1.Mrakia terrae sp. nov. and Mrakia soli sp. nov., Two Novel Basidiomycetous Yeast Species Isolated from Soil in Korea
Yuna PARK ; Soohyun MAENG ; Junsang OH ; Gi-Ho SUNG ; Sathiyaraj SRINIVASAN
Mycobiology 2021;49(5):469-475
Three strains, YP416 T , YP421 T, and Y422, were isolated from soil samples in Pocheon City, Gyeonggi province, South Korea. The strains belong to two novel yeast species in the genus Mrakia. Molecular phylogenetic analysis showed that the strain YP416 T was closely related to Mrakia niccombsii. Still, it differed by 9 nucleotide substitutions with no gap (1.51%) in the D1/D2 domain of the LSU rRNA gene and 14 nucleotide substitutions with 7 gaps (2.36%) in the ITS region. The strain YP421 T differed from the type strain of the most closely related species, Mrakia aquatica, by 5 nucleotide substitutions with no gap (0.81%) in the D1/D2 domain of the LSU rRNA gene and 9 nucleotide substitutions with one gap (1.43%) in the ITS region. The names Mrakia terrae sp. nov. and Mrakia soli sp. nov. are proposed, with type strains YP416 T (KCTC 27886 T ) and YP421 T (KCTC 27890 T ), respectively. MycoBank numbers of the strains YP416 T and YP421 T are MB 836844 and MB 836847, respectively.
2.Applications of Single-Cell Omics Technologies for Induced Pluripotent Stem Cell-Based Cardiovascular Research
Hyunjoon KIM ; Sohee CHOI ; HyoJung HEO ; Su Han CHO ; Yuna LEE ; Dohyup KIM ; Kyung Oh JUNG ; Siyeon RHEE
International Journal of Stem Cells 2025;18(1):37-48
Single-cell omics technologies have transformed our investigation of genomic, transcriptomic, and proteomic landscapes at the individual cell level. In particular, the application of single-cell RNA sequencing has unveiled the complex transcriptional variations inherent in cardiac cells, offering valuable perspectives into their dynamics. This review focuses on the integration of single-cell omics with induced pluripotent stem cells (iPSCs) in the context of cardiovascular research, offering a unique avenue to deepen our understanding of cardiac biology. By synthesizing insights from various single-cell technologies, we aim to elucidate the molecular intricacies of heart health and diseases. Beyond current methodologies, we explore the potential of emerging paradigms such as single-cell/spatial omics, delving into their capacity to reveal the spatial organization of cellular components within cardiac tissues. Furthermore, we anticipate their transformative role in shaping the future of cardiovascular research. This review aims to contribute to the advancement of knowledge in the field, offering a comprehensive perspective on the synergistic potential of transcriptomic analyses, iPSC applications, and the evolving frontier of spatial omics.
3.Applications of Single-Cell Omics Technologies for Induced Pluripotent Stem Cell-Based Cardiovascular Research
Hyunjoon KIM ; Sohee CHOI ; HyoJung HEO ; Su Han CHO ; Yuna LEE ; Dohyup KIM ; Kyung Oh JUNG ; Siyeon RHEE
International Journal of Stem Cells 2025;18(1):37-48
Single-cell omics technologies have transformed our investigation of genomic, transcriptomic, and proteomic landscapes at the individual cell level. In particular, the application of single-cell RNA sequencing has unveiled the complex transcriptional variations inherent in cardiac cells, offering valuable perspectives into their dynamics. This review focuses on the integration of single-cell omics with induced pluripotent stem cells (iPSCs) in the context of cardiovascular research, offering a unique avenue to deepen our understanding of cardiac biology. By synthesizing insights from various single-cell technologies, we aim to elucidate the molecular intricacies of heart health and diseases. Beyond current methodologies, we explore the potential of emerging paradigms such as single-cell/spatial omics, delving into their capacity to reveal the spatial organization of cellular components within cardiac tissues. Furthermore, we anticipate their transformative role in shaping the future of cardiovascular research. This review aims to contribute to the advancement of knowledge in the field, offering a comprehensive perspective on the synergistic potential of transcriptomic analyses, iPSC applications, and the evolving frontier of spatial omics.
