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Fig. 2 in Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing

Fig. 2. Summary of the tag length distribution following the sequencing of genes from the four samples.

Fig. 9 in Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing

Fig. 9. Pie chart of the distribution of viral abundances in different samples. Note: "%" represents the proportion of the virus in the total community from each sample, and the different colours represent different viruses. A: The primary micropathogens analysed in G1. B: The primary micropathogens analysed in G2. C: The main micropathogens analysed in G3. D: The main micropathogens analysed in G4.

Fig. 4 in Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing

Fig. 4. Venn diagram based on the KEGG Orthology database. Note: DIAMOND was used to compare gene sequences with the KEGG database, and the corresponding metabolic pathway information and KEGG orthology results of the genes were obtained from the KEGG database.

Fig. 6 in New data on Thelohanellus nikolskii Achmerov, 1955 (Myxosporea, Myxobolidae) a parasite of the common carp (Cyprinus carpio, L.): The actinospore stage, intrapiscine tissue preference and molecular sequence

Fig. 6. Phylogenetic position of Thelohanellus nikolskii spores from the fins and scales of common carp based on SSU rDNA analysis by the Maximum Likelihood algorithm. Myxobolus cerebralis was used as the outgroup. Bootstrap values are given at the nodes. The scale-bar indicates the number of expected substitutions per site.

Fig. 1 in Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing

Fig. 1. The genomic DNA library was generated according to the PacBio Sequel sample preparation instructions.

Fig. 5 in New data on Thelohanellus nikolskii Achmerov, 1955 (Myxosporea, Myxobolidae) a parasite of the common carp (Cyprinus carpio, L.): The actinospore stage, intrapiscine tissue preference and molecular sequence

Fig. 5. Microphotograph of fresh, unstained actinospore of Aurantiactinomyxon type (AUM5) from Nais sp. Insert – apical view of spore with protruding polar capsules.

Fig. 7 in New data on Thelohanellus nikolskii Achmerov, 1955 (Myxosporea, Myxobolidae) a parasite of the common carp (Cyprinus carpio, L.): The actinospore stage, intrapiscine tissue preference and molecular sequence

Fig. 7. Schematic illustration of T. nikolskii life cycle: Aurantiactinomyxon-type actinospores (A) infect the vertebrate host C. carpio (V) in which they develop myxospores (M) that infect the invertebrate host Nais sp. (I).

Fig. 2. A in New data on Thelohanellus nikolskii Achmerov, 1955 (Myxosporea, Myxobolidae) a parasite of the common carp (Cyprinus carpio, L.): The actinospore stage, intrapiscine tissue preference and molecular sequence

Fig. 2. A: Section of an infected fin, containing T. nikolskii cysts, stained with hematoxilin-eosin. Cartilage of finray (cf) is next to the cyst. Plasmodium (p) is in the achromatic tegument, mature myxospores (s) are in the middle, sporoblasts (sb) are at the edges. Around the plasmodium, there is a thick connective tissue (ct) layer, containing cartilaginous elements (c). Multilayer epithelium (e) is the outer layer. B: T. nikolskii myxospores from the plasmodium.

Fig. 4. A in New data on Thelohanellus nikolskii Achmerov, 1955 (Myxosporea, Myxobolidae) a parasite of the common carp (Cyprinus carpio, L.): The actinospore stage, intrapiscine tissue preference and molecular sequence

Fig. 4. A: Cross section of infected scales, stained with hematoxilin-eosin. The plasmodia (p) are filled with myxospores (s) and are surrounded by cartilaginous tissue (c) of the scales, covered by the epithelium layer (e). B: T. nikolskii myxospores from a plasmodium in the scale.

Fig. 4 in The neglected diversity: Description and molecular characterisation of Trypanosoma haploblephari Yeld and Smit, 2006 from endemic catsharks (Scyliorhinidae) in South Africa, the first trypanosome sequence data from sharks globally

Fig. 4. Bayesian Inference (BI)/Maximum Likelihood (ML) analysis showing the phylogenetic position of Trypanosoma haploblephari (Yeld and Smit, 2006) genotypes representing morphotypes A and B inferred from partial 18S rRNA gene sequences. Comparative sequences representing known Trypanosoma species, with Trypanosoma avium (KT728402) as outgroup, were obtained from GenBank. Tree topologies for both the BI and ML trees were identical; the nodal support values (BI/ML) are represented on the BI tree. Some branches have been shortened with each //= 0.04 substitutions per site.

Fig. 3 in The neglected diversity: Description and molecular characterisation of Trypanosoma haploblephari Yeld and Smit, 2006 from endemic catsharks (Scyliorhinidae) in South Africa, the first trypanosome sequence data from sharks globally

Fig. 3. Micrographs of Trypanosoma haploblephari (Yeld and Smit, 2006) morphotype A (A–C) and T. haploblephari morphotype B (D–F) in Giemsa-stained blood films of Haploblepharus pictus and Poroderma pantherinum, respectively. Blood stage with kinetoplast (k) and undulating membrane (μm) visible (A–C); slender forms (B, E); presence of a flagellum (f) in deeply stained individuals (C, F). Scale bar: 10 μm.

Fig. 2 in The neglected diversity: Description and molecular characterisation of Trypanosoma haploblephari Yeld and Smit, 2006 from endemic catsharks (Scyliorhinidae) in South Africa, the first trypanosome sequence data from sharks globally

Fig. 2. Line drawing of Trypanosoma haploblephari (Yeld and Smit, 2006) from the host Poroderma pantherinum (Slide HE18-18) next to a drawing of a red blood cell.

