Charge-Directed Peptide Backbone Dissociations of o-TEMPO-Bz-C(O)-Peptides

Jeon, Aeran,Lee, Ji Hye,Kwon, Hyuk Su,Park, Hyung Soon,Moon, Bong Jin,Oh, Han Bin Korean Society for Mass Spectrometry 2013 Mass spectrometry letters Vol.4 No.4

In the present study, we report that the charge-directed (assisted) peptide dissociation products, such as b- and y-type peptide backbone fragments, were the major products in MS/MS and $MS^3$ applications of some o-TEMPO-Bz-C(O)-peptide ions, while radical-driven dissociation products, such as a/x and c/z-type fragments, were previously shown to be the major products in the free radical initiated peptide sequencing mass spectrometry (FRIPS MS). Those o-TEMPO-Bz-C(O)-peptides share a common feature in their sequences, that is, the peptides do not include an arginine residue that has the highest proton affinity among free amino acids. The appearance of b- and y-type fragments as major products in FRIPS MS can be understood in terms of the so-called "mobile-proton model". When the proton is highly mobilized by the absence of arginine, the chare-directed peptide dissociation pathways appear to be more competitive than the radical-driven dissociation pathways, in our FRIPS experiments.

Charge-Directed Peptide Backbone Dissociations of o-TEMPO-Bz-C(O)-Peptides

( Aeran Jeon ),( Ji Hye Lee ),( Hyuk Su Kwon ),( Hyung Soon Park ),( Bong Jin Moon ),( Han Bin Oh ) 한국질량분석학회 2013 Mass spectrometry letters Vol.4 No.4

In the present study, we report that the charge-directed (assisted) peptide dissociation products, such as b- and y-type peptide backbone fragments, were the major products in MS/MS and MS3 applications of some o-TEMPO-Bz-C(O)-peptide ions, while radical-driven dissociation products, such as a/x and c/z-type fragments, were previously shown to be the major products in the free radical initiated peptide sequencing mass spectrometry (FRIPS MS). Those o-TEMPO-Bz-C(O)-peptides share a common feature in their sequences, that is, the peptides do not include an arginine residue that has the highest proton affinity among free amino acids. The appearance of b- and y-type fragments as major products in FRIPS MS can be understood in terms of the so-called “mobile-proton model”. When the proton is highly mobilized by the absence of arginine, the chare-directed peptide dissociation pathways appear to be more competitive than the radical-driven dissociation pathways, in our FRIPS experiments.

2009 개정 교육과정에 따른 화학II교과서에 포함된 탐구 활동 분석: 8가지 과학 실천을 중심으로

전영,최애란,Jeon, Young,Choi, Aeran 대한화학회 2016 대한화학회지 Vol.60 No.1

최근 과학교육에서 강조되고 있는 과학적 소양의 함양은 과학 지식이 형성되는 일련의 탐구 과정을 경험하고 이해함으로써 향상될 수 있다. 이러한 관점에서 미국연구회(NRC)의 차세대과학기준(NGSS)은 학생들의 과학 탐구 과정 경험과 이해를 돕기 위하여 8가지 과학 실천(8 Practices of Science)을 제안하였고, 8가지 과학 실천 각각에 대하여 학년 군별 세부성취 목표를 제시하고 있다. 본 연구에서는 2009 개정 교육과정에 따른 고등학교 화학II교과서 4종에 포함된 탐구 활동을 8가지 과학 실천과 9-12학년군 세부 성취 목표를 기준으로 분석하였다. 4종의 화학II교과서에 포함된 탐구 활동은 총 173개 이고 분석된 과학 실천은 총 678개 이었다. 4종 화학II교과서의 탐구 활동에 포함된 과학 실천은 ‘자료 분석하고 해석하기’가 가장 많았고, ‘증거에 입각하여 논의하기’, ‘정보를 얻고 평가하고 의사소통하기’등은 상대적으로 그 기회가 부족하였으며, ‘질문하고 문제 규정하기’와 ‘모형 개발하고 사용하기’는 거의 포함되어 있지 않았다. The cultivation of scientific literacy in recent science education can be improved by experiencing and understanding scientific inquiry by which scientific knowledge is formed. The National Research Council(NRC) released the Next Generation Science Standards (NGSS) including 8 practices of science that help students experience scientists' inquiry and subdividing achievement standards to perform 8 practices of science into by grade clusters. This study was intended to examine science inquiry activities included in 4 high school chemistry II textbooks developed by the 2009 revised curriculum using the 8 scientific practices and their achievement standards for 9th-12th grade. The science inquiry activities and the science practices included in the 4 textbooks were 173 and 678. The science practices included in the inquiry activities of 4 textbooks included the most ‘analyzing and interpreting data.’ The ‘engaging in argument from evidence’, ‘Obtaining, Evaluating, and Communicating Information’ were less than other practices. The ‘asking questions and defining problem’ and ‘developing and using models’ were not nearly included in the 4 high school chemistry II textbooks.

