• Journal of Veterinary Science
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• 제23권5호
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• pp.67.1-67.11
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• 2022

Background: Budgerigar fledgling disease polyomavirus (BFDV) is the pathogen that causes budgerigar fledgling disease in psittacine species. The clinical signs of PBFV infection include ascites, hepatitis, and crop stasis. BFDV is associated with a high mortality rate in nestling birds. In contrast, adult birds only have mild symptoms such as feather dystrophy. Objectives: This study aimed to determine the prevalence, genetic characteristics, and phylogenetic analysis of BFDV in pet parrots in Korea. Methods: Fecal and tissue samples were collected from 217 pet parrots from 10 veterinary hospitals including Chungbuk National University Veterinary Hospital. The molecular screening was performed using polymerase chain reaction (PCR) analysis of the small t/large T antigen gene segment. Full-length genome sequencing with the Sanger and phylogenetic analysis were performed on BFDV-positive samples. Results: The PCR results based on the small t/large T antigen gene marker indicated that BFDV DNA was present in 10 out of 217 screened samples. A whole-genome sequence was obtained from six strains and phylogenetic analysis revealed no significant relationship existed between the species and geographical locations amongst them. Conclusions: The prevalence of BFDV infection in South Korea is not high when compared to the prevalence of BFDV in other parts of the world, however, it has been reported sporadically in various species and geographic locations. The whole-genome analysis revealed 0.2%-0.3% variation in intragenomic homogeneity among the six strains analyzed. Korean strains are separately on the phylogenetic tree from their counterparts from China and Japan which might reflect the substantial genetic variation.

• BMB Reports
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• 제38권4호
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• pp.386-390
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• 2005

Based on the reported cDNA sequences of $BmK{\alpha}Txs$, the genes encoding toxin $BmK{\alpha}Tx11$ and $BmK{\alpha}Tx15$ were amplified by PCR from the Chinese scorpion Buthus martensii Karsch genomic DNA employing synthetic oligonucleotides. Sequences analysis of nucleotide showed that an intron about 500 bp length interrupts signal peptide coding regions of $BmK{\alpha}Tx11$ and $BmK{\alpha}Tx15$. Using cDNA sequence of $BmK{\alpha}Tx11$ as probe, southern hybridization of BmK genome total DNA was performed. The result indicates that $BmK{\alpha}Tx11$ is multicopy genes or belongs to multiple gene family with high homology genes. The similarity of $BmK{\alpha}$-toxin gene sequences and southern hybridization revealed the evolution trace of $BmK{\alpha}$-toxins: $BmK{\alpha}$-toxin genes evolve from a common progenitor, and the genes diversity is associated with a process of locus duplication and gene divergence.

• 한국어병학회지
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• 제23권3호
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• pp.323-334
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• 2010

Bactericidal/permeability-increasing protein (BPI) and lipopolysaccharide-binding protein (LBP) are important components of the mammalian innate defence system against Gram-negative infections. The BPI/LBP cDNA was identified from the black rockfish ConA/PMA or LPS stimulated leukocyte cDNA library. The full-length BR-BPI/LBP cDNA was 2118 bp long and contained an open reading frame (ORF) of 1422 bp that encoded 473 amino-acid residues. The 5' UTR had a length of 57 bp, and the 3' UTR 639 bp. The molecular weight and theoretical isoelectric point (pI) values were calculated 51.4 kDa and 9.72, respectively. Compared with other known BPI or BPI/LBP peptide sequences, the most conserved regions of the black rockfish BPI/LBP peptide were found to be the BPI1 N-terminal, BPI2 C-terminal domains and a LPS binding domain. Phylogenetic analysis based on the deduced amino acid sequence revealed a homologous relationship between the BPI/LBP sequence of black rockfish and that of other teleosts. The black rockfish BPI/LBP gene was predominantly expressed in the PBLs, head kidney, trunk kidney and spleen. The expression of the black rockfish BPI/LBP molecule was induced in the peripheral blood leukocytes (PBLs) from 1 to 24 h following LPS stimulation, with a peak at 12 h post-stimulation.

