Analysis of nano-crystals: Evaluation of heavy metal-embedded biological specimen by high voltage electron microscopy

Jeong, Hyeongseop,Yoo, Seung Jo,Won, Jonghan,Lee, Hyun-Ju,Chung, Jeong Min,Kim, Han-ul,Kim, Gwang Joong,Kim, Jin-Gyu,Jung, Hyun Suk,Hyun, Jaekyung Elsevier 2018 Ultramicroscopy Vol.194 No.-

<P><B>Abstract</B></P> <P>Heavy metal compounds are adsorbed onto biological specimen in order to enhance the contrast as well as to preserve the structural features of the specimen against electron beam-induced radiation damage. In particular, in combination with computational image processing, negative staining is widely used for structural analysis of protein complexes to moderate resolutions. Image analysis of negatively stained biological specimen is known to suffer from limited achievable resolution due to dehydration and large grain size of staining molecules although the extent of such effect remains somewhat dubious.</P> <P>Stain molecules exist as grains under electron beam. However, clear observation of the crystalline nature of the grains and their association with biological specimen has not been thoroughly demonstrated. In this study, we attempted high-resolution TEM (HRTEM) using high voltage electron microscopy and electron crystallography analysis for the detailed characterization of negatively stained biological specimen, focusing on physical state and chemical composition of the stain molecules. The electron crystallography analysis allowed for the identification of the crystal constituents of widely used stains, hence revealing the chemical nature and the morphology of the stain molecules at specimen level. This study re-evaluated generally accepted notions on negative staining, and may help correctly interpreting the structural analysis of stained biological specimen.</P> <P><B>Highlights</B></P> <P> <UL> <LI> High voltage electron microscopy (HVEM) visualized nano-crystals surrounding of heavy metal-embedded biological specimen. </LI> <LI> Electron crystallography determined chemical composition of the stain molecules. </LI> <LI> The grain size of nano-crystals of stained molecules from uranyl acetate and uranyl formate were nearly identical, and consistent with that of uranium dioxide (UO<SUB>2</SUB>). </LI> <LI> It identified that UO<SUB>2</SUB> is the main contributor of image contrast of heavy metal-embedded biological specimen. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Construction of regional mouse brain ganglioside library using UHPLC-QTOF MS and MS/MS

Jaekyung Yunl,Jua Lee,Hyun Joo An 한국당과학회 2018 한국당과학회 학술대회 Vol.2018 No.07

Gangliosides are amomc glycosphingolipids containing one to several sialic acid residues. Although they play an important role in neuro-biological functions including synaptic plasticity and memory formation, there are only few studies in ganglioside due to their structural complexity and lack of effective analytical methods. In particular, isomeric investigation of gangliosides is necessarily required in order to understand the ganglioside biology with the consideration of its biosynthesis however, isomer separation based on reversed-phase (RP) chromatography is highly challengeable. In this study, for the purpose of construction of localized mouse brain ganglioside library, we examined ganglioside from anatomically dissected nine mouse brain regions using UHPLC-QTOF MS and MS/MS. Briefly, gangliosides were extracted by modified Folch method with chloroform and methanol, followed by purification and enrichment by Cl8-SPE. Then they were identified and quantified by UHPLC (Cl8 column) QTOF MS. Ganglioside isomers were completely separated depending on their glycan traits on a Cl8 column by addition of formic acid in the mobile phase. Furthermore, tandem MS analysis was performed to confirm the identification based on diagnostic fragment ions. Through LC-MS/MS based isomeric investigation of gangliosides, region- specific mouse brain ganglioside biosynthetic pathway including 0-, a-, b- and c- series could be suggested. Interestingly, major ganglioside were distributed with distinguished qualitative and quantitative pattern for each nine brain regions. In the future, the constructed library of mouse brain ganglioside will be used for monitoring alteration in KO mouse models including glycosylation transferase KO mice.

Effect of Metal-sulfate as Electron Acceptor to Reduce Nitrous Oxide Emission on Denitrification

Hyun Ho Lee(이현호),Jaekyung Song(송재경),Chang Oh Hong(홍창오) 한국토양비료학회 2018 한국토양비료학회 학술발표회 초록집 Vol.2018 No.10

문풀을 가지는 2차원 부유체의 강제 상하동요에 대한 CFD 해석

허재경(Jaekyung Heo),박종천(Jong-Chun Park),Moo-Hyun Kim 한국해양공학회 2011 韓國海洋工學會誌 Vol.25 No.2

A two-dimensional floating body with a moon pool under forced heave motion, including a piston mode, is numerically simulated. A dynamic CFD simulation is carried out to thoroughly investigate the flaw field around a two-dimensional moon pool aver various heaving frequencies. The numerical results are compared with experimental results and a linear potential program by Faltinsen et al. (2007). The effects of vortex shedding and viscosity are investigated by changing the corner shapes of the floating body and solving the Euler equation, respectively. The flaw fields, including the velocity, vorticity, and pressure fields, are discussed to understand and determine the mechanisms of wave elevation, damping, and sway force.

