De novo assembly and phasing of a Korean human genome

Seo, Jeong-Sun,Rhie, Arang,Kim, Junsoo,Lee, Sangjin,Sohn, Min-Hwan,Kim, Chang-Uk,Hastie, Alex,Cao, Han,Yun, Ji-Young,Kim, Jihye,Kuk, Junho,Park, Gun Hwa,Kim, Juhyeok,Ryu, Hanna,Kim, Jongbum,Roh, Mira Nature Publishing Group, a division of Macmillan P 2016 Nature Vol.538 No.7624

<P>Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing(2), next-generation mapping(3), microfluidics-based linked reads(4), and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.</P>

Development of InDel markers based on chloroplast DNA for the identification of Ziziphus jujuba Mill. cultivars

Kim Moonkyo,Yeruult Enkhtsetseg,Lee Dong Geun,Oh Ha Kyung,Lee Mi Sun,Kim Juhyeok,Park Sang Ik,Gil Jinsu,Lee Kyeong Hee,이문순,Lee Yi 한국원예학회 2024 Horticulture, Environment, and Biotechnology Vol.65 No.3

Jujube ( Ziziphus jujuba Mill.) is a plant belonging to the genus Ziziphus of the family Rhamnaceae. Z. jujuba is generally rich in nutrients—vitamin C, thiamin, and ribofl avin—making it an excellent source of functional food. Z. jujuba cultivation has a long history, resulting in the creation of numerous cultivars, and the economic value of this plant has recently been on the rise. Therefore, there is a need for easy and accurate methods to distinguish the cultivars. We developed insertion or deletion (InDel) markers using chloroplast (CP) DNA to identify Z. jujuba cultivars. A total of 192 InDel loci were found and 21 InDel markers were developed. Twenty-two InDel markers were used for diversity analysis, including the Zj-InDel-1 marker developed in the previous study. The size of the InDel loci varied from 4 to 200 bp. The maximum value of polymorphism information content (PIC) was 0.35, the minimum value was 0.03, and the average was 0.31. The 61 Z. jujuba cultivars were grouped into 8 CP types by the 22 CP InDel markers. The ‘Dongjo’, ‘Sanjo’, ‘Tibetwang’ and ‘Wolgwang’ cultivars were classifi ed independently among the 61 cultivars. The InDel markers developed in this study could be used for cultivar identifi cation and breeding of Z. jujuba .

스피리컬 조인트를 이용하여 다중 쿼드로터를 결합한 공중조작시스템의 모델링 및 제어

김주혁(Juhyeok Kim),뉴엔하이뉴엔(Hai-Nguyen Nguyen),이동준(Dongjun Lee) 대한기계학회 2015 대한기계학회 춘추학술대회 Vol.2015 No.11

We introduce a new aerial manipulator system that consists of an airborne base actuated by spherically-connected multiple quadrotors and a manipulator rigidly connected to that base. We first model the dynamics of the system and show that attitude dynamics of each quadrotor is decoupled from the base-manipulator dynamics. We then use Lyapunov approach to design a pose-tracking control for the end-effector of the manipulator and optimally distribute that control input to each quadrotor on the base and each joint rotor of the manipulator. The simulation of a system of three quadrotors and a 2 degree-of-freedom(DOF) manipulator is presented to support the theory.

층상형 광물의 마찰물성에 대한 나노수준의 이해를 위해

김주혁(Juhyeok Kim),권기덕(Kideok D. Kwon) 대한지질학회 2022 대한지질학회 학술대회 Vol.2022 No.10

수정진동자미세저울을 이용한 광물-나노플라스틱 상호작용 연구

김주혁(Juhyeok Kim),명현아(Hyeonah Myeong),권기덕(Kideok D. Kwon) 한국암석학회 2021 한국암석학회 학술발표회 논문집 Vol.2021 No.8

