Comprehensive genomic analyses with 115 plastomes from algae to seed plants: structure, gene contents, GC contents, and introns

Eun‑Chae Kwon,Jong‑Hwa Kim,Nam‑Soo Kim 한국유전학회 2020 Genes & Genomics Vol.42 No.5

Background Chloroplasts are a common character in plants. The chloroplasts in each plant lineage have shaped their own genomes, plastomes, by structural changes and transferring many genes to nuclear genomes during plant evolution. Some plastid genes have introns that are mostly group II introns. Objective This study aimed to get genomic and evolutionary insights on the plastomes from green algae to flowering plants. Methods Plastomes of 115 species from green algae, bryophytes, pteridophytes (spore bearing vascular plants), gymnosperms, and angiosperms were mined from NCBI organelle genome database. Plastome structure, gene contents and GC contents were analyzed by the in-house developed Phyton code. Intronic features including presence/absence, length, intron phases were analyzed by manually in the annotated information in NCBI. Results The canonical quadripartite structures were retained in most plastomes except of a few plastomes that had lost an invert repeat (IR). Expansion or reduction or deletion of IRs resulted in the length variation of the plastomes. The number of protein coding genes ranged from 40 to 92 with an average 79.43 ± 5.84 per plastome and gene losses were apparent in specific lineages. The number of trn genes ranged from 13 to 33 with an average 21.19 ± 2.42 per plastome. Ribosomal RNA genes, rrn, were located in the IRs so that they were present in a duplicate except of the species that had lost one of the IR. GC contents were variable from 24.9 to 51.0% with an average 38.21 ± 3.27%, indicating bias to high AT contents. Plastid introns were present in 18 protein coding genes, six trn genes, and one rrn gene. Intron losses occurred among the orthologous genes in different plant lineages. The plastid introns were long compared with the nuclear introns, which might be related with the spliceosome nuclear introns and self-splicing group II plastid introns. The trnK-UUU intron contained the maturase encoding matK gene except in the chlorophyte algae and monilophyte ferns in which the trnK-UUU was lost, but matK retained. There were many annotation artefacts in the intron positions in the NCBI database. In the analysis of intron phases, phase 0 introns were more frequent than those of phase 2 and 3 introns. Phase polymorphism was observed in the introns of clpP which was derived from nucleotide insertion. Plastid trn introns were long compared to the archaeal or eukaryotic nuclear tRNA introns. Of the six plastid trn introns, one was at the D loop and other five were at the anticodon loop. The insertion sites were conserved among the trn genes in archaea, eukaryotic nuclear and plastid tRNA genes. Conclusions Current study refurbrished the previous findings of structural variations, gene contents, and GC contents of the chloroplast genomes from green algae to flowering plants. The study also included some noble findings and discussions on the plastome introns including their length variations and phase variation. We also presented and corrected some false annotations on the introns in protein coding and tRNA genes in the genome database, which might be confirmed by the chloroplast transcriptome analysis in the future.

