Mitochondrial genome editing: strategies, challenges, and applications

Kayeong Lim 생화학분자생물학회 2024 BMB Reports Vol.57 No.1

Mitochondrial DNA (mtDNA), a multicopy genome found inmitochondria, is crucial for oxidative phosphorylation. Mutationsin mtDNA can lead to severe mitochondrial dysfunction intissues and organs with high energy demand. MtDNA mutationsare closely associated with mitochondrial and age-relateddisease. To better understand the functional role of mtDNAand work toward developing therapeutics, it is essential toadvance technology that is capable of manipulating the mitochondrialgenome. This review discusses ongoing efforts inmitochondrial genome editing with mtDNA nucleases and baseeditors, including the tools, delivery strategies, and applications. Future advances in mitochondrial genome editing toaddress challenges regarding their efficiency and specificity canachieve the promise of therapeutic genome editing.

Au nanoparticle-encapsulated hydrogel substrates for robust and reproducible SERS measurement

Shin, Kayeong,Ryu, Kyungtag,Lee, Hoik,Kim, Kwangsoo,Chung, Hoeil,Sohn, Daewon The Royal Society of Chemistry 2013 The Analyst Vol.138 No.3

<P>A reliable and reproducible surface-enhanced Raman scattering (SERS) measurement utilizing Au nanoparticle-encapsulated hydrogels as a substrate has been demonstrated. A hydrogel matrix was adopted to: (i) take advantage of its excellent water uptake capacity for facile access of an analyte into the substrate and (ii) securely hold Au nanoparticles. Silica-coated Au (Au@SiO<SUB>2</SUB>) nanoparticles were initially prepared and uniquely used as an initiator as well as a cross-linker for the polymerization of acrylic acid to synthesize Au nanoparticle-encapsulated hydrogels. Then, the outer silica layer of the Au nanoparticles in the hydrogel was etched out using hydrofluoric acid (HF) to make it possible for an analyte to approach the surface of the Au nanoparticles for generation of the SERS signal. In parallel, locally occurring SERS signals over the hydrogel were integrated using a wide area illumination scheme capable of covering a large area to improve quantitative representation of analyte concentration. To evaluate reproducibility of the proposed method, 6 independent hydrogels were prepared every two months over one year and then Raman spectra of 2-naphthalenethiol (2-NAT) captured hydrogels were collected. The resulting SERS intensities of 2-NAT acquired at each concentration were reproducible and clearly increased according to the elevation of 2-NAT concentration.</P> <P>Graphic Abstract</P><P>A reliable and reproducible surface-enhanced Raman scattering (SERS) measurement utilizing Au nanoparticle-encapsulated hydrogels as a substrate has been demonstrated. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c2an35862j'> </P>

Development of a particle-settling tolerant transmission Raman scheme for analysis of suspension samples

Shin, Kayeong,Duy, Pham Khac,Park, Sijun,Woo, Young-Ah,Chung, Hoeil The Royal Society of Chemistry 2014 The Analyst Vol.139 No.11

<P>We have demonstrated a simple and effective strategy, the so-called axial illumination scheme, that is able to obtain representative Raman spectra of suspension samples with minimal influence from internal particle settling. In a partially settled suspension sample, since particle concentrations at given points throughout the sample differ, the acquisition of Raman spectra representative of the entire sample composition is critically important for accurate quantitative analysis. The proposed scheme used axially irradiated laser radiation in the same or opposite direction of settling, thus allowing laser photons to migrate through the settling-induced particle-density gradient formed in the suspension and to widely interact with particles regardless of their settled locations. Therefore, transmitted Raman signals gathered opposite to the illumination could be more representative of the overall suspension composition even with partial settling. In this study, the performance of axial illumination schemes (TB (Top-to-Bottom) and BT (Bottom-to-Top) illumination) was evaluated for the determination of the aceclofenac (a non-steroidal anti-inflammatory drug) concentration in suspensions. Although the spectral features exhibited minute variations during settling, settling did not significantly degrade the accuracy of the concentration determination, thereby indicating effective acquisition of settling-tolerant Raman spectra. In addition, the characteristics of photon migration in a partially settled suspension sample were studied using a simulation based on Monte-Carlo method.</P> <P>Graphic Abstract</P><P>We have demonstrated a simple and effective strategy, the so-called axial illumination scheme, that is able to obtain representative Raman spectra of suspension samples with minimal influence from internal particle settling. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c4an00213j'> </P>

A Au nanoparticle-incorporated sponge as a versatile transmission surface-enhanced Raman scattering substrate

