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opencc-by-4.0Dec 2023View details →

Fig. 6 in Morphological and molecular phylogenetic characterization of Sarcocystis kani sp. nov. and other novel, closely related Sarcocystis spp. infecting small mammals and colubrid snakes in Asia

Fig. 6. Mapping of (A) potential heme ligand binding sites and (B) amino acid variability among different lineages of tissue cyst-forming coccidia in the barcode area of the mitochondrial COX1 protein. A) Map of putative heme ligand binding sites (arrowheads) in a protein sequence alignment of selected taxa used in the phylogenetic tree of cox1. Identical/conservative aa positions are highlighted by light background, variable positions and gaps are shown against black background. Helix 1 (H1) is shown partial, starting at position 14 of the global barcode alignment (Pentinsaari et al., 2016); aa sequences of helices 2 (H2) and 6 (H6) are shown in full length, while putative heme binding sites of loop 3–4 (L3-4) were in its anterior part only. Domain boundaries and putative ligand binding sites were derived from COX1 of template organisms Saccharomyces cerevisiae and Bos taurus by sequence alignment against Toxoplasma gondii applying three-dimensional homology modelling of protein structure. The complete alignment of the six helices of the barcode area is shown in Supplementary Fig. S2. Note that aa numbering of the barcode area of the Apicomplexan sequence is different to the global alignment, because the former showed one additional aa and domain boundaries were slightly altered. The nucleotide sequence KC209732 of S. tenella (GenBank) is also registered in the barcode reference database BOLD (accession number JRPAA5858-15; http://boldsystems.org); the aa barcode position 14 (Glycine) shown here corresponds to position 16 of the aa translation of GenBank record KC209732. B) 'Heat map' of aa changes (darker shades of green = more changes, number of changes indicated) in the barcode area among chemically/structurally different aa groups in different lineages of tissue cyst-forming coccidia relative to the COX1 protein sequence of T. gondii. Because helix 1 was truncated, records of aa changes in this area are incomplete.

opencc-by-4.0Dec 2022View details →

Fig. 2 in Novel genotypes of Cryptosporidium and Enterocytozoon bieneusi detected in plateau zokors (Myospalax baileyi) from the Tibetan Plateau

Fig. 2. Phylogenetic relationships of E. bieneusi genotypes identified in the present study and other known genotypes deposited on GenBank was inferred by a maximum-likelihood phylogenetic analysis of ITS sequences using the Tamura 3-parameter model with 500 replicates. The Enterocytozoon hepatopenaei (GenBank: KR021167.1) was used as the outgroup. The blue triangle and squares indicate the novel genotypes identified in this study, respectively. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

opencc-by-4.0Dec 2022View details →

Fig. 1 in Novel genotypes of Cryptosporidium and Enterocytozoon bieneusi detected in plateau zokors (Myospalax baileyi) from the Tibetan Plateau

Fig. 1. Phylogenetic relationships of Cryptosporidium sp. genotypes identified in the present study and other known genotypes and species on GenBank was inferred by a maximum-likelihood phylogenetic analysis of SSU rRNA gene sequences using the Tamura 3-parameter model and with 500 replicates. The Eimeria (GenBank: U40264.1) were used as the outgroup. The red circles and squares indicate the novel genotypes identified in this study. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Fig. 5. Phylogenetic tree Note: (A): Maximum likelihood (ML) phylogenetic tree inferred from the mitochondrial genome based on the 13 PCGs dataset; (B): Bayesian inference (BI) phylogenetic tree inferred from the mitochondrial genome based on the 13 PCGs dataset.

Fig. 4 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Fig. 4. Mitochondrial genome organization of Platygaster robiniae and 11 species of Platygastroidea, compared with the ancestral pancrustacean mt genome organization. Note: tRNA genes are indicated by single letter amino acid codes, L1, L2, S1 and S2 denote tRNALeu(CUN), tRNALeu(UUR), tRNASer(AGN) and tRNASer(UCN), respectively. Genes are transcribed from left to right except those indicated by underlining. Gene movements, relative to the ancestral organization, are indicated with arrows.

Fig. 2 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Fig. 2. Amino acids (A) and relative synonymous codons (B) of protein-coding genes of the mitochondrial genome of Platygaster robiniae.

Fig. 1 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Fig. 1. Genetic map of the complete mitochondrial genome of Platygaster robiniae. Notes: the blue arrow represents the direction of gene transcription; the black peak represents the deviation of GC%; the purple and green peaks represent the deviation in GC skew; green refers to positive skew, and purple indicates negative skew. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

opencc-by-4.0Apr 2022View details →

Fig. 3 in A novel intermediate host for Taenia serialis (Gervais, 1847): The European roe deer (Capreolus capreolus L. 1758) from the Monti Sibillini National Park (MSNP), Italy

Fig. 3. Phylogenetic relationships between two species of Taenia (T. serialis and T. multiceps) and the sample obtained for this study (sample from roe deer).