연성해석을 이용한 원통형 전자기식 액추에이터의 설계

임재경(JaeKyung Lim),우정현(Jung-Hyun Woo),박영필(Young-Pil Park),박경수(Kyung-Su Park),박노철(No-Cheol Park),백윤수(Yoon Su Beak),유원희(Won Hee You) 한국소음진동공학회 2011 한국소음진동공학회 학술대회논문집 Vol.2011 No.4

철도 차량용 원통형 선형 구동기의 설계

임재경(JaeKyung Lim),우정현(Jung-Hyun Woo),박영필(Young-Pil Park),박경수(Kyung-Su Park),박노철(No-Cheol Park),백윤수(Yoon Su Beak),유원희(Won Hee You) 한국소음진동공학회 2010 한국소음진동공학회 학술대회논문집 Vol.2010 No.10

초저온 전자현미경법을 통한 고분해능 생물분자 구조분석

현재경,Hyun, Jaekyung 한국진공학회 2017 진공 이야기 Vol.4 No.4

Transmission electron microscopy (TEM) is a versatile and powerful technique that enables direct visualization of biological samples of sizes ranging from whole cell to near-atomic resolution details of a protein molecule. Thanks to numerous technical breakthroughs and monumental discoveries, 3D electron microscopy (3DEM) has become an indispensable tool in the field of structural biology. In particular, development of cryo-electron microscopy(cryo-EM) and computational image processing played pivotal role for the determination of 3D structures of complex biological systems at sub-molecular resolution. Here, basis of TEM and 3DEM will be introduced, especially focusing on technical advancements and practical applications. Also, future prospective of constantly evolving 3DEM field will be discussed, with an anticipation of great biological discoveries that were once considered impossible.

중세철학의 연구 동향과 토미즘의 미래 - 이재룡 신부의 물음 되새기기 -

이재경 ( Lee Jaekyung ),정현석 ( Chung Hyun Sok ) 한국중세철학회 2023 중세철학 Vol.- No.29

이 글은 “21세기를 맞아 토미즘의 과제는 무엇일까?”라는 이재룡 신부의 물음을 되새기고자 한다. 19세기 말 교황 레오 13세가 회칙 「영원하신 아버지」를 반포한 이후 토미즘은 물론 중세철학 연구도 획기적인 발전을 이루어 냈지만, 최근 들어 토마스 중심적인 연구 경향 탓에 중세철학 연구의 불균형 현상이 생길 뿐만 아니라 토미즘도 고립을 자초한다는 비판이 제기되기도 한다. 우리는 이런 비판에 귀 기울이면서 토미즘의 미래를 위한 과제를 알아보고자 한다. 이를 위해 비판의 대상인 중세철학의 표준적 해석들에 대해 살펴보고 중세철학과 토마스 또는 토미즘의 대안적 해석이나 연구 방법을 모색하고자 한다. This paper aims to reflect on Fr. Jae-Ryong Lee’s question, “What are the challenges of Thomism in the 21st century?” Since Pope Leo XIII promulgated the encyclical ‘Aeterni Patris’ at the end of the 19th century, the study of medieval philosophy as well as Thomism have made great strides, but there have recently been criticisms that Aquinas-centered research has not only led to an imbalance in the study of medieval philosophy but also to the isolation of Thomism. We wish to respond to these criticisms and explore the challenges for the future of Thomism. To this end, we will examine the standard interpretations of medieval philosophy that have been criticized and find out alternative interpretations and methods of studying medieval philosophy and Aquinas or Thomism.

