Com probe implemented STexS II greatly enhances specificity in SARS-CoV-2 variant detection.

The initial introduction of utilizing double helix structural oligonucleotides known as SNP typing with excellent specificity (STexS) in a standard PCR greatly improved the detection of single nucleotide polymorphisms (SNP) by enhancing amplification rates of primer-matching strands and interrupting mismatched strands by constant instability of kinetics regarding alignment attaching and detaching. The model was beneficial overall in detecting SNP variants consisting of large amounts of wildtype strands such as EGFR mutation genotyping for early detection of non-small cell lung cancer. While the STexS PCR is advantageous in detecting SNPs and biomarkers, limitations were yet observed. Despite the ability to detect variants 10 times more effective than a typical amplification-refractory mutation system PCR, it could only perform optimally in DNA concentrations around 101 ~ 105. To further enhance STexS specificity to perform detecting viral-RNA variants such as the infamous SARS-CoV-2, a novel improvement of the regular TaqMan Probe using Com-probes to inhibit high copy wild targets and amplify low copy mutant targets. By introducing the novel STexS II, omicron variants of SARS-CoV-2 were able to be successfully detected in high concentrations of normal genes.

The complete mitochondrial genome information of Phoxinus phoxinus (Cypriniformes: Cyprinidae) on the Korean Peninsula and the phylogenetic implication.

Phoxinus phoxinus is a small Leuciscinae species predominantly found in cool and well-oxygenated streams throughout a wide area encompassing Europe, Siberia and East Asia. It is believed that the populations in Korea hold important clues to how the species has been distributed south along the Eurasian continent to the Korean Peninsula. We characterized the complete mitochondrial genomes of two individual fin-clip samples collected from the two Korean river systems. The whole sequences were 17,665 and 18,220 bp, respectively, and included 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. The genome size difference was due to the considerably different sizes of the control region. The overall genome structures were identical to those observed in other Leuciscinae species.

Complete Genome Sequence of Sphingorhabdus sp. YGSMI21, Exhibiting High Enantioselective Epoxide Hydrolase Activity.

Sphingorhabdus sp. YGSMI21 is a novel strain exhibiting high enantioselective hydrolysis activity for styrene oxide. Here, we present its complete genome sequence, consisting of one circular chromosome (3.86 Mb) and one plasmid (0.196 Mb).

Complete Genome Sequence of Indigo-Producing Bacterium Celeribacter sp. Strain TSPH2.

Celeribacter sp. strain TSPH2, a novel producer of indigo, was isolated from oil-contaminated sediment. We present here its genome sequence consisting of one circular chromosome (4 Mb) and one plasmid (0.15 Mb), with an overall G+C content of 60.9%. This strain contains oxygenase genes involved in indigo synthesis, such as flavin-containing monooxygenase.

Complete genome sequence of Streptomyces venezuelae ATCC 15439, a promising cell factory for production of secondary metabolites.

Streptomyces venezuelae ATCC 15439, which produces 12- and 14-membered ring macrolide antibiotics, is a platform strain for heterologous expression of secondary metabolites. Its 9.05-Mb genome sequence revealed an abundance of genes involved in the biosynthesis of secondary metabolites and their precursors, which should be useful for the production of bioactive compounds.

Complete mitochondrial genome of endangered Rhodeus pseudosericeus and its implications for the reconstruction of phylogenetic relationship among Acheilognathinae species.

Rhodeus pseudosericeus is a native bitterling to the Korean Peninsula and found in very limited areas with small census size. Here, its complete mitochondrial genome was analyzed to provide novel data for the reconstruction of phylogenetic relationship among Acheilognathinae species. The genome was a 16,574 bp long consisting of 1 putative control region, 2 rRNA genes, 22 tRNA and 13 protein-coding genes. The gene arrangement was completely identical to those observed in other Acheilognathinae species as well as in other cyprinid species. In our phylogenetic analyses, three major genera of Acheilognathinae indepedently formed monophyletic groups in the tree reconstructed based on the whole genome sequences, whereas Rhodeus was not recovered as a single monophyly when solely considering protein-coding genes, indicating that the taxonomic reevaluation is still required in this subfamily.

Complete genome sequence of Bacillus anthracis H9401, an isolate from a Korean patient with anthrax.