Free Radical-Initiated Peptide Sequencing Mass Spectrometry for Phosphopeptide Post-translational Modification Analysis

Jang, Inae,Jeon, Aeran,Lim, Suk Gyu,Hong, Duk Ki,Kim, Min Soo,Jo, Jae Hyeong,Lee, Sang Tak,Moon, Bongjin,Oh, Han Bin Springer New York LLC 2019 Journal of the American Society for Mass Spectrome Vol.30 No.3

<P>Free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) was employed to analyze a number of representative singly or doubly protonated phosphopeptides (phosphoserine and phosphotyrosine peptides) in positive ion mode. In contrast to collision-activated dissociation (CAD) results, a loss of a phosphate group occurred to a limited degree for both phosphoserine and phosphotyrosine peptides, and thus, localization of a phosphorylated site was readily achieved. Considering that FRIPS MS supplies a substantial amount of collisional energy to peptides, this result was quite unexpected because a labile phosphate group was conserved. Analysis of the resulting peptide fragments revealed the extensive production of <I>a</I>-, <I>c</I>-, <I>x</I>-, and <I>z</I>-type fragments (with some minor <I>b</I>- and <I>y</I>-type fragments), suggesting that radical-driven peptide fragmentation was the primary mechanism involved in the FRIPS MS of phosphopeptides. Results of this study clearly indicate that FRIPS MS is a promising tool for the characterization of post-translational modifications such as phosphorylation.</P> [FIG OMISSION]</BR>

Capsular serotypes, virulence-associated genes and antimicrobial susceptibility of <i>Streptococcus suis</i> isolates from pigs in Korea

OH, Sang-Ik,JEON, Albert Byungyun,JUNG, Byeong-Yeal,BYUN, Jae-Won,GOTTSCHALK, Marcelo,KIM, Aeran,KIM, Jong Wan,KIM, Ha-Young JAPANESE SOCIETY OF VETERINARY SCIENCE 2017 The Journal of veterinary medical science Vol.79 No.4

<P><I>Streptococcus suis</I> is an important pig pathogen with potential for human transmission. The serotype distributions and phenotypic characteristics vary over time and among regions; however, little is known about the characteristics of <I>S. suis</I> isolates in Korea. In this study, 240 <I>S. suis</I> isolates collected from pigs in Korea in 2009–2010 were serotyped by coagglutination tests, subsequently screened for three virulence-associated genes (<I>mrp</I>, <I>epf</I> and <I>sly</I>) and tested for antimicrobial susceptibility. As for 80 isolates, the serotypes of which were relevant to human infections, clonal complexes (CCs) were further identified by PCR. Serotype 3 was the most prevalent (15.8%), followed by serotype 2 (15.0%), with geographical variation for each serotype. Overall, 55.4% of the isolates carried <I>mrp</I>, whereas only 3.8% carried <I>epf.</I> CC25 was the most prevalent (41.3%) and was related to serotypes 2 and 9. The isolates showed higher susceptibility to ampicillin (93.4%) and ceftiofur (90.8%) than to the other antimicrobial agents tested. The highest resistance rate was observed to tetracycline (98.0%), followed by erythromycin (88.8%). In addition, the resistance to certain antimicrobials was significantly associated, in part, with virulence-associated genes or serotypes. Therefore, continuous characterization of <I>S. suis</I> is essential for the benefit of veterinary and human medicine.</P>

One-Step Peptide Backbone Dissociations in Negative-Ion Free Radical Initiated Peptide Sequencing Mass Spectrometry

Lee, Jihye,Park, Hyeyeon,Kwon, Hyuksu,Kwon, Gyemin,Jeon, Aeran,Kim, Hugh I.,Sung, Bong June,Moon, Bongjin,Oh, Han Bin American Chemical Society 2013 ANALYTICAL CHEMISTRY - Vol.85 No.15