Regulation Mechanism of the <i>ald</i> Gene Encoding Alanine Dehydrogenase in <i>Mycobacterium smegmatis</i> and <i>Mycobacterium tuberculosis</i> by the Lrp/AsnC Family Regulator AldR

Jeong, Ji-A,Hyun, Jaekyung,Oh, Jeong-Il American Society for Microbiology 2015 Journal of Bacteriology Vol.197 No.19

<P>In the presence of alanine, AldR, which belongs to the Lrp/AsnC family of transcriptional regulators and regulates <I>ald</I> encoding alanine dehydrogenase in <I>Mycobacterium smegmatis</I>, changes its quaternary structure from a homodimer to an octamer with an open-ring conformation. Four AldR-binding sites (O2, O1, O4, and O3) with a consensus sequence of GA/T-N<SUB>2</SUB>-NWW/WWN-N<SUB>2</SUB>-A/TC were identified upstream of the <I>M. smegmatis</I> <I>ald</I> gene by means of DNase I footprinting analysis. O2, O1, and O4 are required for the induction of <I>ald</I> expression by alanine, while O3 is directly involved in the repression of <I>ald</I> expression. In addition to O3, both O1 and O4 are also necessary for full repression of <I>ald</I> expression in the absence of alanine, due to cooperative binding of AldR dimers to O1, O4, and O3. Binding of a molecule of the AldR octamer to the <I>ald</I> control region was demonstrated to require two AldR-binding sites separated by three helical turns between their centers and one additional binding site that is in phase with the two AldR-binding sites. The cooperative binding of AldR dimers to DNA requires three AldR-binding sites that are aligned with a periodicity of three helical turns. The <I>aldR</I> gene is negatively autoregulated independently of alanine. Comparative analysis of <I>ald</I> expression of <I>M. smegmatis</I> and <I>Mycobacterium tuberculosis</I> in conjunction with sequence analysis of both <I>ald</I> control regions led us to suggest that the expression of the <I>ald</I> genes in both mycobacterial species is regulated by the same mechanism.</P><P><B>IMPORTANCE</B> In mycobacteria, alanine dehydrogenase (Ald) is the enzyme required both to utilize alanine as a nitrogen source and to grow under hypoxic conditions by maintaining the redox state of the NADH/NAD<SUP>+</SUP> pool. Expression of the <I>ald</I> gene was reported to be regulated by the AldR regulator that belongs to the Lrp/AsnC (feast/famine) family, but the underlying mechanism was unknown. This study revealed the regulation mechanism of <I>ald</I> in <I>Mycobacterium smegmatis</I> and <I>Mycobacterium tuberculosis</I>. Furthermore, a generalized arrangement pattern of <I>cis</I>-acting regulatory sites for Lrp/AsnC (feast/famine) family regulators is suggested in this study.</P>

The Use of LIF-based Instrument with 405 nm for Real-time Monitoring of Aerosolized Bio-particles

Sung Nyo Yoon,Jaekyung Lee,Duckho Kim,Hyun Sang Yoo,Kyung Yool Min,Min Cheol Kim 한국대기환경학회 2019 Asian Journal of Atmospheric Environment (AJAE) Vol.13 No.3

Bio-aerosols can affect public health depending on the origin of bio-particles (bacteria, virus etc.). Here, we attempted to assess the applicability of laser-induced fluorescence (LIF) instrument with 405 nm to real-time monitoring of bacteria and viruscontaining aerosols. For the purpose, the LIF-based BDS (Bio-aerosol Detection System) was used. The bio-particle monitoring of the BDS is based on fluorescence signals from two wavelength ranges [short wavelength range (SWR): 430-550 nm & long wavelength range (LWR): 500-600 nm] and the scattering signal. Firstly, auto-fluorophores (NADH, riboflavin, tyrosine, tryptophan) were tested to expect the monitoring ranges of the BDS for the auto-fluorophores. NADH and riboflavin showed fluorescence signals from two wavelength ranges, and the fluorescence efficiency of NADH was higher in the SWR than in the LWR and that of riboflavin was reversed. While tyrosine and tryptophan showed negligible fluorescence signals from two wavelength ranges as expected. Next, the lyophilized powders of Bacillus subtilis (BS), virus vaccines [ND (Newcastle Disease), IB (Infectious Bronchitis)] and the bacteriophage MS2 were tested to investigate the monitoring ranges of the BDS for the bio-particles. Individual virus and bacteriophage have been expected no fluorescence signals because of the absence of NADH and riboflavin fluorescing by 405 nm. Nonetheless, all the tested samples showed the fluorescence signals in the size range of 2 to 15 μm, generally known as bio-aerosol size. Considering that atmospheric virus particles are released through the respiratory organs of their hosts, just as virus vaccines from chicken embryo and MS2 from E. coli, it can be thought in turn that the BDS can also monitor bio-aerosols including virus as well as bacteria. Taken together, we suggests that the BDS, LIF-based instrument with 405 nm, is applicable for real-time monitoring of virus-containing aerosols as well as other bio-aerosols by counting the fluorescence particles and resolving their particle sizes.