opencc-by-4.0Apr 2022View details →

Fig. 1. Microscope view 100 in A novel intermediate host for Taenia serialis (Gervais, 1847): The European roe deer (Capreolus capreolus L. 1758) from the Monti Sibillini National Park (MSNP), Italy

Fig. 1. Microscope view 100 magnifications of the scolex collected from one of the cysts recovered in a wild European roe deer.

opencc-by-4.0Apr 2022View details →

Fig. 2 in A novel intermediate host for Taenia serialis (Gervais, 1847): The European roe deer (Capreolus capreolus L. 1758) from the Monti Sibillini National Park (MSNP), Italy

Fig. 2. Note the meningeal vessels' congestion and the suppurative exudate covering the meningeal surface.

opencc-by-4.0Aug 2023View details →

Fig. 1 in Molecular detection and characterization of a novel Theileria genotype in Dama Gazelle (Nanger dama)

Fig. 1. Phylogenetic analyses of sequence data for 393bp 18S rRNA gene of Theileria spp. in gazelles by Maximum Likelihood method with bootstrap of 1000 replications using MEGA software version10.

opencc-by-4.0Jun 2024View details →

Inducing Novel Endosymbioses by Bacteria Implantation into Fungi

The data in this repository was incorporated in the manuscript "Inducing Novel Endosymbioses by Bacteria Implantation into Fungi". The repository contains the original FACS data collected for the study, the GraphPad Prism file used to generate the plots and statistics, and the raw image data used in the figures, extended data figures, LC MS MS data, and SI Videos 1-4. The raw data for SI Videos 5-8 was too large and can be found in a second repository (10.5281/zenodo.12189101). A FlowJo workplace with approximate gating which was used for the analysis of the data to extract the numbers used in the study is also added. Note that the workplace had to be recreated to collect all the samples in the same workplace and the gating might have been slightly different for the initial analysis and may have yielded slight, if only minor changes in the exact output. The exact numbers used in the study can be found in the file Suppl Data Zenodo.xlsx and in the source data of the publication.

opencc-by-4.0Aug 2024View details →

Detection of novel P. falciparum haplotypes under treatment pressure in pediatric severe malaria

The dataset contains Amplicon sequencing data targeting three Plasmodium falciparum polymorphic markers—cpmp, cpp, and ama1. These markers were analyzed to investigate the association between parasite clearance rate and the multiplicity of infection in Beninese children undergoing treatment for severe malaria.

Fig. 11. Plectanocotyle jeanloujustinei n in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden

Fig. 11. Plectanocotyle jeanloujustinei n. sp. ex Chelidonichthys lastoviza from the western Mediterranean. Detail of the reproductive organs in the region of ovary, ventral view (HEL 1715).

Fig. 10. Plectanocotyle jeanloujustinei n in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden

Fig. 10. Plectanocotyle jeanloujustinei n. sp. ex Chelidonichthys lastoviza from the western Mediterranean. Disposition of clamps sclerites. A, Dorsal jaw. B, Ventral jaw. C, Clamp, dorsal view (HEL 1713).

Fig. 9. Plectanocotyle jeanloujustinei n in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden

Fig. 9. Plectanocotyle jeanloujustinei n. sp. ex Chelidonichthys lastoviza from the western Mediterranean. A, Body, holotype, ventral view (HEL 1721). B, Clamp, hologenophore, ventral view (HEL 1731). C, Clamp, paratype, dorsal view (HEL 1717). D, terminal lappet, paratype (HEL 1717). E, Anterior end showing male copulatory organ, paratype, ventral view (HEL 1720). F, Egg, paratype (HEL 1714).

Fig. 4 in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden

Fig. 4. Tree inferred using the ML method based on the cox1 sequence data; only bootstrap values higher than 70 are indicated. The newly generated sequences of Plectanocotyle gurnardi sensu stricto are indicated in blue. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 8 in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden

Fig. 8. Plectanocotyle gurnardi (Van Beneden and Hesse, 1863) sensu stricto ex Eutrigla gurnardus from the North Sea, Sweden, Detail of the reproductive organs in the region of ovary, ventral view (SMNH 216584).

Fig. 5 in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden

Fig. 5. Tree inferred using the ML method based on the 28S rDNA sequence data; only bootstrap values higher than 70 are indicated. The newly generated sequences are indicated in bold. All sequences of Plectanocotyle gurnardi from the type-host Eutrigla gurnardus clustered in a single clade. * The polyopisthocotylean parasite annotated on GenBank as "Plectanocotyloides obscurum"; the host as "Aspitrigla obscura".

Fig. 3. Plectanocotyle jeanloujustinei n in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden

Fig. 3. Plectanocotyle jeanloujustinei n. sp. ex Chelidonichthys lastoviza from the western Mediterranean (Algeria), hologenophores. A-E, Body lacking only the haptor. F. Body lacking a lateral part posterior part. G-H, anterior end of the body including the male copulatory organ. The missing parts were excised and used for DNA extraction. A, (HEL1729). B, (HEL1730). C, (HEL1732). D, (HEL1733). E, (HEL1734). F, (HEL1731). G, (HEL1727). H, (HEL17287).