4.Applications of Single-Cell Omics Technologies for Induced Pluripotent Stem Cell-Based Cardiovascular Research
Hyunjoon KIM ; Sohee CHOI ; HyoJung HEO ; Su Han CHO ; Yuna LEE ; Dohyup KIM ; Kyung Oh JUNG ; Siyeon RHEE
International Journal of Stem Cells 2025;18(1):37-48
Single-cell omics technologies have transformed our investigation of genomic, transcriptomic, and proteomic landscapes at the individual cell level. In particular, the application of single-cell RNA sequencing has unveiled the complex transcriptional variations inherent in cardiac cells, offering valuable perspectives into their dynamics. This review focuses on the integration of single-cell omics with induced pluripotent stem cells (iPSCs) in the context of cardiovascular research, offering a unique avenue to deepen our understanding of cardiac biology. By synthesizing insights from various single-cell technologies, we aim to elucidate the molecular intricacies of heart health and diseases. Beyond current methodologies, we explore the potential of emerging paradigms such as single-cell/spatial omics, delving into their capacity to reveal the spatial organization of cellular components within cardiac tissues. Furthermore, we anticipate their transformative role in shaping the future of cardiovascular research. This review aims to contribute to the advancement of knowledge in the field, offering a comprehensive perspective on the synergistic potential of transcriptomic analyses, iPSC applications, and the evolving frontier of spatial omics.
5.Comparison Study of Image Quality of Direct and Indirect Conversion Digital Mammography System.
Hye Suk PARK ; Yuna OH ; Hee Jeong JO ; Sang Tae KIM ; Yu Na CHOI ; Hee Joung KIM
Korean Journal of Medical Physics 2010;21(3):239-245
The purpose of this study is to comprehensively compare and evaluate the characteristics of image quality for digital mammography systems which use a direct and indirect conversion detector. Three key metrics of image quality were evaluated for the direct and indirect conversion detector, the modulation transfer function (MTF), normalized noise power spectrum (NNPS), and detective quantum efficiency (DQE), which describe the resolution, noise, and signal to noise performance, respectively. DQE was calculated by using a edge phantom for MTF determination according to IEC 62220-1-2 regulation. The contrast to noise ratio (CNR) was evaluated according to guidelines offered by the Korean Institute for Accreditation of Medical Image (KIAMI). As a result, the higher MTF and DQE was measured with direct conversion detector compared to indirect conversion detector all over spatial frequency. When the average glandular dose (AGD) was the same, direct conversion detector showed higher CNR value. The direct conversion detector which has higher DQE value all over spatial frequency would provide the potential benefits for both improved image quality and lower patient dose in digital mammography system.
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6.Construction and validation of a synthetic phage-displayed nanobody library
Minju KIM ; Xuelian BAI ; Hyewon IM ; Jisoo YANG ; Youngju KIM ; Minjoo MJ KIM ; Yeonji OH ; Yuna JEON ; Hayoung KWON ; Seunghyun LEE ; Chang-Han LEE
The Korean Journal of Physiology and Pharmacology 2024;28(5):457-467
Nanobodies derived from camelids and sharks offer unique advantages in therapeutic applications due to their ability to bind to epitopes that were previously inaccessible. Traditional methods of nanobody development face challenges such as ethical concerns and antigen toxicity. Our study presents a synthetic, phagedisplayed nanobody library using trinucleotide-directed mutagenesis technology, which allows precise amino acid composition in complementarity-determining regions (CDRs), with a focus on CDR3 diversity. This approach avoids common problems such as frameshift mutations and stop codon insertions associated with other synthetic antibody library construction methods. By analyzing FDA-approved nanobodies and Protein Data Bank sequences, we designed sub-libraries with different CDR3 lengths and introduced amino acid substitutions to improve solubility. The validation of our library through the successful isolation of nanobodies against targets such as PD-1, ATXN1 and STAT3 demonstrates a versatile and ethical platform for the development of high specificity and affinity nanobodies and represents a significant advance in biotechnology.
7.Construction and validation of a synthetic phage-displayed nanobody library
Minju KIM ; Xuelian BAI ; Hyewon IM ; Jisoo YANG ; Youngju KIM ; Minjoo MJ KIM ; Yeonji OH ; Yuna JEON ; Hayoung KWON ; Seunghyun LEE ; Chang-Han LEE
The Korean Journal of Physiology and Pharmacology 2024;28(5):457-467
Nanobodies derived from camelids and sharks offer unique advantages in therapeutic applications due to their ability to bind to epitopes that were previously inaccessible. Traditional methods of nanobody development face challenges such as ethical concerns and antigen toxicity. Our study presents a synthetic, phagedisplayed nanobody library using trinucleotide-directed mutagenesis technology, which allows precise amino acid composition in complementarity-determining regions (CDRs), with a focus on CDR3 diversity. This approach avoids common problems such as frameshift mutations and stop codon insertions associated with other synthetic antibody library construction methods. By analyzing FDA-approved nanobodies and Protein Data Bank sequences, we designed sub-libraries with different CDR3 lengths and introduced amino acid substitutions to improve solubility. The validation of our library through the successful isolation of nanobodies against targets such as PD-1, ATXN1 and STAT3 demonstrates a versatile and ethical platform for the development of high specificity and affinity nanobodies and represents a significant advance in biotechnology.
