• Korean Journal of Ecology and Environment
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• v.55 no.3
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• pp.212-220
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• 2022

An estuary is a water ecosystem with a high abundance of the species diversity, due to a variety of complex physicochemical factors of the area where freshwater and ocean mixed. The identification of Corbicula species in the estuary environments is difficult because of various morphological characteristics. In this study, we provide taxonomic information on Corbicula species with taxonomic difficulties using morphological and genetic analysis. This study was conducted on clams from the Seomjin River-Gwangyang Bay, one of the major production area of marsh clam in Korea. As a result, we characterized Cytocrome C Oxidase subunit I (COI) sequences of the Corbicula. The 636 bp nucleotide sequences of COI have 98% homology among Corbicula species collected from 2 sites of Seomjin River-Gwangyang Bay. The phylogenetic analysis with 17 species of Corbicula indicated that most of the species collected from Seomjin River-Gwangyang Bay were brackish water clam (Corbicula japonica), and only one Asian clam (Corbicula fluminea). The evolutionary distance between C. japonica and C. fluminea was less than 0.003. Therefore, it was confirmed that C. japonica is phylogenetically closely related to C. fluminea. In 9 species of Cyrenidae, phylogenetic tree was classified into three lineages. These results will be used as an important data for an identification of clam species by providing genetic information for Corbicula species with a morphological diversity.

• Journal of Microbiology and Biotechnology
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• v.34 no.5
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• pp.1146-1153
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• 2024

The increasing economic losses associated with growth retardation caused by Enterocytozoon hepatopenaei (EHP), a microsporidian parasite infecting penaeid shrimp, require effective monitoring. The internal transcribed spacer (ITS)-1 region, the non-coding region of ribosomal clusters between 18S and 5.8S rRNA genes, is widely used in phylogenetic studies due to its high variability. In this study, the ITS-1 region sequence (~600-bp) of EHP was first identified, and primers for a polymerase chain reaction (PCR) assay targeting that sequence were designed. A newly developed nested-PCR method successfully detected the EHP in various shrimp (Penaeus vannamei and P. monodon) and related samples, including water and feces collected from Indonesia, Thailand, South Korea, India, and Malaysia. The primers did not cross-react with other hosts and pathogens, and this PCR assay is more sensitive than existing PCR detection methods targeting the small subunit ribosomal RNA (SSU rRNA) and spore wall protein (SWP) genes. Phylogenetic analysis based on the ITS-1 sequences indicated that the Indonesian strain was distinct (86.2% nucleotide sequence identity) from other strains collected from Thailand and South Korea, and also showed the internal diversity among Thailand (N = 7, divided into four branches) and South Korean (N = 5, divided into two branches) samples. The results revealed the ability of the ITS-1 region to determine the genetic diversity of EHP from different geographical origins.

• Journal of Microbiology and Biotechnology
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• v.34 no.7
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• pp.1484-1490
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• 2024

The gut microbiota is a key factor significantly impacting host health by influencing metabolism and immune function. Its composition can be altered by genetic factors, as well as environmental factors such as the host's surroundings, diet, and antibiotic usage. This study aims to examine how the characteristics of the gut microbiota in pigs, used as source animals for xenotransplantation, vary depending on their rearing environment. We compared the diversity and composition of gut microbiota in fecal samples from pigs raised in specific pathogen-free (SPF) and conventional (non-SPF) facilities. The 16S RNA metagenome sequencing results revealed that pigs raised in non-SPF facilities exhibited greater gut microbiota diversity compared to those in SPF facilities. Genera such as Streptococcus and Ruminococcus were more abundant in SPF pigs compared to non-SPF pigs, while Blautia, Bacteroides, and Roseburia were only observed in SPF pigs. Conversely, Prevotella was exclusively present in non-SPF pigs. It was predicted that SPF pigs would show higher levels of processes related to carbohydrate and nucleotide metabolism, and environmental information processing. On the other hand, energy and lipid metabolism, as well as processes associated with genetic information, cell communication, and diseases, were predicted to be more active in the gut microbiota of non-SPF pigs. This study provides insights into how the presence or absence of microorganisms, including pathogens, in pig-rearing facilities affects the composition and function of the pigs' gut microbiota. Furthermore, this serves as a reference for tracing whether xenotransplantation source pigs were maintained in a pathogen-controlled environment.

• Journal of Microbiology
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• v.35 no.4
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• pp.347-353
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• 1997

We have characterized a phage library displaying random 22mer peptides which were produced as N-terminal fusions to the pIII coat protein of M13 filamentous phages. Among the sixty phages randomly picked from the library, 25 phages had the 22mer peptide inserts. The DNA sequence analysis of the 25 inserts showed the following results: first, each nucleotide was represented almost equally at each codon position except that there were some biases toward G bases at the first position of the codons. Secondly, the expected 47 sense codons were represented. The deduced amino acid sequences of the 25 inserts were analyzed to examine its diversity. Glycine and glutamate were the two most overrepresented residues above the expected value, whereas cysteine and threonine residues were underrepresented. The range of dicersity in dipeptide sequences showed that the amino acid residues were randomly distributed along the peptide insert. Acidic, basic, polar, and nonpolar amino acid residues were represented to the extent expected at most positions of the peptide inserts. The predicted isoelectric points and hydropathy indices of the 25 peptides showed that a variety of the peptide were represented in the library. These results indicate that this phage display library could be useful in fiuding ligands for a broad spectrum of receptors by affinity screening.

