• Asian-Australasian Journal of Animal Sciences
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• v.32 no.12
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• pp.1942-1949
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• 2019

Objective: Leukocyte cell-derived chemotaxin 2 (LECT2) is associated with several physiological processes including inflammation, tumorigenesis, and natural killer T cell generation. Chicken LECT2 (chLECT2) gene was originally identified as one of the differentially expressed genes in chicken kidney tissue, where the chickens were fed with different calcium doses. In this study, the molecular characteristics and gene expression of chLECT2 were analyzed under the stimulation of toll-like receptor 3 (TLR3) ligand to understand the involvement of chLECT2 expression in chicken metabolic disorders. Methods: Amino acid sequence of LECT2 proteins from various species including fowl, fish, and mammal were retrieved from the Ensembl database and subjected to Insilco analyses. In addition, the time- and dose-dependent expression of chLECT2 was examined in DF-1 cells which were stimulated with polyinosinic:polycytidylic acid (poly [I:C]), a TLR3 ligand. Further, to explore the transcription factors required for the transcription of chLECT2, DF-1 cells were treated with poly (I:C) in the presence or absence of the nuclear factor ${\kappa}B$ ($NF{\kappa}B$) and activated protein 1 (AP-1) inhibitors. Results: The amino acid sequence prediction of chLECT2 protein revealed that along with duck LECT2 (duLECT2), it has unique signal peptide different from other vertebrate orthologs, and only chLECT2 and duLECT2 have an additional 157 and 161 amino acids on their carboxyl terminus, respectively. Phylogenetic analysis suggested that chLECT2 is evolved from a common ancestor along with the actinopterygii hence, more closely related than to the mammals. Our quantitative polymerase chain reaction results showed that, the expression of chLECT2 was up-regulated significantly in DF-1 cells under the stimulation of poly (I:C) (p<0.05). However, in the presence of $NF{\kappa}B$ or AP-1 inhibitors, the expression of chLECT2 is suppressed suggesting that both $NF{\kappa}B$ and AP-1 transcription factors are required for the induction of chLECT2 expression. Conclusion: The present results suggest that chLECT2 gene might be a target gene of TLR3 signaling. For the future, the expression pattern or molecular mechanism of chLECT2 under stimulation of other innate immune receptors shall be studied. The protein function of chLECT2 will be more clearly understood if further investigation about the mechanism of LECT2 in TLR pathways is conducted.

• Parasites, Hosts and Diseases
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• v.58 no.6
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• pp.653-660
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• 2020

Spirometra tapeworms (Cestoda: Diphyllobothriidae) collected from carnivorous mammals in Tanzania were identified by the DNA sequence analysis of the mitochondrial cytochrome c oxidase subunit 1 (cox1) and internal transcribed spacer 1 (ITS1), and by morphological characteristics. A total of 15 adult worms were collected from stool samples and carcasses of Panthera leo, Panthera pardus, and Crocuta crocuta in the Serengeti and Selous ecosystems of Tanzania. Three Spirometra species: S. theileri, S. ranarum and S. erinaceieuropaei were identified based on morphological features. Partial cox1 sequences (400 bp) of 10 specimens were revealed. Eight specimens showed 99.5% similarity with Spirometra theileri (MK955901), 1 specimen showed 99.5% similarity with the Korean S. erinaceieuropaei and 1 specimen had 99.5% similarity with Myanmar S. ranarum. Sequence homology estimates for the ITS1 region of S. theileri were 89.8% with S. erinaceieuropaei, 82.5% with S. decipiens, and 78.3% with S. ranarum; and 94.4% homology was observed between S. decipiens and S. ranarum. Phylogenetic analyses were performed with 4 species of Spirometra and 2 species of Dibothriocephalus (=Diphyllobothrium). By both ML and BI methods, cox1 and ITS1 gave well supported, congruent trees topology of S. erinaceieuropaei and S. theileri with S. decipiens and S. ranarum forming a clade. The Dibothriocephalus species were sisters of each other and collectively forming successive outgroups. Our findings confirmed that 3 Spirometra species (S. theileri, S. ranarum, and S. erinaceieuropaei) are distributed in the Serengeti and Selous ecosystems of Tanzania.

