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open access
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ISSN : 1225-3480
The PANM database (Protostome DB) is a public repository of protein sequences available from the Protostomia group (includes Arthropoda, Mollusca, and Nematoda). The latest version of PANM DB v5.0 (released in 2022) contained 21,276,123 protein sequences that comprised 4% of the total NCBInr protein data. In this study, an update of PANM DB, i.e., version 5.1, is presented that could accurately analyze the large-scale transcriptome data of molluscs for the contaminating fungal gene sequences. This version can filter out the fungal genes, thereby restricting the annotation to molluscs-only sequences. Using the database, we confirmed 1,589,546 amino acid sequences from 32 fungal species, which can be essentially filtered from the unigenes of 20 species of endangered molluscs. In general, the updated version of PANM DB is expected to enhance the accuracy of bioinformatics analyses of invertebrate NGS data, providing a valuable resource for researchers. PANM version 5.1 can be downloaded for free at https://panm.sch.ac.kr/ for local BLAST analysis.
Observation and division of sedimentary facies, and establishment of molluscan fossil assemblage in 5 sediment horizons of the early Middle Miocene sediment body (Shinhyeon Formation of Ulsan Basin) distributed at Kangdong-dong, Ulsan City, conducted to understand the mechanism of development and changing history of molluscan fossil assemblages. Sedimentary facies and Molluscan fossil assemblages composed of composed of 7 types (facies 1-7) and, Crassostrea assembage (layer I) - Vicarya-Cultellus assemblage (layer II) - Crassostrea assemblage (layer III) - Vicarya-Cultellus asemblage (layer IV) - Vicarya-Tatewaia-Striarca assemblage (layer V) toward upper from lower layer, respectively. Crassostrea assemblage of layer I and III indicating the intertidal-subtidal environment and Vicarya assemblage of layer II, IV and V indicating the marsh-intertidal environment appeared repeatedly. It is caused by the transgression and regression of sea level.
To characterize the contamination state of shellfish farming waters around Saryangdo Island, the surface sediment was evaluated for Acid Volatile Sulfide (AVS), organic matter (ignition loss and chemical oxygen demand), and heavy metals (Al, Cd, Cu, Fe, Ni, Pb and Zn). AVS was relative low all the sampling sites except station 1 influeced by low current velocity at open sea, as well as organic matter was the highest at Station 2 influenced from fish cage. The trace elements (Cd, Cu, Ni, Pb, Zn) showed relatively low level at the narrow channel in Station 3-6, but the highest at Station 7 near Gumpyeong port in Saryang Island. The concetration of metal was satisfied the criteria of TEL and PEL in all metal elements. For Igeo, Zn was strongly polluted at all stations, as well as, the sediments were polluted with excess of 1.0 for PLI. ERI represented realtively low risk at all sampling sites. The finding indicated that the study waters was relatively low contaminated because of low sedimentation at narrow channel between Sarayng Islands.
When abalones were farmed in a Recirculating Aquaculture System (RAS) with inadequate water conditioning for a long time, the salt concentration gradually increased to more than 36 psu. This study raised abalones in different salt concentrations (30, 33, 36, and 39 psu) in a RAS and examined growth (shell and weight), cumulative mortality, changes in blood components, and histological changes to explore the effect of salt concentration on these parameters. During the two-week experiment, the daily growth rate decreased and the cumulative mortality increased as the salt concentration in the water increased. Concentrations of K+, Na+, and Cl- ions in the hemolymph changed significantly, and the cell mortality of blood cells increased. In addition, histopathological alterations in gill and digestive tubule of the abalone showed more obvious with experimental condition of salinity increase. Based on the results, a salinity of 36 psu or higher is not a suitable environment for the survival of abalones.
This study designed species-specific primers for quick and convenient molecular biological species identification of three species belonging to Architaenioglossa widely distributed in Korea and developed a single triplex PCR primer set by verifying specificity and reproducibility. Species-specific primers were designed to amplify species-specific bands (Pomacea canaliculata, 223 bp; Sinotaia quadrata, 261 bp; Cipangopaludina chinensis malleata, 431 bp) in consideration of positions representing genetic variation within species and between species on the cytochrome c oxidase subunit 1 (co1) gene base sequence of mitochondrial DNA. In addition, conventional PCR verification experiments were performed according to the amplification cycle and concentration range of genomic DNA (gDNA) to verify the amplification efficiency when configuring the triplex PCR primer set. As a result, considering the PCR reaction cycle and sample amount, the minimum PCR reaction cycle and gDNA concentration were found to be each 25 cycles and 10 ng/μL. Therefore, it is judged that the triplex PCR primer set between the three species belonging to Architaenioglossa developed in this study can contribute to accurate species identification in the industrial field with a quick and simple analysis method at the conventional PCR level.