부산지역 소방공무원의 폐기능과 호흡기증상

김성훈,김정원,,김종은,손병철,김정호,이창희,장상환,이채관 大韓産業醫學會 2006 대한직업환경의학회지 Vol.18 No.2

목적: 본 연구에서는 소방관 집단의 호흡기 증상과 폐기능을 조사하여 호흡기 질환의 유병 정도를 비교 분석함으로써 소방관의 호흡기 질환과 화재 노출과의 관련성을 규명하고자 하였다. 방법: 2004년 11월 13일부터 동년 12월 15일까지 부산 소재 4개 소방서와 부속 파출소의 남성 소방공무원 699명을 대상으로 폐기능 검사와 호흡기 설문조사를 실시하였다. 호흡기 증상 설문은 BMRC에서 개발한 설문조사표를 이용하였다. FVC, FEV_(1), MMEF 예측치는 Morris의 폐기능 예측식을 사용하여 계산하였고, 폐기능 검사 이상을 판정하기 위하여 미국 NHNES 기준에 따라 정하였다. 폐기능 측정치와 호흡기 증상은 노출유무와 흡연여부로 집단을 나누어 각각 비교분석하였다. 유의수준은 p<0.05로 정하였다. 결과: 폐기능 비교에서 화재노출군이 FVC, FVC%, FEV_(1), FEV_(1)%, FEF_(25%)는 비노출군에 비해 통계학적으로 유의하게 저하되어 있었고, 이를 흡연여부에 따라 층화하였을 때, FVC 와 FEV_(1)은 흡연여부와 관계없이 노출 여부에 따른 차이를 보이나 FVC%, FEV_(1)%, PEFR은 흡연군에서만 차이를 보였다. 폐기능 검사 이상을 비교하면 전체적으로 화재노출군이 비노출군보다 폐기능 이상자의 수가 많았고 흡연군에서 FEV_(1) 이상자의 차이는 통계적으로 유의하였다. FVC, FEV_(1), MMEF를 종속변수로 하여 다중회귀분석을 시행하였을 때, FVC와 FEV_(1)은 부분적으로 화재노출유무와 관련성이 있었다. 호흡기 증상 조사에서 화재노출군은 비노출군에 비해 코막힘, 목아픔, 흉부압박감의 증상의 호소율이 통계학적으로 유의하게 높았으나, 이를 흡연여부에 따라 층화하면 이들 증상들은 경계역의 차이를 보였다. 결론: 이러한 결과들을 종합하면 소방관은 화재진압과정에서 노출되는 많은 호흡기 유독물질로 인해 급성 폐기능 저하와 높은 호흡기 증상 호소율을 보이며, 이는 화재노출 외에 흡연의 부가적 효과가 영향을 미친다고 생각된다. 따라서 폐기능이 저하된 경방군에서 주기적인 폐기능 검사가 실시되어야 하며, 금연과 호흡기 보호구의 철저한 착용이 권장되어야 하겠다. Objective: The purpose of this study was to evaluate the relationship between respiratory disorders and fire exposure by investigating and analyzing the lung function and respiratory symptoms of firefighters. Methods: The health effects of firefighting on respiratory function were investigated in 699 male fire officers in 4 fire departments in Busan by recording respiratory symptoms and measuring lung function. The data were analysed according to fire exposure and smoking habits. Results: Mean spirometric data showed significantly decreased levels in the fire-exposed group (FVC, -0.20 L; FVC%, -4.2%; FEV_(1) -0.21 L; FEV_(1)%, -5.1%; FEF25%, -0.13 L/SEE p<0.05). After stratification by smoking habits, FVC and FEV1 showed a significant difference between groups. The prevalence of spirometric abnormality was greater for the fire-exposed group than for the non-exposed group. Significantly higher prevalences of nasal stiffness (16.7% vs. 10.9%), sore throat (17.7% vs. 14.2%) and chest tightness (6.5% vs. 2.5%) were recorded in fire fighters compared to controls (p<0.05). However, after stratification by smoking habits, the 3 symptoms were showed only marginal differences in the smoking group. Conclusions: This study demonstrated that fire-exposed firefighters generally suffer a decline of lung function and a higher prevalence of respiratory symptoms. These results suggest that the exposure to routine firefighting activity is associated with adverse health effects to the respiratory system.

cDNA array 방법을 이용한 망간에 노출된 흰쥐 뇌기저핵의 유전자발현 분석

이채관,노성민,문덕환,,김정호,손병철,김대환,이창희,김휘동,김정원,김종은,안진홍,이채언 大韓産業醫學會 2005 대한직업환경의학회지 Vol.17 No.4

Objectives: This study investigated the gene expression profile in basal ganglia of manganese-exposed rats based on cDNA array analysis. Methods: For cDNA array, 25 male Sprague-Dawley rats (250±25 g) were intraperitoneally injected with 25 ㎎/㎏ B. W./day of MnCl2 (0.3 ㎖) for 10 days. For dose-related gene expression analysis, rats were intraperitoneally injected with 0.2, 1.0, and 5.0 ㎎/㎏ B. W/day of MnCl2 for 10 days. Control rats were injected with an equal volume of saline. RNA samples were extracted from brain tissue and reverse-transcribed in the presence of [α^(32)P]-dATP. Membrane sets of the Atlas Rat 1.2 array Ⅱ and Toxicology array 1.2 kit (Clontech, Palo Alto, CA) were hybridized with cDNA probe sets. Northern blot hybridization method was employed to assess the dose-related gene expression. Results: Fifty-two genes showed significant changes in expression of more than two-fold. Twenty-eight were up-regulated and 24 were down-regulated in the manganese-exposed group compared to the control. Among the 52 genes, 28 genes including nuclear factor I-X1 (NF1-X1), neuroligin 2 and 3, mitochondrial stress-70 protein (MTHSP70), neurodegeneration-associated protein 1 (Neurodap 1), multidrug resistance protein (MDR), and endoplasmic reticulum stress protein 72 (ERP72), were reported for the first time related to the manganese-induced neurotoxic-metabolism in the rat basal ganglia. According to the dose-related gene expression analyses, MTHSP70, Neurodap 1 and ERP72 genes were up-regulated compared to the control even in the group exposed to low manganese dose ( 0.2 ㎎/㎏ B.W./day). Conclusions: Twenty-eight genes detected for the first time in this study were closely related to the manganese-induced neurotoxic-metabolism in the rat basal ganglia and further study of these genes can give some more useful information about the manganese metabolism.