• Journal of Marine Life Science
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• v.6 no.2
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• pp.97-105
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• 2021

Tegillarca granosa, is one of the most important fishery resources throughout Asia. However, due to industrialization factories, marine environmental pollution, and global warming, the marine fishery production has drop sharply. In order to understand the genetic factors of the blood clam, which is a major fishery resource on the southern coast of Korea, the whole genome of blood clam was studied. The assembled genome of T. granosa was 915.4 Mb, and 19 chromosomes were identified. 25,134 genes were identified, and 22,745 genes were functionally annotated. As a result of performing gene gain and loss analysis between the blood clam genome and eight other types of shellfish, it was confirmed that 725 gene groups were expanded, and 479 gene groups were contracted. The homeobox gene cluster of blood clam showed a well-preserved genetic structure within lophotrochozoan ancestor. T. granosa genome showed high similarity between three hemoglobin genes with Scarpharca broughtonii. The blood clam genome will provide information for the genetic and physiological characteristics of blood clam adaptation, evolution, and the development of aquaculture industry.

• Journal of the Korean Applied Science and Technology
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• v.39 no.5
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• pp.605-613
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• 2022

The genus Flavobacterium, type genus of the family Flavobacteriaceae and a member of the phylum Bacteriodetes includes gram-negative and yellow-pigmented rods. Those bacteria have been isolated from various environments of the earth. A yellow-pigmented, gram-negative rod was isolated from a pond in the campus of the Changwon University, Changwon, Kyeongnam and designated as strain B1. Strain B1 was further analyzed physiologically, biochemically and phylogenetically, and concluded to be a member of genus Flavobacterium. BLAST search of the 16S rRNA gene sequence of strain B1 shows homology no higher than 99.0% with those sequences of other bacteria. The major fatty acids of strain B1 are iso-C_15:0 (19.6%), summed feature 3(C_16:1 ω7c and/or C_16:1 ω6c, 16.1%), iso-C_17:0 3OH(10.2%), iso-C_15:0 3OH(8.4%) and iso-C_15:1 G(6.6%) showing significant differences in fatty acid compositions between strain B1 and the other known Flavobacterium species. DNA sequence of 16S rRNA gene of strain B1 was deposited in genbank under accession number OP060681.

• Korean Journal of Environmental Biology
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• v.40 no.4
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• pp.387-397
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• 2022

The germination characteristics of the resting cysts of Pheopolykrikos hartmannii collected from the southern coastal sediments of Korea were studied at different temperature conditions, and the morphology and phylogeny of the germlings were examined. The resting cysts of Ph. hartmannii were round and characterized by a red accumulation body and many arrow-like spines and could germinate at temperature of 10 to 30℃. High germination rates (>90%) were observed at 15 and 20℃, indicating that the resting cysts could act as seed populations for the bloom initiation of Ph. hartmannii in Korean coastal waters in early summer or early fall. The morphology of the germlings was generally consistent with the previous description, and an apical groove characterized by a fully enclosed loop was observed. Phylogenetic analysis based on large SubUnit (LSU) rRNA gene sequences revealed that the germlings shared an identical sequence with the Korean and American isolates of Ph. hartmannii and was a sister clade of Polykrikos species.

• Journal of Microbiology and Biotechnology
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• v.33 no.10
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• pp.1292-1298
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• 2023

PAMB 00755^T, a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20℃, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755^T was most closely related to Sphingomonas chungangi MAH-6^T (97.7%) and Sphingomonas polyaromaticivorans B2-7^T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9-81.3%), average amino acid identity (73.3-75.9%), and digital DNA-DNA hybridization (73.3-75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755^T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C_18:1ω7c and/or C_18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755^T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755^T as the type strain (= KCTC 92781^T = GDMCC 1.3779^T).

• Journal of Marine Life Science
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• v.8 no.2
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• pp.128-135
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• 2023

The present study was tried to identify whether the eel's larva was close to a conger (Conger myriaster), a pipe conger (Muraenesox cinereus) or four species of Anguilla. Experimental fishes were collected by set net in the gulf of enggang, Namhae, Korea from May to June. Their morphological characteristics were compared with adult fishes of a conger, a pipe conger and four species of Anguilla. For genetic classification, DNA was isolated and amplified by using 12S rRNA and 16S rRNA primer set. The PCR products were direct sequencing in both directions. The nucleotide sequences were analyzed using softwares. As results of morphological measurement on eel's larva, the percentages of head length and preanal length against total length were similar with a conger. Based on the nucleotide sequences, the phylogenetic tree also revealed a close relationship to a conger. Therefore, eel's larva, caught in Namhae from May to June, was identified into a conger's larva.