8.Construction and validation of a synthetic phage-displayed nanobody library
Minju KIM ; Xuelian BAI ; Hyewon IM ; Jisoo YANG ; Youngju KIM ; Minjoo MJ KIM ; Yeonji OH ; Yuna JEON ; Hayoung KWON ; Seunghyun LEE ; Chang-Han LEE
The Korean Journal of Physiology and Pharmacology 2024;28(5):457-467
Nanobodies derived from camelids and sharks offer unique advantages in therapeutic applications due to their ability to bind to epitopes that were previously inaccessible. Traditional methods of nanobody development face challenges such as ethical concerns and antigen toxicity. Our study presents a synthetic, phagedisplayed nanobody library using trinucleotide-directed mutagenesis technology, which allows precise amino acid composition in complementarity-determining regions (CDRs), with a focus on CDR3 diversity. This approach avoids common problems such as frameshift mutations and stop codon insertions associated with other synthetic antibody library construction methods. By analyzing FDA-approved nanobodies and Protein Data Bank sequences, we designed sub-libraries with different CDR3 lengths and introduced amino acid substitutions to improve solubility. The validation of our library through the successful isolation of nanobodies against targets such as PD-1, ATXN1 and STAT3 demonstrates a versatile and ethical platform for the development of high specificity and affinity nanobodies and represents a significant advance in biotechnology.
9.Construction and validation of a synthetic phage-displayed nanobody library
Minju KIM ; Xuelian BAI ; Hyewon IM ; Jisoo YANG ; Youngju KIM ; Minjoo MJ KIM ; Yeonji OH ; Yuna JEON ; Hayoung KWON ; Seunghyun LEE ; Chang-Han LEE
The Korean Journal of Physiology and Pharmacology 2024;28(5):457-467
Nanobodies derived from camelids and sharks offer unique advantages in therapeutic applications due to their ability to bind to epitopes that were previously inaccessible. Traditional methods of nanobody development face challenges such as ethical concerns and antigen toxicity. Our study presents a synthetic, phagedisplayed nanobody library using trinucleotide-directed mutagenesis technology, which allows precise amino acid composition in complementarity-determining regions (CDRs), with a focus on CDR3 diversity. This approach avoids common problems such as frameshift mutations and stop codon insertions associated with other synthetic antibody library construction methods. By analyzing FDA-approved nanobodies and Protein Data Bank sequences, we designed sub-libraries with different CDR3 lengths and introduced amino acid substitutions to improve solubility. The validation of our library through the successful isolation of nanobodies against targets such as PD-1, ATXN1 and STAT3 demonstrates a versatile and ethical platform for the development of high specificity and affinity nanobodies and represents a significant advance in biotechnology.
10.Construction and validation of a synthetic phage-displayed nanobody library
Minju KIM ; Xuelian BAI ; Hyewon IM ; Jisoo YANG ; Youngju KIM ; Minjoo MJ KIM ; Yeonji OH ; Yuna JEON ; Hayoung KWON ; Seunghyun LEE ; Chang-Han LEE
The Korean Journal of Physiology and Pharmacology 2024;28(5):457-467
Nanobodies derived from camelids and sharks offer unique advantages in therapeutic applications due to their ability to bind to epitopes that were previously inaccessible. Traditional methods of nanobody development face challenges such as ethical concerns and antigen toxicity. Our study presents a synthetic, phagedisplayed nanobody library using trinucleotide-directed mutagenesis technology, which allows precise amino acid composition in complementarity-determining regions (CDRs), with a focus on CDR3 diversity. This approach avoids common problems such as frameshift mutations and stop codon insertions associated with other synthetic antibody library construction methods. By analyzing FDA-approved nanobodies and Protein Data Bank sequences, we designed sub-libraries with different CDR3 lengths and introduced amino acid substitutions to improve solubility. The validation of our library through the successful isolation of nanobodies against targets such as PD-1, ATXN1 and STAT3 demonstrates a versatile and ethical platform for the development of high specificity and affinity nanobodies and represents a significant advance in biotechnology.