<P>Peptide dissociation behavior in TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl)-based FRIPS (free radical initiated peptide sequencing) mass spectrometry was analyzed in both positive- and negative-ion modes for a number of peptides including angiotensin II, kinetensin, glycoprotein IIb fragment (296–306), des-Pro<SUP>2</SUP>-bradykinin, and ubiquitin tryptic fragment (43–48). In the positive mode, the ·Bz-C(O)–peptide radical species was produced exclusively at the initial collisional activation of <I>o</I>-TEMPO-Bz-C(O)–peptides, and two consecutive applications of collisional activation were needed to observe peptide backbone fragments. In contrast, in the negative-ion mode, a single application of collisional activation to <I>o</I>-TEMPO-Bz-C(O)–peptides produced extensive peptide backbone fragmentations as well as ·Bz-C(O)–peptide radical species. This result indicates that the duty cycle in the TEMPO-based FRIPS mass spectrometry can be reduced by one-half in the negative-ion mode. In addition, the fragment ions observed in the negative-ion experiments were mainly of the <I>a</I>-, <I>c</I>-, <I>x</I>-, and <I>z</I>-types, indicating that radical-driven tandem mass spectrometry was mainly responsible for the TEMPO-based FRIPS even with a single application of collisional activation. Furthermore, the survival fraction analysis of <I>o</I>-TEMPO-Bz-C(O)–peptides was made as a function of the applied normalized collision energy (NCE). This helped us to better understand the differences in FRIPS behavior between the positive- and negative-ion modes in terms of dissociation energetics. The duty-cycle improvement made in the present study provides a cornerstone for future research aiming to achieve a single-step FRIPS in the positive-ion mode.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancham/2013/ancham.2013.85.issue-15/ac303517h/production/images/medium/ac-2012-03517h_0010.gif'></P>

Establishment of PCR Conditions for the Identification of Stenotrophomonas maltophilia Isolated from Boar Semen and Antimicrobial Susceptibility Patterns of the Isolates

Byeong Yeal Jung(정병열),Bum Soo Park(박범수),Ha-Young Kim(김하영),Jae Won Byun(변재원),Aeran Kim(김애란),Albert Byungyun Jeon(전병윤),In Cheul Kim(김인철),Ki Hwa Chung(정기화) 한국생명과학회 2012 생명과학회지 Vol.22 No.8

돼지 정액의 세균오염은 정자활력 감소나 수태율 저하 등을 유발하는데, 특히 Stenotrophomonas maltophilia는 자연환경에 널리 존재하여 비위생적으로 채취된 정액에 많이 오염될 뿐 아니라 사람에게도 병원성을 일으킨다. 본 연구에서는 S. maltophilia의 검사 시간 단축과 정확도를 높이고자 PCR 기법을 개발하였으며, 돼지 원정액에서 이들 세균의 오염율을 조사하고 유효 항생제를 선발하고자 하였다. 돼지 원정액에서 분리 빈도가 높은 18 균종을 대상으로 PCR을 적용한 결과, S. maltophilia에서만 445 bp의 특이 유전자 증폭산물이 확인되었다. 또한 순수 배양된 S. maltophilia는 1.5×10³ CFU/ml까지, 원정액에 혼합된 S. maltophilia에 대해서는 1.5×10⁴ CFU/ml까지 검출이 가능하였다. 2009년에 116건과 2011년 324건 등 총 440건의 원정액 중 26건(5.9%)에서 S. maltophilia가 분리되었으며, 여름과 가을철에 오염율이 상대적으로 높게 나타났다. 균분리법과 PCR간의 일치율은 98.9%, kappa value는 0.906이었으며, PCR의 민감도와 특이도는 각각 100%, 98.7%로 나타났다. 분리균주의 항생제 감수성 시험 결과, enrofloxacin (100%)과 florfenicol (92.3%)에 높은 감수성을 보였으나 amoxicillin/clavulanic acid, apramycin, ceftiofur, penicillin, spectinomycin에는 내성율이 높게 나타났다. 결론적으로 개발된 PCR기법은 민감도, 특이도, 일치율이 높아 균분리법을 보조하고 신속?정확하게 정액 내 오염세균을 확인할 수 있어 효율적인 정액관리가 가능할 것으로 기대된다. Bacteria are frequently contaminated during the collection and processing procedures of boar semen. Of the contaminants, Stenotrophomonas (S.) maltophilia is a Gram-negative bacterium that is widely distributed in a variety of habitats. Although PCR assays have been developed for the detection of S. maltophilia, they cross-react with some species of Xanthomonas. In this study, we designed a primer set for the detection of S. maltophilia in order to target the chiA (GenBank accession no. NC_010943) gene. The specific PCR products were amplified from S. maltophilia only, not from other tested strains that are frequently found in semen. The detection limit of the PCR was 1.5×10³ CFU/ml with pure-cultured S. maltophilia and 1.5×10⁴ CFU/ml with S. maltophilia spiked in semen. Twenty-six (5.9%) S. maltophilia were isolated from 440 semen samples. The PCR results exhibited 98.9% agreement with a comparison of S. maltophilia isolation. Also, the sensitivity and specificity of the PCR were 100% and 98.7%, respectively. In the antimicrobial susceptibility test, S. maltophilia isolates were highly susceptible to enrofloxacin and florfenicol, while the majority of them were resistant to amoxicillin/clavulanic acid, apramycin, ceftiofur, penicillin, and spectinomycin. These results indicated that the PCR using the chiA gene was proven to be reliable and effective for the detection of S. maltophilia with high levels of sensitivity and specificity.