• Research in Plant Disease
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• v.30 no.1
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• pp.60-65
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• 2024

In July 2020, total RNA was extracted from passion fruit (Passiflora edulis) leaves showing virus symptoms such as chlorotic spots and vein banding in Haenam, South Korea. Cucumber mosaic virus (CMV)-HN2 was identified through reverse transcription polymerase chain reaction and sequencing analysis. To confirm the biological characteristics of the CMV infecting passion fruit, 10 indicator plants were inoculated with CMV-HN2, and the results showed a typical CMV symptoms. Phylogenetic analysis based on the amino acid of the coat protein (CP) of CMVs revealed that the CMV passion fruit isolates belonged to subgroup I, among which CMV-HN2 belonged to subgroup IA. Additionally, CMVs isolated from passion fruit in Korea have amino acid sequence variation between the subgroup. Among them, CMV-HN2 had four to eight amino acid differences in CP from other CMV isolates from passion fruit. These results confirm the presence of genetic diversity in the CPs of passion fruit CMV isolates.

• Journal of Applied Biological Chemistry
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• v.66
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• pp.394-403
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• 2023

In the pursuit of sustainable and environmentally-friendly agricultural practices, we conducted an extensive study on the rhizosphere bacteria inhabiting soils that have been devoid of chemical fertilizers for an extended period exceeding 40 years. Through this investigation, we isolated a total of 80 species of plant growth-promoting rhizosphere bacteria and assessed their potential to enhance plant growth. Among these isolates, Burkholderia cepacia CD2 displayed remarkable plant growth-promoting activity, making it an optimal candidate for further analysis. Burkholderia cepacia CD2 exhibited a range of beneficial characteristics conducive to plant growth, including phosphate solubilization, siderophore production, denitrification, nitrate utilization, and urease activity. These attributes are well-known to positively influence the growth and development of plants. To validate the taxonomic classification of the strain, 16S rRNA gene sequencing confirmed its placement within the Burkholderia genus, providing further insights into its phylogenetic relationship. To delve deeper into the potential mechanisms underlying its plant growth-promoting properties, we sought to confirm the presence of specific genes associated with plant growth promotion in CD2. To achieve this, whole genome sequencing (WGS) was performed by Plasmidsaurus Inc. (USA) utilizing Oxford Nanopore technology (Abingdon, UK). The WGS analysis of the genome of CD2 revealed the existence of a subsystem function, which is thought to be a pivotal factor contributing to improved plant growth. Based on these findings, it can be concluded that Burkholderia cepacia CD2 has the potential to serve as a microbial fertilizer, offering a sustainable alternative to chemical fertilizers.

• Microbiology and Biotechnology Letters
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• v.52 no.1
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• pp.1-14
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• 2024

This study focused on isolating and identifying strains from the gut of Epinephelus akaara cultivated in aquaculture facilities on Jeju Island. The aim was to evaluate the potential of utilizing these strains as probiotics for industrial applications. A total of 129 strains were isolated from the gut of E. akaara and screened based on their ability to create a clear zone of 10 mm or more in a preliminary antimicrobial activity test. Twelve strains were selected for further analysis, including bile resistance, acid tolerance at different pH levels, antioxidant activity, antibiotic susceptibility, and biochemical characteristics using the API kit. Through these characteristic experiments, eight strains (G1, G3, G15, G21, B1, B2, B3, B5) were identified as having potential as probiotics. Among these, the B group strains (B1, B2, B3, B5) exhibited significantly higher activity compared to the G group strains (G1, G3, G15, G21). Based on the phylogenetic analysis of the 16S rRNA gene sequences of the selected microorganisms, the strains were named as follows: B1 strain as Lactobacillus paracasei B1, B2 strain as Lactococcus lactis B2, B3 strain as Lactobacillus plantarum B3, B5 strain as Lactococcus lactis subsp. hordniae B5, G1 strain as Bacillus licheniformis G1, G3 strain as Bacillus velezensis G3, G15 strain as Brevibacterium frigoritolerans G15, and G21 strain as Bacillus pumilus G21.