Fig. 5 in Sequence of post-moult exoskeleton hardening preserved in a trilobite mass moult assemblage from the Lower Ordovician Fezouata Konservat-Lagerstätte, Morocco

Fig. 5. Mid-moult specimen of Limulus polyphemus Linnaeus, 1758 (YPMIZ 55597), Recent, USA, in dorsal (A1), ventral (A2), and anterior (A3) views. The moult is fully hardened and shows a robust convex exoskeleton, whereas the carcass partially emerged but trapped within the old exoskeleton shows extensive lateral wrinkling of its new exoskeleton (arrowed). Photo Russell Bicknell.

Fig. 1 in Sequence of post-moult exoskeleton hardening preserved in a trilobite mass moult assemblage from the Lower Ordovician Fezouata Konservat-Lagerstätte, Morocco

Fig. 1. Trilobite referred to Symphysurus ebbestadi Gutiérrez-Marco, Rábano, and García-Bellido, 2018, from the early Ordovician of Morocco (Tigzigzaouine area), in dorsal views, under standard lighting. A. MGL 102127. B. MGL 102128. C. MGL 102129. D. MGL 102130; D2 close up of thorax axial rings in D1, showing the clear terrace ridges. E. MGL 102131. F. MGL 102132. G. MGL 102133. H. MGL 102134. I. MGL 102135. Scale bars 5 mm.

Fig. 4 in Sequence of post-moult exoskeleton hardening preserved in a trilobite mass moult assemblage from the Lower Ordovician Fezouata Konservat-Lagerstätte, Morocco

Fig. 4. Graphs showing means (points) and ranges of exoskeleton thickness for cephala (A) and thoraces (B) of the thin sectioned trilobites Symphysurus ebbestadi.

Fig. 3 in Sequence of post-moult exoskeleton hardening preserved in a trilobite mass moult assemblage from the Lower Ordovician Fezouata Konservat-Lagerstätte, Morocco

Fig. 3. Thin sections showing the cuticular structure of trilobites Symphysurus ebbestadi Gutiérrez-Marco, Rábano and García-Bellido 2018, from the early Ordovician of Tigzigzaouine area, Morocco. A. MGL 102127, the putative moult. B. MGL 102130, a fully-hardened individual. C. MGL 102133, individual with medium levels of wrinkling. D. MGL 102134, the most wrinkled individual. A1–D1, anterodorsal sections through the cephalon (except C1, transverse section); A2–D2, anterodorsal sections through the thorax. Scale bars 1 mm.

Fig. 2 in Sequence of post-moult exoskeleton hardening preserved in a trilobite mass moult assemblage from the Lower Ordovician Fezouata Konservat-Lagerstätte, Morocco

Fig. 2. Wrinkled specimens of trilobite Symphysurus ebbestadi Gutiérrez-Marco, Rábano, and García-Bellido 2018, from the early Ordovician of Tigzigzaouine area, Morocco, photographed under low-angle incident lighting, in order to emphasise the three-dimensional surface texture of their exoskeletons. Specimens are organised in relative order of exoskeleton hardening, from that with the most wrinkled and soft exoskeleton (A) to the least wrinkled (D) before being fully hardened. A. MGL 102132. B. MGL 102134. C. MGL 102128. D. MGL 102133. Scale bars 5 mm.

opencc-zeroJul 2024View details →

Deep Learning Neural Network Development for the Classification of Bacteriocin Sequences Produced by Lactic Acid Bacteria

This project contains the following underlying data: <h3>      Software-Related Files</h3>                ·         BacLABNet_script.ipynb (Deep Learning Neural Network for classification of Bacteriocin Sequences)                 ·         embed_proteins.py (Recurrent Neural Network to obtained the embedding vectors)                ·         model_I22.h5 (This file contains the trained weights of the trained model)                ·         model_I22.json (This file contains the structure of the trained model)                ·         rnn_gru.pt (Initial weights of the Recurrent Neural Network to obtain embedding vectors)                ·         List_kmers.csv (List of 5-mers and 7-mers obtained from dataset after it filtered sequences shorter than 50 aa and                           longer than 2000 aa)                     Files Used for Training, Testing, and Validation of the Neural Network                ·         data_nonBacLAB.csv (25000 nonBacLAB amino acid sequences retrieved from Uniprot)                ·         data_BacLAB.csv (24964 BacLAB amino acid sequences retrieved from Uniprot)              Additional Files                 ·         data_BacLAB_and_nonBacLAB.csv (Combination of sequences from data_BacLAB.csv and data_nonBacLAB.csv)                  ·         all k.mers list.xlsx (Table of all k-mers obtained for k=3,5,7,15,20)   Note: Codes are additionally available on GitHub.  Data are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication)(http://creativecommons.org/publicdomain/zero/1.0/)

opencc-by-4.0Aug 2023View details →

Fig. 2 in Diversity of fecal parasitomes of wild carnivores inhabiting Korea, including zoonotic parasites and parasites of their prey animals, as revealed by 18S rRNA gene sequencing

Fig. 2. Relative abundance of all parasite genera detected from fecal samples of wild carnivores in Korea. The relative abundance of each parasite is defined as the ratio of the number of sequence reads assigned to that parasite to the total number of sequence reads assigned to all target parasites.