Bacillus anthracis H9401 (NCCP 12889) is an isolate from a Korean patient with gastrointestinal anthrax. The whole genome of H9401 was sequenced. It is a circular chromosome containing 5,480 open reading frames (ORFs) and two plasmids, pXO1 containing 202 ORFs and pXO2 containing 110 ORFs. H9401 shows high pathogenicity and genome sequence similarity to Ames Ancestor.

Complete genome sequence of multidrug-resistant Acinetobacter baumannii strain 1656-2, which forms sturdy biofilm.

Acinetobacter baumannii is a Gram-negative bacterium causing nosocomial infections worldwide. To gain quick insight into the molecular basis of biofilm formation in A. baumannii, we determined the complete genome sequence of A. baumannii strain 1656-2, which forms sturdy biofilm and is resistant to multiple drugs.

A Sexually Transmitted Disease (STD) DNA chip for the diagnosis of genitourinary infections.

The results of an investigation aimed at the development of a DNA chip for the detection of genitourinary infections are described. Through analysis of over 35,000 clinical cases, 14 pathogens which are most abundantly found among Koreans were selected and candidate sequences for capture probes were accordingly chosen by considering their sequences and ß-globin house-keeping gene. Among this group, the most suitable capture probe sequences were selected by employing repeated chip tests in which they are immobilized on a glass chip by using a recently developed novel gold nanoparticles-based method. A multiplex PCR method was established to generate fluorescence-labeled sequences for all 14 pathogens along with the ß-globin gene. By using optimized hybridization conditions, the final chip was constructed and employed to diagnose reliably both single and multiple infections in clinical human samples for 14 target pathogens. The results show that the novel chip methodology serves as a highly reliable and convenient tool for the diagnosis of Sexually Transmitted Diseases (STDs). Furthermore, this study has its great significance in that it demonstrates the entire process from statistical analysis of a large number of clinical cases to the final development of STD DNA chip just ready to be applied or commercialized in the clinical diagnostic field.

Complete genome sequence of Rhodobacter sphaeroides KD131.

Rhodobacter sphaeroides is a purple nonsulfur photosynthetic bacterium that is considered a possible source of H(2) production. R. sphaeroides KD131, which was isolated from sea mud in South Korea, was found to produce high levels of H(2). Here we report the complete and annotated genome sequence of R. sphaeroides KD131.

Complete genome sequence of Neisseria gonorrhoeae NCCP11945.

Neisseria gonorrhoeae is an obligate human pathogen that is the etiological agent of gonorrhea. We explored variations in the genes of a multidrug-resistant N. gonorrhoeae isolate from a Korean patient in an effort to understand the prevalence, antibiotic resistance, and importance of horizontal gene transfer within this important, naturally competent organism. Here, we report the complete annotated genome sequence of N. gonorrhoeae strain NCCP11945.

Oligonucleotide DNA chips are useful adjuncts in epigenetic studies of glioblastomas.

Several studies have suggested that hypermethylation and hypomethylation of CpG islands within the promoters and 5' exons of tumor-related genes are closely associated with carcinogenesis. However, large-scale analysis of candidate genes has been hampered by the lack of a high throughput approach for analyzing methylation patterns. Using methylation-specific oligonucleotide (MSO) chips, we evaluated the methylation patterns of eight samples of fresh frozen glioblastoma tissue. The MSO chip used contained DNA probes with the CpG sites of p16 (p16INK4A, CDKN2A), MGMT (O6-Methylguanine-DNA-methyltransferase), APC (adenomatous polyposis coil), RASSF1A (human RAS effect homolog), which are usually hypermethylated in cancer cells and MAGE (melanoma antigen), which is usually hypomethylated in cancer cells. We selected CpG sites for analysis; 28 CpG sites (263 bp) for p16, 26 CpG sites (249 bp) for MGMT, 16 CpG sites (195 bp) for APC, 22 CpG sites (262 bp) for RASSF1A and 18 CpG sites (235 bp) for MAGE. We then constructed primer sets not including CpG sites. Bisulfite modification of genomic DNA, methylation specific PCR, hybridization and image scan with data analysis and sequencing of the bisulfite modified DNA were carried out. Of the eight glioblastomas, hypermethylation of the 5'-CpG sites of the MGMT were found in two, RASSF1A were found in five, and p16 and APC genes were not found in any cases and hypomethylation of that of the MAGE was found in eight cases. These results obtained from the oligo DNA chip study were correlated well with the sequencing data of bisulfite modified genomic DNA except in regard to the RASSF1A and MAGE genes. The devised MSO DNA chip is a useful tool for studies on methylation.