8년간(1992~1999) 산업안전보건연구원에 의뢰된 직업병 심의 사례 분석

강성규,김규상,김양호,최정근,안연순,진영우,최병순,양정선,김은아,채창호,최용휴,김대성,박정선,정호근 대한산업의학회 2000 대한직업환경의학회지 Vol.12 No.2

Objectives : Pneumoconisis and noise-induced hearing loss (NIHL) have been reported as main occupational diseases by the Special Health Examination. The Industrial Accident Compensation Insurance has reported various work-related diseases, however, these two diseases occupied almost a half of compensated cases. Therefore, it was not well known about the status of occupational diseases other than pneumoconiosis, NIHL, and cardio-cerebrovascular accident (CVA). This study was conducted to analyze claimed cases as an occupational disease, that was requested to the Korea Industrial Safety and Health Agency (KOSHA). Methods : The local office of the Korea Labor Welfare Corporation (KLWC) has asked the KOSHA for confirmation of claimed cases as an occupational disease. We analyzed 379 cases requested from KLWC, the Ministry of Labor, employers, unions and occupational health agencies from 1992 to 1999. Results : Male was 80.7 % of the requested cases. Their mean age was 42 years old and 75.5 % of them were more than 35 years old. The requested cases were increased rapidly from 25 cases in 1992 to 108 cases in 1999 and the accept rate was 50.7 %. The majority of requested cases were respiratory diseases(22.4%), cancers(18.5%), Neuropsychiatric problems(14.5%), and musculoskeletal problems(13.5%). The accept rate was high in reproductive, respiratory, musculoskeletal and digestive disorders and low in neuropsychiatric, renal and otologic problems and occupational cancers. 73.6% of them were caused by chemical agents, especially 28.5 % were by organic solvents. 67% of them were clinically confirmed at university hospitals. A half of the cases were from KyongIn area, even the request came from the whole country. Conclusions : A claim was common in workers whose age was over 35 years old and exposure history was over 10 years. The respiratory diseases and neuropsychiatric disorders were still main problems in occupational health and occupational cancers was increasing even though its accept rate was not high yet.

우리나라 지역 직업성질환 감시체계의 현황과 전망

임종한,장성실,김성아,문재동,채창호,홍윤철,김수영,김진석,김영욱,한상환,이혜숙,원종욱,송동빈,하은희,강성규 대한산업의학회 2001 대한직업환경의학회지 Vol.13 No.2

기존의 특수건강진단과 작업환경측정을 통한 직업병 관리가 진폐증, 소음성난청 등의 소수 특정질환에 국한되고 실제 직업병 발생 규모 파악이나 신종 직업병의 발견에 한계를 보인다는 사실은 산업의학전문가들 사이에서도 공감을 이루고 있다. 미국과 영국 등에서의 직업성질환 감시체계에 대한 경험은 우리 나라의 직업성질환 감시체계 구축에도 새로운 자극제가 되면서, 1998년이후 인천, 대전, 여천, 구미, 부울경 지역에서 지역 직업성질환감시체계를 산업보건관리의 중요한 시스템으로 구축하려는 노력이 확산되고 있다. 새로이 구축되어지는 이들 지역 직업성질환 감시체계는 감시하고자 하는 대상질환, 활용 가능한 인적자원 및 자료원, 지역 의료체계의 특수성 등에 따라서 목적과 방법을 달리하면서 독특한 형태로 발전을 하고 있다. 각 지역단위 감시체계들이 그 상황에 맞게 독특한 목적과 전략들을 발전 시키면서도, 향후 발전할 국가적인 차원의 직업성질환 감시체계 구축을 위하여 직업성질환 감시의 기본 전략 등을 공유하는 등의 노력이 필요하다. 환례 정의 및 기본적인 등록 서식의 공유, 직업성질환 감시 자료원의 발굴, 공동의 정보 네트워크 및 직업성질환 감시 데이터베이스 구축 등 직업성질환 감시활동을 지원하기 위한 여러 기초 인프라 구축에 힘을 모아야 할 것이다. 우리 나라에서 직업성질환 감시체계를 성공적으로 구축하기 위해서는 수집된 자료의 질 관리를 위한 직업성질환 감시의 원칙 제정과 감시 전략의 공유 등이 필요하며, 전국적인 직업성질환 감시체계의 하부구조라고 할 수 있는 지역감시체계의 기초 토대 마련과 강화작업이 절실하게 필요하다.

성인 IgA 신병증의 임상적 고찰

김영학,권용은,허경무,윤채중,김종인,김건영,배학연,정종훈 조선의대 1998 The Medical Journal of Chosun University Vol.23 No.1

通貨需要函數와 通貨指票의 選定에 관한 實證的 考察

金銀埰 釜山水産大學校 1992 論文集 Vol.48 No.-

Since 1980 the behavior of economic agents on the demand for money has been observed to change. As a result traditional money indicator, M₂ is not sufficient to describe the recent change in surpluses in balnace of trade and the deregulation on financial markets in Korea. Therefore microfundation of money demand is required to develop.

보호무역의 정치경제에 관한 고찰

김은채 釜山水産大學校 1993 論文集 Vol.49 No.-

Economic theory argues that free trade leads to the most efficient allocation of resources and maximizes on country's economic welfare. Empirical research shows that unilateral and multilateral tariff reduction yield significant welfare gains. In reality, however, we have shown that tariffs and other trade restrictions are prevalent in all periods and countries, and that there is a continual danger of increasing protectionism in the world. Until recently, there has been a strong tendency to assume that protection structures were dicided upon by persons who were ignorant of economic principles. More recently, however, there has been increasing concerns about the political market for protection. Protection is demanded by particular groups such as firms and associated interest groups and parties, and supplied by politicians and public bureaucrats. They improve their position by turning to the political system. Interest groups(e.g. protected producers and nonprotected producers) invest resources in order to influence political decision in their favor. Such activities, which are directly unproductive, are a special form of profit-maximization which can be gained by lobbying for trade barriers. In this papers, we are attempting to demonstrate the political determinants of trade barriers, and suggesting that tariff structures themselves may be in part endogeneous, as political decisions may be made in responsive to economic phenomena and vice versa. We also have shown that a declining industry well continue to decline which is established by Hillman (1982). He uses a Stigler/Peltzman political support model in which he assumes political support and blame is aimed at the component of price for which the government is directly responsible in this case the tariff. Suppose an industry is faced with a fall in the world price of its good, it is possible to show that the domestic price of the good must fall as represented in mathematical proof in the context and to suggest structural change will proceed in the right direction because of diminishing maginal return to political pressure. To develop the argument, the next section briefly reviews the trade protection and public choices which can help why larger groups have been unsuccessful in forming a coalition to oppose tariffs and other distortions. Then, in section 3, we are attempting to demonstrate the political determintants of trade barriers, and associated with declining industry, Section 4 considers alternative trade restrictions such as quota and VERs. A final section provides conclusions.

