Molecular and genomic features of <i>Mycobacterium bovis</i> strain 1595 isolated from Korean cattle

Kim, Narae,Jang, Yunho,Kim, Jin Kyoung,Ryoo, Soyoon,Kwon, Ka Hee,Kim, Miso,Kang, Shin Seok,Byeon, Hyeon Seop,Lee, Hee Soo,Lim, Young-Hee,Kim, Jae-Myung The Korean Society of Veterinary Science 2017 Journal of Veterinary Science Vol.18 No.-

<P>The aim of this study was to investigate the molecular characteristics and to conduct a comparative genomic analysis of <I>Mycobacterium</I> (<I>M.</I>) <I>bovis</I> strain 1595 isolated from a native Korean cow. Molecular typing showed that <I>M. bovis</I> 1595 has spoligotype SB0140 with mycobacterial interspersed repetitive units-variable number of tandem repeats typing of 4-2-5-3-2-7-5-5-4-3-4-3-4-3, representing the most common type of <I>M. bovis</I> in Korea. The complete genome sequence of strain 1595 was determined by single-molecule real-time technology, which showed a genome of 4351712 bp in size with a 65.64% G + C content and 4358 protein-coding genes. Comparative genomic analysis with the genomes of <I>Mycobacterium tuberculosis</I> complex strains revealed that all genomes are similar in size and G + C content. Phylogenetic analysis revealed all strains were within a 0.1% average nucleotide identity value, and MUMmer analysis illustrated that all genomes showed positive collinearity with strain 1595. A sequence comparison based on BLASTP analysis showed that <I>M. bovis</I> AF2122/97 was the strain with the greatest number of completely matched proteins to <I>M. bovis</I> 1595. This genome sequence analysis will serve as a valuable reference for improving understanding of the virulence and epidemiologic traits among <I>M. bovis</I> isolates in Korea.</P>

Proteomic analysis for the effects of non-saponin fraction with rich polysaccharide from Korean Red Ginseng on Alzheimer's disease in a mouse model

Sujin Kim,Yunkwon Nam,Min-jeong Kim,Seung-hyun Kwon,Junhyeok Jeon,Soo Jung Shin,Soyoon Park,Sungjae Chang,Hyun Uk Kim,Yong Yook Lee,Hak Su Kim,Minho Moon The Korean Society of Ginseng 2023 Journal of Ginseng Research Vol.47 No.2

Background: The most common type of dementia, Alzheimer's disease (AD), is marked by the formation of extracellular amyloid beta (Aβ) plaques. The impairments of axons and synapses appear in the process of Aβ plaques formation, and this damage could cause neurodegeneration. We previously reported that non-saponin fraction with rich polysaccharide (NFP) from Korean Red Ginseng (KRG) showed neuroprotective effects in AD. However, precise molecular mechanism of the therapeutic effects of NFP from KRG in AD still remains elusive. Methods: To investigate the therapeutic mechanisms of NFP from KRG on AD, we conducted proteomic analysis for frontal cortex from vehicle-treated wild-type, vehicle-treated 5XFAD mice, and NFP-treated 5XFAD mice by using nano-LC-ESI-MS/MS. Metabolic network analysis was additionally performed as the effects of NFP appeared to be associated with metabolism according to the proteome analysis. Results: Starting from 5,470 proteins, 2,636 proteins were selected for hierarchical clustering analysis, and finally 111 proteins were further selected for protein-protein interaction network analysis. A series of these analyses revealed that proteins associated with synapse and mitochondria might be linked to the therapeutic mechanism of NFP. Subsequent metabolic network analysis via genome-scale metabolic models that represent the three mouse groups showed that there were significant changes in metabolic fluxes of mitochondrial carnitine shuttle pathway and mitochondrial beta-oxidation of polyunsaturated fatty acids. Conclusion: Our results suggested that the therapeutic effects of NFP on AD were associated with synaptic- and mitochondrial-related pathways, and they provided targets for further rigorous studies on precise understanding of the molecular mechanism of NFP.