• Animal cells and systems
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• 제2권4호
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• pp.451-454
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• 1998

Gulgastrura reticulosa, first described by Yosii (1966) as a monotypic new genus from a Korean limestone cave, was reviewed for its systematic position by c1adistic analysis of morphological characteristics, investigation of its intermaulting period and reproductive cycle as well as allozyme and 18S rDNA analysis. The great extent of divergence was strongly suggested by its combined lack of sensory organs (third antennal organ, postantennal organ, eyes, pseudocelli) with simultaneous development of an 'apical organ'at the tip of the antennae. The obvious divergence from any existing Collembola families was additionally supported by the extremely prolonged intermoulting period as well as by the low strap value it showed with Onychiuridae as obtained by 18S DNA sequence analysis. All these were considered Justifying the creation of a new family, Gulgastruridae, but still revealing more allied to Onychiuvidae rather than to Hypogastruridae.

• 식물조직배양학회지
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• 제27권4호
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• pp.259-268
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• 2000

Senescence is a sequence of biochemical and physiological events that lead to death of a cell, organ, or whole organism. Senescence is now clearly regarded as a genetically determined and evolutionarilly acquired developmental process comprising the final stage of development. However, in spite of the biological and practical importance, genetic mechanism of senescence has been very limited. Through forward and reverse genetic approaches, we are trying to reveal the molecular and genetic mechanism of senescence in plants, employing leaf organs of Arabidopsis as a model system. Using forward genetic approach, we have initially isolated several delayed senescence mutants either from T-DNA insertional lines or chemical-mutagenized lines. In the case of ore 4 and ore 9 mutants, the mutated genes were identified. The recent progress on characterization of mutants and identification of the mutated genes will be reported. We are also screening mutations from other various sources of mutant pools, such as activation tagging lines and promoter trap lines. Two dominant senescence-delayed mutants were isolated from the activation tagging pool. Cloning of the genes responsible for this phenotype is in progress. For reverse genetic approach, the genes that induced during leaf senescence were first isolated by differential screening method. We are currently using PCR-based suppression subtractive hybridization, designed to enrich a cDNA library for rare differentially expressed transcripts. Using this method, we have identified over 35 new sequences that are upregulated at leaf senescence stage. We are investigating the function of these novel genes by systemically generating antisense lines.

• The Plant Pathology Journal
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• 제25권4호
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• pp.429-432
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• 2009

An unreported disease of apricot was observed in orchards in Zhejiang province, China. Symptoms started as water soaked lesions on the fruit surface. Later, water-soaked areas developed and spread to the entire fruit, resulting in soft rot of the whole fruit. The causal organism isolated from symptomatic fruits was identified as Burkholderia cepacia based on its biochemical and physiological characteristics and confirmed by the cellular fatty acid composition and Biolog data as well as 16S rRNA gene sequence analysis. The bacterial isolates caused similar symptoms when inoculated onto fruits of apricot. In addition, European plum, Japanese plum, nectarine and kiwifruit were susceptible to the B. cepacia pathogen. However, the B. cepacia pathogen failed to cause any visible symptoms when it was inoculated onto 16 other fruits. This is the first report of a bacterial disease of apricot caused by B. cepacia in China.

• Environmental Engineering Research
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• 제19권4호
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• pp.317-329
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• 2014

The diversity of cyanobacteria in Sri Lanka was studied in different water reservoirs, paddy fields, brackish water and tsunami affected areas using light microcopy, 16S rRNA sequences, followed by phylogenetic analysis. Based on light microscopy, 24 genera were identified from environmental samples belonging to the orders Chroococcales, Oscillatoriales, Pleurocapsales and Nostocales. In cultures, 33 genera were identified from all five cyanobacterial orders, including Stigonematales. Based on 16S rRNA gene sequences and their morphology, two isolates were identified up to species level, 72 to genus level, one isolate up to family and 11 up to order level. Twelve isolates couldn't be assigned to any taxonomic level. The results of 16S rRNA gene sequences along with the phylogenetic analysis indicated that some cyanobacterial isolates could be accommodated to genus or order level. The 16S rRNA sequence analysis data in this study confirmed that order Nostocales and order Pleurocapsales cyanobacteria are monophyletic while orders Chroococcales, Oscillatoriales and Stigonematales cyanobacteria are polyphyletic. Polyphasic approach including the combination of light microscopy, cultures and the analysis of 16S rRNA gene sequences provide a promising approach to ascertain the diversity of cyanobacteria in different habitats.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.407-411
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• 2005