혈관내피세포-U937세포의 부착에 미치는 Eicosapentaenoic Acid의 효과

김은지,전재은,임현주,차성철,정의룡,조용근,조용근 경북대학교 병원 1998 경북대학교병원의학연구소논문집 Vol.2 No.1

연구배경: 역학적연구에서 어류의 섭취가 많은 집단에서 관상동맥질환의 빈도가 낮은 것이 보고되었고, 이것은 어류에 많이 함유된 불포화지방산(polyunsaturated fatty acid) 특히 eicosapentaenoic acid 때문으로 생각되어지고 있다. 본 연구에서는 동맥경화증 발생의 초기단계로 여겨지는 단핵구와 혈관내피세포 사이의 adhesion에 미치는 다불포화지방산의 영향을 in vitro system에서 관찰하고자 하였다. 방 법: 제대정맥에서 얻은 혈관내피세포를 배양하여 96 well에 옮기고 25, 50, 100, 200 ㎛ 농도의 eicosapentaenoic acid(EPA)를 6시간 동안 처리한 U937세포를 부착시켜 adhesion assay를 시행하였다. 혈관내피세포를 자극하기 위해서는 lipopolysaccharide(LPS)를 well당 100 ng씩을 투여하였다. 음성대조군으로는 LPS로 자극하지 않은 혈관내피세포에 EPA처리를 하지 않은 U937세포로 adhesion assay한 성적을 사용했고, 양성대조군으로는 LPS로 자극한 혈관내피세포에 EPA처리를 하지 않은 U937세포로 adhesion assay한 성적을 사용했다. 그리고 EPA(3.3 mM)을 5㎛ CuSO4 및 300 ㎛ asscorbic acid와 혼합하여 섭씨 37도에서 16시간 두어 산화-EPA를 만들어 같은 실험을 반복하였다. 결 과: U937세포에 25, 50, 100, 200 ㎛의 EPA로 6시간 처리하였을 때 U937세포의 생존율은 99% 이상이었다. 혈관내피세포를 LPS로 자극했을 때 adhesion assay에서 혈관내피세포에 붙는 U937세포의 수는 현저히 증가하였다. 그러나 EPA를 U937세포에 25, 50, 100, 200 ㎛의 농도로 6시간 처리 후에 lipopolysac-charide를 처리한 제대정맥 내피세포에 부착(adhesion)시켰을 때 처리한 EPA의 각 농도에 따른 부착된 U937세포의 수는 통계적으로 유의한 차이를 나타내지 못했다. EPA처리가 부착된 U937세포의 수에 영향을 미치지 못하였다. 결 론: EPA는 U937세포에 영향을 미쳐 혈관내피세포-U937 세포부착을 감소시키지는 못하였다. 따라서 EPA에 의한 혈관내피세포-단핵구 부착 억제 효과는 EPA의 단핵구에 미치는 영향에 의하지는 않는 것으로 생각되나 추후 더 많은 연구가 필요하리라 생각된다. Background : Epidemiological studies have shown correlation between low incidence of coronary heart disease and high consumption of fish products. It has been suggested that this may be due to the high content of polyunsaturated fatty acids of the n-3 fatty acid group in fish oil. In animal studies eicosapentaenoic and (EPA) inhibited attachment of monocytes to the arterial endothlium. Method : Adhesion assay was performed on the endothelial cells of the human umbilical vein with 25, 50, 100, 200 ㎛ EPA-treated U937 cells. The endothelial cells were activated with lipopoysaccharide (LPS). The adhesion assay was repeated with oxidized EPA. EPA was oxidized with CuSO4 and ascorbic acid. Result : Viability of U937 cells were not afected by concentrations up to 200 ㎛ of EPAand oxidized EPA. LPS treatment of endothelium notably increased the number of U937 cells attached to endothelial cells on the adhesion assay. However, treatment of EPA, native or oxidized, to U937 cells did not afect the number of U937 cells attached to LPS activated endothelial cells. Conclusion : EPA treatment, native or oxidized, of U937 cells did not affect U937 cell-endothlial cell adhesion. This suggests that inhibition of monocyte-endothlial cells ◎attachment by EPA is not due to the effects of EPS on monocytes.(Korean Circulatin J 1998;28(4):606-610)

대학급식의 미생물적 품질보증을 위한 HACCP의 적용 : 참치샐러드 Tuna Salad

김운주,최은희,최현미,배주희,채현숙 충북대학교 교육 ·생활연구소 생활과학연구센터 2002 생활과학연구논총 Vol.6 No.1

The purpose of this study was to evaluate the microbiological quality, and to assure the safety of the food production process in the university foodservice facilities in accordance with the Hazard Analysis Critical Control Point(HACCP) concepts. The kitchen layout and time-temperature relationship, miciobiological quality(total plate count, coliform) were assessed to identify the critical point during each of the production phases. The results were as follows: 1) The kitchen layout had to be improved because contamination area was not separated from non-contamination area, and work table was in contact with washing sink. 2) Some employee did not follow personal hygiene standards(hand washing), and did not wear proper working uniforms(hair restraints). 3) The production time of tuna salad was 120 min, and environment temperature was 20.1~26.0℃. Improper receiving temperature, inproper holding practices(without cover at room temperature) were observed. 4) In the purchasing phase of the raw materials, the microbiological quality of green pepper was not at acceptable level based on the TPC(2.3×10^6CFU/g)and coliform(>14,000 MPN/g). During washing phase TPC was decreased about 3 log cycle. After cutting and holding phase the level of TPC and coliform were increased rapidly. At serving phase the microbiological quality of tuna salad were not at acceptable level(TPC 3.3×10^6 CFU/g, coliform 11,000 MPN/g) according to the standard set(TPC <10^5 CFU/g, coliform <100 MPN/g) by Sorberg et al. 5) For tuna salad, critical control points were purchasing and receiving of fresh vegetables, washing, cutting, holding, mixing and serving phase.