치어기 넙치(Paralichthys olivaceus) 사료 내 돈모분(Pig Bristle Meal)의 어분대체 가능성 평가

김유정 ( Youjeong Kim ),신재형 ( Jaehyeong Shin ),권황원 ( Hwangwon Kwon ),이소연 ( Soyoon Lee ),김주민 ( Joo-min Kim ),김민기 ( Min-gi Kim ),김정대 ( Jeong-dae Kim ),이경준 ( Kyeong-jun Lee ) 한국수산과학회(구 한국수산학회) 2018 한국수산과학회지 Vol.51 No.2

This study was conducted to evaluate dietary hydrolyzed pig bristle meal (PBM) for juvenile olive flounder Paralichthys olivaceus. In Experiment 1 (EXP-1), six experimental diets were prepared to contain 0, 3, 6, 9, 12 and 15% PBM (designated Con, PBM3, PBM6, PBM9, PBM12 and PBM15, respectively). Triplicate groups of olive flounder (initial body weight, 8.69 g) were fed the diets to apparent satiation for 8 weeks during the optimal water temperature season (20.5±2.12℃). All PBM supplemented groups except for PBM3 showed significantly lower growth performance and feed utilization compared to the control group. The protein digestibility of PBM3, PBM6, and PBM9 diets did not significantly differ from that of the control diet. In Experiment 2, 1% mono-calcium phosphate was added into the experimental diets used in Exp-1. Triplicate groups of olive flounder (10.6 g) were fed the diets to apparent satiation for 8 weeks during the low water temperature season (12.5±1.12℃). The growth performances and feed utilization of fish fed all diets except for PBM15 diet did not significantly differ from those of the control diet. This study indicates that hydrolyzed PBM can replace fish meal by up to 12% with limiting amino acids and mono-calcium phosphate in diets for juvenile olive flounder.

Healthcare Workforce Response to The Coronavirus Disease Outbreak in Daegu, Korea: A Multi-Center, Cross-Sectional Survey

Kwon Hyun Hee,Kim Hye In,Kwon Ki Tae,Hwang Soyoon,Kim Shin-Woo,Kim Yoonjung,Kim Hyun ah,Hyun Miri,Hong Hyo-Lim,Kim Min Jung,Hur Jian,Hong Kyung Soo 대한감염학회 2022 Infection and Chemotherapy Vol.54 No.2

Background Securing an available healthcare workforce is critical to respond to coronavirus disease 2019 (COVID-19); however, research investigating Korea’s COVID-19 staffing response is rare. To present the fundamental data of healthcare staff in response to the surge in COVID-19 cases, we investigated the healthcare workforce response in Daegu, South Korea, which experienced the first largest outbreak of COVID-19 outside of China. Materials and Methods In response to the COVID-19 outbreak, this retrospective cross-sectional study analyzed data on the scale and characteristics of healthcare workers (HCWs). Additionally, it analyzed the clinical and epidemiological characteristics of HCWs infected with COVID-19 in six major teaching hospitals (five tertiary and one secondary) in Daegu from January 19 to April 30, 2020. Results During this study period, only 1.3% (n = 611) of the total hospitalized patients (n = 48,807) were COVID-19 inpatients, but they occupied 6.0% (n = 303) of the total hospital beds (n = 5,056), and 23.7% (n = 3,471) of all HCWs (n = 14,651) worked in response to COVID-19. HCWs participating in COVID-19-related works comprised 50.6% (n = 1,203) of doctors (n = 2,379), 26.3% (n = 1,571) of nurses (n = 5,982), and 11.4% (n = 697) of other HCWs (n = 6,108). Only 0.3% (n = 51) of HCWs (n = 14,651) developed COVID-19 infections from community-acquired (66.7%) or hospital-acquired (29.4%). Nurses were affected predominantly (33.3%), followed by doctors (9.8%), caregivers (7.8%), radiographers (5.9%), and others (45.1%), including nurse aides and administrative, facility maintenance, telephone appointment centers, and convenience store staff. All HCWs infected with COVID-19 recovered completely. The 32.7% (n = 333) of individuals (n = 1,018) exposed to HCWs who had COVID-19 were quarantined, and only one case of secondary transmission among them occurred. Conclusion The COVID-19 pandemic has necessitated significant staffing and facility usage, which is disproportionate to the relatively low number of COVID-19 inpatients, imposing a substantial burden on healthcare resources. Therefore, beyond the current reimbursement level of the Korean National Health Insurance, a new type of rewarding system is needed to prepare hospitals for the emerging outbreaks of infectious diseases. Keeping HCWs safe from COVID-19 is crucial for maintaining the healthcare workforce during a sudden massive outbreak. Further studies are needed to determine the standards of required HCWs through detailed research on the working hours and intensity of HCWs responding to COVID-19.

