, Control

Journal: BMC Plant Biology

Article Title: Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium

doi: 10.1186/s12870-024-04818-x

Figure Lengend Snippet: Cell viability test ( n = 2) of each strain of Methylobacterium spp. against two concentrations of pure glyphosate (GLY), with and without Tween20 (polysorbate-20). Negative control involved nutrient-rich trypic soy broth (TSB) with no addition of glyphosate or Tween20

Article Snippet: Freeze-dried cultures of Methylobacterium spp . were obtained from four microbe collections: the Belgian Coordinated Collections of Microorganisms (BCCM/LMG), the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) [“German Collection of Microorganisms and Cell Cultures”], the Japan Collection of Microorganisms (JCM), and the National Institute of Technology and Evaluation’s (NITE) Biological Resource Center (NBRC).

Techniques: Negative Control, Control

Journal: BMC Plant Biology

Article Title: Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium

doi: 10.1186/s12870-024-04818-x

Figure Lengend Snippet: Representative photograph illustrating results of cell viability test from cultures containing 0.1% pure glyphosate (1 mg/mL) with Methylobacterium gnaphali (NBRC 107716) with varying concentrations of Tween20 (polysorbate-20); ( A ) control, ( B ) 0.5%, ( C ) 1.0%, ( D ) 2.0%, ( E ) 4.0% (v/v). Frame ( A ) depicts confluent growth of NBRC 107716

Article Snippet: Freeze-dried cultures of Methylobacterium spp . were obtained from four microbe collections: the Belgian Coordinated Collections of Microorganisms (BCCM/LMG), the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) [“German Collection of Microorganisms and Cell Cultures”], the Japan Collection of Microorganisms (JCM), and the National Institute of Technology and Evaluation’s (NITE) Biological Resource Center (NBRC).

Techniques: Control

Journal: BMC Plant Biology

Article Title: Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium

doi: 10.1186/s12870-024-04818-x

Figure Lengend Snippet: Graphical representation of dry pellet weight of three distinct Methylobacterium strains when cultured in tryptic soy broth (TSB) containing a fixed quantity of pure glyphosate (0.1% w/v) in relation to changes in the presence of Tween20 (polysorbate-20), relative to controls containing Tween20 alone ( n = 4). The Student’s t-test was used to assess statistical difference between groups. A star (*) indicates statistical difference in pellet weight between control conditions (TSB only) and following the application of a treatment ( p < 0.05 = *, p < 0.01 = **, p < 0.001 = ***). A dagger (†) indicates statistical difference comparing pellet weight between the application of Tween20 and the corresponding application of Tween20 with the addition of glyphosate ( p < 0.05 = †, p < 0.01 = ††, p < 0.001 = †††)

Article Snippet: Freeze-dried cultures of Methylobacterium spp . were obtained from four microbe collections: the Belgian Coordinated Collections of Microorganisms (BCCM/LMG), the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) [“German Collection of Microorganisms and Cell Cultures”], the Japan Collection of Microorganisms (JCM), and the National Institute of Technology and Evaluation’s (NITE) Biological Resource Center (NBRC).

Techniques: Cell Culture, Control

Journal: BMC Plant Biology

Article Title: Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium

doi: 10.1186/s12870-024-04818-x

Figure Lengend Snippet: Graphical representation of average pellet fresh weight (line, right axis) of three distinct Methylobacterium strains when cultured in tryptic soy broth (TSB) containing fixed quantities of the active ingredient (AI), glyphosate, obtained from the Transorb ® commercial product, and corresponding intracellular formaldehyde concentrations (bar, left axis) after 4 days of growth at 27 o C ( n = 4)

Article Snippet: Freeze-dried cultures of Methylobacterium spp . were obtained from four microbe collections: the Belgian Coordinated Collections of Microorganisms (BCCM/LMG), the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) [“German Collection of Microorganisms and Cell Cultures”], the Japan Collection of Microorganisms (JCM), and the National Institute of Technology and Evaluation’s (NITE) Biological Resource Center (NBRC).

Techniques: Cell Culture

Journal: BMC Plant Biology

Article Title: Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium

doi: 10.1186/s12870-024-04818-x

Figure Lengend Snippet: Schematic illustrating basic metabolic pathways that may lead to increased intracellular formaldehyde load in Methylobacterium spp

Article Snippet: Freeze-dried cultures of Methylobacterium spp . were obtained from four microbe collections: the Belgian Coordinated Collections of Microorganisms (BCCM/LMG), the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) [“German Collection of Microorganisms and Cell Cultures”], the Japan Collection of Microorganisms (JCM), and the National Institute of Technology and Evaluation’s (NITE) Biological Resource Center (NBRC).

Techniques: