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Bioinformatics (Oxford, England) Sep 2023We present an interactive Deep Learning-based software tool for Unsupervised Clustering of DNA Sequences (iDeLUCS), that detects genomic signatures and uses them to...
SUMMARY
We present an interactive Deep Learning-based software tool for Unsupervised Clustering of DNA Sequences (iDeLUCS), that detects genomic signatures and uses them to cluster DNA sequences, without the need for sequence alignment or taxonomic identifiers. iDeLUCS is scalable and user-friendly: its graphical user interface, with support for hardware acceleration, allows the practitioner to fine-tune the different hyper-parameters involved in the training process without requiring extensive knowledge of deep learning. The performance of iDeLUCS was evaluated on a diverse set of datasets: several real genomic datasets from organisms in kingdoms Animalia, Protista, Fungi, Bacteria, and Archaea, three datasets of viral genomes, a dataset of simulated metagenomic reads from microbial genomes, and multiple datasets of synthetic DNA sequences. The performance of iDeLUCS was compared to that of two classical clustering algorithms (k-means++ and GMM) and two clustering algorithms specialized in DNA sequences (MeShClust v3.0 and DeLUCS), using both intrinsic cluster evaluation metrics and external evaluation metrics. In terms of unsupervised clustering accuracy, iDeLUCS outperforms the two classical algorithms by an average of ∼20%, and the two specialized algorithms by an average of ∼12%, on the datasets of real DNA sequences analyzed. Overall, our results indicate that iDeLUCS is a robust clustering method suitable for the clustering of large and diverse datasets of unlabeled DNA sequences.
AVAILABILITY AND IMPLEMENTATION
iDeLUCS is available at https://github.com/Kari-Genomics-Lab/iDeLUCS under the terms of the MIT licence.
Topics: Base Sequence; Deep Learning; Algorithms; Archaea; Cluster Analysis
PubMed: 37589603
DOI: 10.1093/bioinformatics/btad508 -
Scientific Data Oct 2023Calcite shells of planktic foraminifera (Protista, Rhizaria) constitute a large portion of deep-sea sediments. The shells are constructed by sequential addition of...
Calcite shells of planktic foraminifera (Protista, Rhizaria) constitute a large portion of deep-sea sediments. The shells are constructed by sequential addition of partly overlapping chambers with diverse shapes, resulting in complex shell architectures, which are genetically fixed and diagnostic at the species level. The characterisation of the complete architecture requires three-dimensional imaging of the shell, including the partially or entirely covered juvenile chambers. Here we provide reconstructed x-ray micro computed tomography image stacks of 179 specimens of extant planktic foraminifera collected from plankton tows, sediment traps and surface sediments. The specimens have fully resolved and curated taxonomy and represent 43 of the currently recognised 48 holoplanktic species and subspecies. The image stacks form a basis for further applications, such as the characterisation of the architectural morphospace of the extant taxa, allowing studies of species functional ecology, calcification intensity and reconstructions of phylogenetic relationships.
Topics: Ecology; Foraminifera; Phylogeny; X-Ray Microtomography
PubMed: 37798341
DOI: 10.1038/s41597-023-02498-0 -
Frontiers in Microbiology 2023Ciliates serve as excellent indicators for water quality monitoring. However, their utilization is hindered by various taxonomic confusions. The ciliate genus Bory de...
Ciliates serve as excellent indicators for water quality monitoring. However, their utilization is hindered by various taxonomic confusions. The ciliate genus Bory de Saint-Vincent, 1824 is commonly found in different aquatic habitats, but its taxonomy has been sparsely investigated using state-of-the-art methods. This study investigated two new species from Nanhui Wetland, Shanghai, China, using living observation, protargol staining, and molecular phylogeny methods. sp. nov. is 180-340 × 20-25 μm in size and possesses 12-16 somatic kineties, 1 terminal contractile vacuole, 2 macronuclear nodules, and 2 types of rod-shaped extrusomes. sp. nov. is distinguished from its congeners by its cell size of 210-400 × 25-35 μm, 14-17 somatic kineties, 1 terminal contractile vacuole, 1 macronucleus, and 2 types of rod-shaped extrusomes. Phylogenetic analyses based on SSU rRNA gene sequences indicate that Lacrymariidae is monophyletic but is not. Additionally, a brief review of the genus is provided in this study. We suggest that Alekperov, 1984, Kahl, 1930, and Burkovsky, 1970 be removed from the genus and propose nov. comb. and nov. comb. for the latter two. ZooBank registration: Present work: urn:lsid:zoobank.org:pub:CDFB1EBD-80BD-4533-B391-CEE89F62EDC4 sp. nov.: urn:lsid:zoobank.org:act:417E7C2D-DAEC-4711-90BB-64AB3CD2F7D5 sp. nov.: urn:lsid:zoobank.org:act:8778D6B0-1F2E-473C-BE19-3F685391A40D.
PubMed: 38029185
DOI: 10.3389/fmicb.2023.1259653 -
Environmental Science and Pollution... Jan 2024Microplastics (MPs), due to their micro size, which overlaps with the typical food size of various aquatic organisms, can be ingested and move up the food chain,...
Microplastics (MPs), due to their micro size, which overlaps with the typical food size of various aquatic organisms, can be ingested and move up the food chain, accumulating in the bodies of organisms at higher trophic levels. Few studies have focused on the uptake of MPs by ciliates, which are an important element of the microbial cycle. Three different ciliate species were used in this study: Blepharisma japonicum, Euplotes sp., and Spirostomum teres, as well as polystyrene beads with diameters of 1 and 2 µm at two concentrations (10 and 10 beads × mL). The results of the experiments showed that MPs have a variable, species-specific effect on the population growth rate of ciliates, which is directly dependent on their concentration in the environment (P < 0.01). It was also observed that the number of MPs ingested changed over time depending on their concentration and size. On average, the highest number of ingested MPs (883.11 ± 521.47) was recorded at 60 min of exposure to a low concentration of small beads in B. japonicum. The lowest number of beads was ingested after 5 min of exposure to a low concentration of large beads in the same species. The rate of MP uptake by the ciliate species was significantly dependent on their concentration, exposure time, and size (P < 0.001). The highest clearance rate was observed in the fifth minute of the experiment in the environment with the lowest MP concentration.
Topics: Microplastics; Plastics; Population Growth; Polystyrenes; Ciliophora; Water Pollutants, Chemical
PubMed: 38157169
DOI: 10.1007/s11356-023-31635-w -
Animals : An Open Access Journal From... Mar 2024We have conducted a 10-year-long coprological study of the animals housed in two zoological institutions (ZooAquarium and Faunia, Madrid, Spain) to assess the parasite...
We have conducted a 10-year-long coprological study of the animals housed in two zoological institutions (ZooAquarium and Faunia, Madrid, Spain) to assess the parasite biodiversity, prevalence, and their relation with host class, diet, and enclosure type (soil type and level of isolation from wild fauna). A total of 4476 faecal samples from 132 mammal species and 951 samples from 86 avian species were examined. The results indicated that only 12.8% of avian species had parasites at least once during the study period, whereas 62.1% of mammal species tested positive. Predominantly, protists (, flagellates, and ciliates) and nematodes (mainly ) were identified in the findings. Carnivorous species were primarily infected by nematodes, while herbivorous and omnivorous species were mainly infected by protists. The number of infected herbivorous and omnivorous species was significantly greater than carnivorous species. Differences were observed based on soil type (artificial, natural, mixed) and isolation level (isolated/accessible), but these differences were not statistically significant. Several parasites ( spp., spp., , spp.) could potentially be transmitted between humans and some mammals and birds. Regular animal analyses and a personnel health program in the institutions would minimise transmission risks between zoo animals, wildlife, and humans.
PubMed: 38473198
DOI: 10.3390/ani14050813