Shin, Kayeong,Chung, Hoeil The Royal Society of Chemistry 2015 The Analyst Vol.140 No.15

<P>We report a sponge-based transmission surface-enhanced Raman scattering (TSERS) substrate that combines the bulk sampling capabilities of a transmission measurement to improve the quantitative representation of sample concentration with several sponge properties useful for analysis such as fast sample uptake, easy sample enrichment, and a stable polymeric structure. Among nine commercially available sponges made of different materials, a melamine sponge was ultimately selected for this study because it provided the fastest sample uptake and a low background Raman signal. Simultaneously, the amino groups and three-nitrogen hybrid rings in its structure could easily hold Au nanoparticles (AuNPs) inside the sponge. AuNP-incorporated sponges (AuNP sponges) were prepared by simply soaking a melamine sponge in a AuNP solution; these sponges were initially used to measure 4-nitrobenzenethiol (4-NBT) samples with different concentrations in order to evaluate their ability as TSERS substrates. The intensities of the 4-NBT peaks clearly varied according to changes in the concentration, and the relative standard deviation (RSD) of the peak intensity estimated by the measurements of five independently prepared AuNP sponges was 10.0%. Sample enrichment was easily completed by repeated suctioning of the sample into the AuNP sponges followed by depletion of the solvent, so three-time enrichment doubled the intensity. Furthermore, paraquat samples were prepared in diverse matrices (de-ionized water, tap water, river water, and orange juice) and measured using the AuNP sponges. The paraquat peaks were clearly observed from these samples and their peak intensities became smaller with the increased compositional complexity of the matrices. Our overall results demonstrate that the TSERS sponge substrates are easy to prepare and practically versatile for SERS analysis of diverse samples.</P> <P>Graphic Abstract</P><P>We report a sponge-based transmission surface-enhanced Raman scattering (TSERS) substrate that combines the bulk sampling capabilities of a transmission measurement to improve the quantitative representation of sample concentration with several sponge properties useful for analysis such as fast sample uptake, easy sample enrichment, and a stable polymeric structure. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c4an02216e'> </P>

Feasibility study for combination of field-flow fractionation (FFF)-based separation of size-coded particle probes with amplified surface enhanced Raman scattering (SERS) tagging for simultaneous detection of multiple miRNAs

Shin, Kayeong,Choi, Jaeyeong,Kim, Yeoju,Lee, Yoonjeong,Kim, Joohoon,Lee, Seungho,Chung, Hoeil Elsevier 2018 Journal of chromatography A Vol.1556 No.-

<P>We propose a new analytical scheme in which field-flow fractionation (FFF)-based separation of target-specific polystyrene (PS) particle probes of different sizes are incorporated with amplified surface enhanced Raman scattering (SERS) tagging for the simultaneous and sensitive detection of multiple microRNAs (miRNAs). For multiplexed detection, PS particles of three different diameters (15, 10, 5 mu m) were used for the size-coding, and a probe single stranded DNA (ss DNA) complementary to a target miRNA was conjugated on an intended PS particle. After binding of a target miRNA on PS probe, polyadenylation reaction was executed to generate a long tail composed of adenine (A) serving as a binding site to thymine (T) conjugated Au nanoparticles (T-AuNPs) to increase SERS intensity. The three size-coded PS probes bound with T-AuNPs were then separated in a FFF channel. With the observation of extinction based fractograms, separation of three size-coded PS probes was clearly confirmed, thereby enabling of measuring three miRNAs simultaneously. Raman intensities of FFF fractions collected at the peak maximum of 15, 10 and 5 mu m PS probes varied fairy quantitatively with the change of miRNA concentrations, and the reproducibility of measurement was acceptable. The proposed method is potentially useful for simultaneous detection of multiple miRNAs with high sensitivity. (C) 2018 Elsevier B.V. All rights reserved.</P>

Transmission Raman measurement directly through packed corn kernels to improve sample representation and accuracy of compositional analysis

Shin, Kayeong,Chung, Hoeil,Kwak, Chul-won The Royal Society of Chemistry 2012 The Analyst Vol.137 No.16