KUGI (Korean UniGene Information) database contains the annotation information of the cDNA sequences obtained from the disease samples prevalent in Korean. A total of about 157,000 5'-EST high throughput sequences collected from cDNA libraries of stomach, liver, and some cancer tissues or established cell lines from Korean patients were clustered to about 35,000 contigs. From each cluster a representative clone having the longest high quality sequence or the start codon was selected. We stored the sequences of the representative clones and the clustered contigs in the KUGI database together with their information analyzed by running Blast against RefSeq, human mRNA, and UniGene databases from NCBI. We provide a web-based search engine fur the KUGI database using two types of user interfaces: attribute-based search and similarity search of the sequences. For attribute-based search, we use DBMS technology while we use BLAST that supports various similarity search options. The search system allows not only multiple queries, but also various query types. The results are as follows: 1) information of clones and libraries, 2) accession keys, location on genome, gene ontology, and pathways to public databases, 3) links to external programs, and 4) sequence information of contig and 5'-end of clones. We believe that the KUGI database and search system may provide very useful information that can be used in the study for elucidating the causes of the disease that are prevalent in Korean.

• 대한의생명과학회지
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• 제17권4호
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• pp.297-304
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• 2011

Influenza A virus of the Orthomyxoviridae family is a contagious respiratory pathogen that continues to evolve and burden in the human public health. It is able to spread efficiently from human to human and have the potential to cause pandemics with significant morbidity and mortality. It has been estimated that every year about 500 million people are infected with this virus, causing about approximately 0.25 to 0.5 million people deaths worldwide. Influenza A viruses are classified into different subtypes by antigenicity based on their hemagglutinin (HA) and neuraminidase (NA) proteins. The sudden emergence of influenza A virus subtypes and access for epidemiological analysis of this subtypes demanded a rapid development of specific diagnostic tools. Also, rapid identification of the subtypes can help to determine the antiviral treatment, because the different subtypes have a different antiviral drug resistance patterns. In this study, our aim is to detect influenza A virus subtypes by using real-time nucleic acid sequence based amplification (NASBA) which has high sensitivity and specificity through molecular beacon. Real-time NASBA is a method that able to shorten the time compare to other molecular diagnostic tools and is performed by isothermal condition. We selected major pandemic influenza A virus subtypes, H3N2 and H5N1. Three influenza A virus gene fragments such as HA, NA and matrix protein (M) gene were targeted. M gene is distinguished influenza A virus from other influenza virus. We designed specific primers and molecular beacons for HA, NA and M gene, respectively. In brief, the results showed that the specificity of the real-time NASBA was higher than reverse transcription polymerase chain reaction (RT-PCR). In addition, time to positivity (TTP) of this method was shorter than real-time PCR. This study suggests that the rapid detection of neo-appearance pandemic influenza A virus using real-time NASBA has the potential to determine the subtypes.

• Fisheries and Aquatic Sciences
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• 제21권10호
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• pp.27.1-27.5
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• 2018

During a survey of marine algal flora, two gigartinalean species were collected from Pohang and Youngdeok located on the eastern coast of Korea. They share the generic morphological features of Dumontia. One is characterized by cylindrical to complanate thallus with multi- and uniaxial structure, somewhat inflated and contorted branches, and hollow medulla and cortex consisting of progressively smaller cells outwards. The other shows basically the same features as the former species but was smaller in size, as having 4-7 cm in thallus length and 1-2 mm in branch width rather than 15 and 2-5 mm. Both species are distinguished from each other only by these morphometric features. However, it is supported by molecular analysis that both species are genetically distinct. In a phylogenetic tree based on internal transcribed spacer sequence, the two species nest in the same clade as Dumontia contorta and D. alaskana, respectively. The genetic distance between both sequences within the clade was calculated as 0.0 0.2%, considered to be intra-specific for Dumontia. Based on the morphological and molecular analyses, the two Korean species are identified as D. contorta and D. alaskana described originally from Netherlands and Alaska, respectively. This is the first record of the two Dumontia species in Korea.