• Animal cells and systems
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• v.8 no.3
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• pp.231-233
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• 2004

Sequences of cytochrome b gene and control region of mitochondrial DNA from Korean common otters (Lutra lutra lutra L.) were examined to provide the genetic information for the conservation of this subspecies. Two haplotypes and one haplotype were revealed in cytochrome b gene and control region, respectively. The available sequences of European common otter (L. l. lutra) from GenBank were compared together with those of Korean common otter in order to determine the degree of sequence variation between them. In cytochrome b gene sequences, two haplotypes from Korea and two haplotypes of Europe showed differences in 12 of 1,045 sites. The Tamura-Nei nucleotide distances between two European haplotypes was 0.10% and those between two Korean haplotypes was also 0.10%, but those between Korean haplotypes and European ones ranged from 0.96% to 1.16%. In the control region, one Korean haplotype and seven European ones showed differences in seven of 300 sites; the Tamura-Nei distances among seven European haplotypes were 0.34% to 1.01%, but those between Korean haplotype and European ones ranged from 1.01% to 1.69%. Although further molecular and morphological studies with specimens from eastern Asia including Amur region and northeast China are needed, it is possible that the Korean common otter might be closer or identical to the far-eastern Asian common otter, L. l. amurensis Dybowski.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.8
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• pp.1065-1071
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• 2013

The swine leukocyte antigen class II molecules are possibly associated with the induction of protective immunity. The study described here was to investigate the relationship between polymorphisms in exon 2 of the swine DQA gene and piglet diarrhea. This study was carried out on 425 suckling piglets from three purebred pig strains (Large White, Landrace and Duroc). The genetic diversity of exon 2 in swine DQA was detected by PCR-SSCP and sequencing analysis, eight unique SSCP patterns (AB, BB, BC, CC, CD, BD, BE and DD) representing five specific allele (A to E) sequences were detected. Sequence analysis revealed 21 nucleotide variable sites and resulting in 12 amino acid substitutions in the populations. A moderate level polymorphism and significant deviations from Hardy-Weinberg equilibrium of the genotypes distribution were observed in the populations (p<0.01). The association analysis indicated that there was a statistically significant difference in the score of piglet diarrhea between different genotypes, individuals with genotype CC showed a lower diarrhea score than genotypes AB ($0.98{\pm}0.09$), BB ($0.85{\pm}0.77$) and BC ($1.25{\pm}0.23$) (p<0.05), and significantly low than genotype BE ($1.19{\pm}0.19$) (p<0.01), CC genotype may be a most resistance genotype for piglet diarrhea.

• The Korean Journal of Mycology
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• v.42 no.1
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• pp.21-27
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• 2014

Several kinds of yeasts from fruits and flowers of orchard in Yesan-gun of Chungcheongnam-do, Korea were isolated and identified by comparison of nucleotide sequences for PCR-amplified D1/D2 region of 26S rDNA using BLAST. Fourty eight yeast strains of twenty five species and one hundred eight yeast strains of fourty eight species were isolated from fruits and flowers of orchard in Sinam-myeon of Yesan-gun, Chungcheongnam-do, respectively. Among total one hundred fifty-six yeast strains, only sixteen species were overlapped from fruits and flowers.

• The Korean Journal of Mycology
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• v.42 no.1
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• pp.28-33
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• 2014

Various yeasts from wild flowers of Ulleungdo in Gyeongsangbuk-do and Yokjido in Gyeongsangnam-do, Korea were isolated and identified by comparison of nucleotide sequences for PCR-amplified D1/D2 region of 26S rDNA using BLAST. Forty eight yeast strains of twenty two species and sixty yeast strains of twenty five species were isolated from wild flowers of Ulleungdo and Yokjido, respectively. Only seven species were overlapped from the two different islands areas: Cryptococcus albidus, Cryptococcus laurentii, Metschnikowia reukafii, Pichia scolyti, Rhodotorula glutinis, Rhodotorula graminis and Rhodotorula mucilaginosa. Among forty species from two different islands, other thirty three species were restricted to specific collection site suggesting that each area has distinctive yeast flora.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.12
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• pp.1637-1643
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• 2011

Korean native chickens are a very valuable chicken population in Korea and their prices are higher than that of commercial broilers. In order to discriminate two commercial Korean native chicken populations (CCP1 and CCP2), single nucleotide polymorphisms (SNPs) from mitochondrial (mt) DNA D-loop sequences and LEI0258 marker polymorphisms in the major histocompatibility complex (MHC) region were investigated. A total of 718 birds from nine populations were sampled and 432 mtDNA sequences were obtained. Of these, two commercial Korean native chicken populations (363 birds) were used for investigation of their genetic relationship and breed differentiation. The sequence data classified the chickens into 20 clades, with the largest number of birds represented in clade 1. Analysis of the clade distribution indicated the genetic diversity and relation among the populations. Based on the mtDNA sequence analysis, three selected SNPs from mtDNA polymorphisms were used for the breed identification. The combination of identification probability (Pi) between CCP1 and CCP2 using SNPs from mtDNA and LEI0258 marker polymorphisms was 86.9% and 86.1%, respectively, indicating the utility of these markers for breed identification. The results will be applicable in designing breeding and conservation strategies for the Korean native chicken populations and also used for the development of breed identification markers.

• Korean Journal of Ichthyology
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• v.21 no.4
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• pp.287-290
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• 2009

A natural hybrid between the striped spine loach Cobitis tetralineata and the king spine loach Iksookimia longicorpa was genetically identified by sequence analyses of nuclear recombination activating gene 1 (RAG1) and mitochondrial cytochrome c oxidase I (COI) genes. Out of 850 base positions of RAG1, a total of 23 nucleotide substitutions were detected between the two parental species, whereas the electropherogram of the natural hybrid displayed double peaks at all of the 23 positions, which reflects their simple Mendelian inheritance pattern. Meanwhile, comparison of partial sequences of mitochondrial genes (COI in this study), which are well characterized by the maternal inheritance pattern, revealed that the maternal species of the hybrid was C. tetralineata because of their 100% sequence identity.