<P>The potential of transmission Raman spectroscopy for direct analysis of packed granular samples, one of the most frequently encountered sample types in the field of non-destructive spectroscopic analysis, has been evaluated. For this purpose, transmission Raman spectra were collected by laser illumination through packed corn kernels to determine their protein concentration. Back-scattering Raman spectra of the same samples were also collected for comparison. Raman spectral features of the major kernel constituents were initially characterized, and Raman mapping over the whole kernel face was performed to investigate the inhomogeneous distribution of constituents in a kernel. Possible variations of transmission spectral features depending on the laser illumination on different locations of a kernel were investigated, since the orientation of kernels in the packing was essentially random. Rotation of kernel packing during spectral collection was helpful in improving the compositional representation of packed kernels. With partial least squares (PLS) regression, the protein concentrations were determined using both spectral collection methods and the resulting accuracies were compared. As a result, the transmission measurement provided a more accurate determination of protein concentration since it enabled deeper sampling across the packed kernels, leading to a better compositional representation of them. By contrast, in the back-scattering measurement, kernels on the top of the packing were mainly sampled for the spectral acquisition. Moreover, the back-scattering spectral feature, more weighted to constituents localized at the outer portion of a kernel, was short of representing the overall composition of a kernel.</P> <P>Graphic Abstract</P><P>The potential of transmission Raman spectroscopy for direct analysis of packed granular samples, one of the most frequently encountered sample types in the field of non-destructive spectroscopic analysis, has been evaluated. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c2an35443h'> </P>

Use of Multiple Peptide-Based SERS Probes Binding to Different Epitopes on a Protein Biomarker To Improve Detection Sensitivity

Shin, Kayeong,Cho, Jun-Haeng,Yoon, Moon-Young,Chung, Hoeil American Chemical Society 2016 ANALYTICAL CHEMISTRY - Vol.88 No.7

<P>We propose an analytical strategy to improve the sensitivity for detecting a protein biomarker through signal multiplication by manipulating multiple peptide-based surface enhanced Raman scattering (SERS) probes to bind the biomarker. Protective antigen (PA) was used as an Anthrax biomarker in this study. For this purpose, five small peptides selective to various PA epitopes with different binding affinities were chosen and peptide conjugated Au nanoparticle (AuNP) SERS probes were individually prepared using each peptide. Initially, five different SERS probes were separately used to detect PA and the sensitivities were compared. Next, the possibility of enhancing sensitivity by employing multiple SERS probes was examined: Rather than applying the probes simultaneously, which would induce competitive binding, each probe was added sequentially and an optimal probe-addition sequence was determined to provide maximal sensitivity. Finally, PA samples at seven different concentrations were measured with the optimal sequence. The limit of detection (LOD) was 0.1 aM, and the enhancement was more effective at lower PA concentrations. The proposed scheme can be further applicable to detect other protein biomarkers to diagnose various diseases.</P>

쿠마 켄고 공간에 나타난 재료와 구축성에 관한 연구

정가영(Jeong, Kayeong),김문덕(Kim, Moon-Duck) 한국실내디자인학회 2009 한국실내디자인학회 학술대회논문집 Vol.11 No.2

In this study, the architectural spaces of Kengo Kuma were analyzed through the recent trend, materials and tectonic methods of Japanese architecture to review his current design characteristics. The study was conducted through reviewing the collections of Kengo Kuma’s works and his books currently published in Korea and foreign countries, work critiques and interviews published in domestic and international monthly magazines and site visits and the scope of study subjects included 10 works that well expressed the characteristics of materials and construction out of Kengo Kuma’s works. Based on the result, Kengo Kuma mainly uses natural materials such as woods or stones and cuts them to small pieces to use them as construction elements. Through this way, he intended to introduce external environments into indoors so that construction and natural environments can be overlapped and coexist with each other. In terms of tectonics, sub material were arranged in vertical forms to construct spaces in the early period and the forms became more diversified into 3-dimensions in later periods. In general, his works in the early period showed architectures that coexisted with natural environments and were hidden while his works in later periods showed the characteristics of existing while considering the meanings of places together.

지속가능성의 바이오필릭 디자인을 활용한 브랜드 아이덴티티 - 호텔 사례를 중심으로 -

최가영(Choi, Kayeong),이현수(Lee, Hyunsoo) 한국실내디자인학회 2020 한국실내디자인학회 학술대회논문집 Vol.22 No.2

바이오필릭 디자인의 응용 사례연구: 1 Hotels을 중심으로

최가영(Choi, Kayeong),이현수(Lee, Hyunsoo) 한국실내디자인학회 2018 한국실내디자인학회 학술대회논문집 Vol.20 No.1

Architectural spaces are organically related to humans, society, and culture, but such relationship has been discarded for a long time as only the accomplishments of technology and engineering fostered the modern built environment. The contemporary society which encountered a paradigm shift in accordance to technological advancement is calling upon biophilic design which attempts to translate the understanding of humans’ innate affiliation with nature into the design of architecture as an alternative design approach. In this regard, the study aims to shed light on a need of biophilic design in today’s built environment and to examine the application of biophilic design through case analysis.