Differential growth of food microorganism on simple HMOs

Soyoon WON,Mina KIM,Jaehan KIM 한국생물공학회 2019 한국생물공학회 학술대회 Vol.2019 No.4

Popularity and adjacency based prefetching for efficient IPTV channel navigation

Soyoon Lee,Hyewon Moon,Hyokyung Bahn,Taeseok Kim,Ik-Soon Kim IEEE 2011 IEEE TRANSACTIONS ON CONSUMER ELECTRONICS - Vol.57 No.3

<P>As Internet Protocol Television (IPTV) is becoming increasingly popular, users can enjoy a variety of contents from hundreds of IPTV channels. However, the increased number of channels makes users even more difficult to find their desired contents. Along with this problem, the channel zapping time of IPTV incurs serious user-perceived latency. To alleviate these problems, this paper presents a new channel prefetching scheme that can be implemented on the IPTV set-top box. The scheme basically fetches the contents of adjacent channels before they are actually requested, similar to the adjacency-based prefetching scheme. However, it differentiates the number of channels to be prefetched among up-direction and down-direction channels based on the popularity of channels. Trace-driven simulations with various experimental conditions show that the proposed prefetching scheme performs better than existing prefetching schemes in terms of the prefetching hit rate to find the desired channel. Specifically, when the number of IPTV channels is 150, the average improvement of the hit rate is 22.3% compared to the adjacency-based prefetching scheme.</P>

Comparative Whole Cell Proteomics of Listeria monocytogenes at Different Growth Temperatures

( Soyoon Won ),( Jeongmin Lee ),( Jieun Kim ),( Hyungseok Choi ),( Jaehan Kim ) 한국미생물 · 생명공학회 2020 Journal of microbiology and biotechnology Vol.30 No.2

Listeria monocytogenes is a gram-positive, facultative anaerobe food pathogen responsible for the listeriosis that mostly occurs during the low-temperature storage of a cold cut or dairy products. To understand the systemic response to a wide range of growth temperatures, L. monocytogenes were cultivated at a different temperature from 10℃ to 42℃, then whole cell proteomic analysis has been performed both exponential and stationary cells. The specific growth rate increased proportionally with the increase in growth temperature. The maximum growth rate was observed at 37℃ and was maintained at 42℃. Global protein expression profiles mainly depended on the growth temperatures showing similar clusters between exponential and stationary phases. Expressed proteins were categorized by their belonging metabolic systems and then, evaluated the change of expression level in regard to the growth temperature and stages. DnaK, GroEL, GroES, GrpE, and CspB, which were the heat&cold shock response proteins, increased their expression with increasing the growth temperatures. In particular, GroES and CspB were expressed more than 100-fold than at low temperatures during the exponential phase. Meanwhile, CspL, another cold shock protein, overexpressed at a low temperature then exponentially decreased its expression to 65-folds. Chemotaxis protein CheV and flagella proteins were highly expressed at low temperatures and stationary phases. Housekeeping proteins maintained their expression levels constant regardless of growth temperature or growth phases. Most of the growth related proteins, which include central carbon catabolic enzymes, were highly expressed at 30℃ then decreased sharply at high growth temperatures.