토양-지하수내 미세플라스틱 거동 연구를 위한 수정진동자미세저울 기술 소개

김주혁 ( Juhyeok Kim ),명현아 ( Hyeonah Myeong ),손상보 ( Sangbo Son ),권기덕 ( Kideok D. Kwon ) 한국암석학회·(사)한국광물학회 2020 광물과 암석 (J.Miner.Soc.Korea) Vol.33 No.4

최근 토양과 지하수에서도 미세플라스틱이 발견되어 미세플라스틱 환경오염 관련 연구의 중요성이 크게 대두되고 있다. 주로 μm - nm의 작은 입자로 존재하는 점토광물과 금속산화광물은 표면적이 넓어 미세플라스틱에 대한 흡착력 등 화학 반응도가 매우 높기 때문에, 광물표면 상호작용은 토양과 지하수 환경 내 미세플라스틱의 거동을 결정하는 중요한 역할을 할 수 있다. 따라서, 광물과 미세플라스틱 간의 상호작용에 대한 환경광물학 연구는 미세플라스틱 거동 예측 기술개발 및 오염대책 마련에 핵심이 되는 연구분야라 할 수 있다. 광물표면과 미세플라스틱(특히, 나노플라스틱) 연구에는 분자-나노수준의 분석기술이 요구된다. 이번 기술보고에서는 나노그람(=10^-9 g) 수준의 질량 변화를 실시간으로 측정할 수 있는 초정밀 분석기기로, 광물 표면에 흡·탈착되는 미세플라스틱 및 나노플라스틱의 미세한 질량 변화를 측정할 수 있는, 수정진동자미세저울(quartz crystal microbalance, QCM)을 소개한다. QCM 작동원리를 소개하고, 대표적인 QCM 연구결과와 기존 컬럼 실험과의 장단점을 비교하여 미세플라스틱 연구에 QCM 활용 가능성을 논의한다. Presence of microplastics in soil and groundwater has recently been reported and environmental concerns are raised as to the plastic pollution. In the subsurface environment, clay minerals and metal oxide minerals are commonly found as finely dispersed states. Because the minerals have high sorption capacities for diverse pollutants, interactions with mineral surface play an important role in the transport of microplastics in groundwater. Accordingly, environmental mineralogy investigating the interactions between microplastics and mineral surfaces is the essential research area to understand the fate and transport of microplastics in the subsurface environment. The microplastic-mineral surface research requires molecular- to nano-scale analyses to be able to probe the relatively weak interactions between them. The current report introduces a nano-scale analysis tool called quartz crystal microbalance (QCM) that can measure the sorbed/desorbed mass of nanoplastics on mineral surfaces at the level of a few nanograms (~10^-9 g). This report briefly reviews the main principles in the QCM measurement and discusses applications of QCM to the environmental mineralogy research.

Comparative Study Between Geopolymer and Cement Waste Forms for Solidification of Corrosive Sludge

Lee, Juhyeok,Kim, Byoungkwan,Kang, Jaehyuk,Kang, Jaeeun,Kim, Won-Seok,Um, Wooyong Korean Radioactive Waste Society 2020 방사성폐기물학회지 Vol.18 No.4

Two waste forms, namely cement and geopolymer, were investigated and tested in this study to solidify the corrosive sludge generated from the surface and precipitates of the tubes of steam generators in nuclear power plants. The compressive strength of the cement waste form cured for 28 days was inversely proportional to waste loading (24.4 MPa for 0wt% to 2.7 MPa for 60wt%). The corrosive sludge absorbed the free water in the hydration reaction to decrease the cementation reaction. When the corrosive sludge waste loading increased to 60wt%, the cement waste form showed decreased compressive strength (2.7 MPa), which did not satisfy the acceptance criteria of the repository (3.45 MPa). Meanwhile, the compressive strength of the geopolymer waste form cured for 7 days was proportional to waste loading (23.6 MPa for 0wt% to 31.9 MPa for 40wt%). The corrosive sludge absorbed the free water in the geopolymer when the water content decreased, such that a compact geopolymer structure could be obtained. Consequently, the geopolymer waste forms generally showed higher compressive strengths than cement waste forms.