Generation of Monoclonal Antibodies Against Recombinant AtSIZ1

Kim, Kangchang,Bae, Suyoung,Hong, Jaewoo,Choi, Jida,Ryoo, Soyoon,Jhun, Hyunjhung,Lee, Siyoung,Her, Erk,Hong, Kwangwon,Kim, Soohyun Mary Ann Liebert 2010 Hybridoma Vol.29 No.4

<P>Post-translational modifications of target proteins by small ubiquitin-like modifier (SUMO) proteins modulate many cellular processes in yeast and animals. Here we present the development of monoclonal antibodies (MAb) and polyclonal antibodies (PAb) against Arabidopsis SIZ1 (AtSIZ1) protein with high specificity. Mice were immunized with recombinant AtSIZ1 protein for generating monoclonal antibodies via the classic hybridoma production technique. Anti-AtSIZ1 MAb and PAb were able to detect endogenous AtSIZ1 in Arabidopsis wild type and its complementary line formed by transforming C-siz1-2 mutant with construct containing the AtSIZ1 gene under the control of the native promoter, but not the siz1-2 deletion mutant. These results show that these anti-AtSIZ MAbs are highly sensitive to detect endogenous AtSIZ1 and can be used for immunoblotting and other experimental methods. The new anti-AtSIZ1 MAbs will be essential tools used to investigate the role of AtSIZ1 in plant developmental biology.</P>

Cross-protective efficacy of the O1 Manisa + O 3039 bivalent vaccine and the O 3039 monovalent vaccine against heterologous challenge with FMDV O/Jincheon/SKR/2014 in pig

Kim, Taeseong,Hong, Jang-Kwan,Oem, Jae-Ku,Lee, Kwang-Nyeong,Lee, Hyang-Sim,Kim, Yong Joo,Ryoo, Soyoon,Ko, Young-Joon,Park, Jong-Hyeon,Choi, Jida,Lee, Seung Heon,Jo, Hye Jun,Lee, Myoung-Heon,Kim, Byoun Elsevier 2019 Vaccine Vol.37 No.12

<P><B>Abstract</B></P> <P>After massive foot-and-mouth disease (FMD) outbreaks originated from Jincheon County from Dec. 2014 to Apr. 2015, the effectiveness of the previous FMD vaccine containing only the O1 Manisa as the O antigen, O1 Manisa + A Malaysia 97 + Asia 1 Sharmir trivalent vaccine, was questioned in South Korea, and a change in the O antigen in FMD vaccines was demanded to control the FMD caused by FMDV O/Jincheon/SKR/2014, the O Jincheon strain. Therefore, the efficacies of O1 Manisa + O 3039 bivalent vaccine and O 3039 monovalent vaccine were studied for cross-protection against heterologous challenge with the O Jincheon strain. In this study, the efficacy of the O1 Manisa + O 3039 bivalent vaccine was better than that of the O 3039 monovalent vaccine, even though the serological relationship (r<SUB>1</SUB> value) between O Jincheon and O 3039 was matched according to the OIE Terrestrial Manual. According to serological test results from vaccinated specific pathogen free pigs, virus neutralization test titers against Jincheon were good estimates for predicting protection against challenge. A field trial of the O1 Manisa + O 3039 bivalent vaccine was performed to estimate the possibility of field application in conventional pig farms, especially due to concerns about the effect of maternally derived antibodies (MDA) in field application of the FMD vaccine. According to the result of the field trial, the O1 Manisa + O 3039 bivalent vaccine was considered to overcome MDA. The results of the efficacy and field trials indicated that the O1 Manisa + O3039 vaccine could be suitable to replace previous FMD vaccines to control the FMD field situation caused by O Jincheon FMDV.</P>

Use of Molecular Typing to Elucidate Mycobacterium bovis Transmission in South Korean Beef Cattle

Kim, Jae-Myung,Jang, Yunho,Ryoo, Soyoon,Jang, Yoonra,Kim, Narae,Heo, In,Park, Yong-Ho,Jung, Suk Chan Science Alert 2014 Asian Journal of Animal & Veterinary Advances Vol.9 No.8