다중 랜덤 워커를 이용한 객체 추적 기법

문주혁(Juhyeok Mun),김한울(Han-Ul Kim),김창수(Chang-Su Kim) 한국방송·미디어공학회 2016 한국방송공학회 학술발표대회 논문집 Vol.2016 No.6

토도로카이트 내 Mg²⁺ 배위구조에 대한 고전분자동력학 연구

김주혁 ( Juhyeok Kim ),이진용 ( Jin-yong Lee ),권기덕 ( Kideok D. Kwon ) 한국광물학회 2019 광물과 암석 (J.Miner.Soc.Korea) Vol.32 No.3

토도로카이트(todorokite)는 3 × 3 망간 팔면체로 이루어진 상대적으로 큰 나노공극(nanopore)을 가지는 터널구조의 산화망간광물로 나노공극에 다양한 양이온 함유가 가능하기 때문에 금속이온 거동에 큰 역할을 할 수 있다. 주로 결정도가 낮고 다른 산화망간광물들과 함께 집합체로 발견되어 나노공극 내부 양이온의 배위(coordination)구조는 실험만으로 여전히 규명하기 매우 어렵다. 이번 논문에서는 고전분자동력학(classical molecular dynamics, MD) 시뮬레이션을 이용하여 토도로카이트 터널에 함유된 Mg²⁺ 이온의 배위구조에 대한 연구결과를 처음으로 소개한다. 기존 실험에서는 토도로카이트 내부에 함유된 Mg²⁺가 공극의 중앙에 우세하게 자리한다고 알려져 있다. MD 시뮬레이션 결과, Mg²⁺ 이온의 약 60 %가 나노공극의 중앙에 위치하지만, 약 40 %의 Mg²⁺는 광물의 표면에 해당하는 공극의 코너에 위치하였다. 공극 중앙의 Mg²⁺는 수용액에서처럼 물 분자와 6배위수를 보였다. 공극 코너의 Mg²⁺ 역시 6배위수를 보였는데, 물 분자 이외에도 망간 팔면체 표면 산소와 배위를 보였다. Mg²⁺ 이온의 동적 거동을 파악하기 위해 계산한 평균 제곱 변위(mean squared displacement) 결과에서는, 수용액 벌크(bulk) 상태에서 갖는 물 분자와 양이온의 동적 성질이 토도로카이트 1D 나노공극에서는 유지되지 못하고 잃어버리는 것을 확인할 수 있었다. Todorokite, a tunnel-structured manganese oxide, can contain cations within the relatively large nanopores created by the 3 × 3 Mn octahedra. Because todorokite is poorly crystalline and found as aggregates mixed with other phases of Mn oxides in nature, the coordination structure of cations in the nanopores is challenging to fully characterize in experiment. In the current article, we report the atomistic coordination structures of Mg²⁺ ions in todorokite tunnel nanopores using the classical molecular dynamics (MD) simulations. In experiment, Mg²⁺ is known to occupy the center of the nanopores. In our MD simulations, 60 % of Mg²⁺ ions were located at the center of the nanopores; 40 % of the ions were found at the corners. All Mg²⁺ located at the center formed the six-fold coordination with water molecules, just as the ion in bulk aqueous solution. Mg²⁺ ions at the corners also formed the six-fold coordination with not only water molecules but also Mn octahedral surface oxygens. The mean squared displacements were calculated to examine the dynamic features of Mg²⁺ ions in the one-dimensional (1D) nanopores. Our MD simulations indicate that the dynamic features of water molecules and the cations observed in bulk aqueous solution are lost in the 1D nanopores of todorokite.

Solidification of Borate Waste Using Metakaolin-Based Geopolymer Waste Form

Byoungkwan Kim,Juhyeok Lee,Jaehyuk Kang,Younglim Shin,Won-Seok Kim,Wooyong Um 한국방사성폐기물학회 2020 한국방사성폐기물학회 학술논문요약집 Vol.2020 No.12