한국산 꿩의다리속(미나리아재비과)의 cpDNA trnL-F 지역의 분자진화와 유연관계: Indel events의 영향

박성준,박선주,김혁진 한국식물분류학회 2012 식물 분류학회지 Vol.42 No.1

The trnL-F region islocated in the large single-copy region of the chloroplast genome. It consists of the trnL gene, the trnL intron, and the trnL-F IGS. Molecular evolution and phylogenetic relationships in Korean Thalictrum L. were investigated using data from the cpDNA trnL-F region. Bayesian and parsimony analyses of the data set with the gap characteristics recovered well-resolved trees that are topologically similar, with clades supported by some indels evolution. Indel events of cpDNA trnL-F in Korean Thalictrum were interpreted as phylogenetically informative characteristics. Sect. Physocarpum (excluding T. osmorhizoides) was an early-diverging group with in the genus and the remaining section formed strongly supported clades. Korean Thalictrum has various evolutionary patterns, such as the spatial distribution of the nucleotide diversity and transversion-type base substitutions in the trnL-F region. trnL-F 지역은 엽록체 게놈 large single-copy 지역에 위치하며, trnL gene, trnL intron, trnL-F IGS로 구성된다. 본 연구는 한국산 꿩의다리속 내에서 trnL-F 지역의 분자진화와 유연관계를 분석하였다. 갭형질을 이용한 자료의 베이시안과 파시모니 분석에서 몇몇 indels evolution는 분계조를 지지하여 해상력이 좋은 계통수가 나타났다. 한국산 꿩의다리속 내에 cpDNA trnL-F 지역의 indel events는 계통학적으로 유용한 정보를 가지고 있는 것으로 판단된다. 산꿩의다리절(그늘꿩의다리 제외)은 속내에서 가장 먼저 분기한 것으로 나타났고, 나머지 절은 강하게 분계조를 형성하며 분기하였다. 한국산 꿩의다리속 내에 trnL-F 지역은 뉴클레오티드의 다양한 공간적 분포 변이와 주로 transversion에 따른 염기치환 등 다양한 진화적 패턴을 가지고 있었다.

새로운 동물계통

Kim, Chang-Bae,Kim, Won 한국동물분류학회 2001 Animal Systematics, Evolution and Diversity Vol.17 No.2

전통적인 동물의 계통수는 초기발생 형질들에 기초하여 몸 구조의 복잡성에 따라 동물문들을 단순한 동물에서 복잡한 동물 순으로 점진적으로 배열하는 것인데 현재 활발히 연구되는 분자계통 연구들이 이 경향을 재평가하고 새로운 계통과 의미를 제시하고 있다. 주로 18S rRNA 에 의한 분자계통에 의하면 무체강동물과 의체강동물과 같이 진체강동물로의 전이단계에 위치했던 무리들이 서로 나뉘어진 진체강동물 안에 속하게 된다. 이러한 새로운 분자계통은 좌우대칭동물의 공동조사에 대한 새로운 가정들을 세울 수 있는 뼈대와 비교발생학 및 비교유전체학 정보가 해석될 수 있는 토대를 제공한다. Animal phyla in the traditional animal phylogeny were organized into an order of increasing body plan complexity, which was based on the similarities in early embryonic stages. Molecular phylogeny mainly by 18S rRNA data provides recently re-evaluation of the traditional evolutionary scenario. The current molecular-based view of animal relationships strongly suggest the burst of two groups regraded as intermediate grades of body complexity in the traditional concept and displacement of them into higher positions in the tree. The new animal tree provides a framework within new picture of bilaterian ancestor could be drawn, and comparative developmental and genomic data to be interpreted.

Predictability of physicochemical properties of polychlorinated dibenzo-p-dioxins (PCDDs) based on single-molecular descriptor models

Kim, M.,Li, L.Y.,Grace, J.R. Elsevier Applied Science Publishers 2016 Environmental pollution Vol.213 No.-

Polychlorinated dibenzo-p-dioxins (PCDDs) are of global concern due to their persistence, bioaccumulation and toxicity. Although the fate of PCDDs in the environment is determined by their physical-chemical properties, such as aqueous solubility, vapor pressure, octanol/water-, air/water-, and octanol/water-partition coefficients, experimental property data on the entire set of 75 PCDD congeners are limited. The quantitative structure-property relationship (QSPR) approach is applied to predict the properties of all PCDD congeners. Experimental property data available from the literature are correlated against 16 molecular descriptors of five types. Reported and newly developed QSPR models for PCDDs are presented and reviewed. The values calculated by the best QSPRs are further adjusted to satisfy fundamental thermodynamic relationships. Although the single-descriptor models with chlorine number, molar volume, solvent accessible surface area and polarizability are based on good statistical results, these models cannot distinguish among PCDDs having the same chlorine number. The QSPR model based on the hyper-Wiener index of quantum-chemical descriptor gives useful statistical results and is able to distinguish among congeners with the same chlorine number, as well as satisfying thermodynamic relationships. The resulting consistent properties of the 75 PCDD congeners can be used for environmental modeling.

Evolutionary history of the monospecific Compsopogon genus (Compsopogonales, Rhodophyta)

Fangru Nan,Jia Feng,Junping Lv,Qi Liu,Shulian Xie 한국조류학회I 2016 ALGAE Vol.31 No.4

Compsopogon specimens collected in China were examined based on morphology and DNA sequences. Five molecularmarkers from different genome compartments including rbcL, COI, 18S rDNA, psbA, and UPA were identified andused to construct a phylogenetic relationship. Phylogenetic analyses indicated that two different morphological typesfrom China clustered into an independent clade with Compsopogon specimens when compared to other global samples. The Compsopogon clade exhibited robust support values, revealing the affiliation of the samples to Compsopogon caeruleus. Although the samples were distributed in a close geographical area, unexpected sequence divergences betweenthe Chinese samples implied that they were introduced by different dispersal events and from varied origins. It wasspeculated that Compsopogon originated in North America, a portion of the Laurentia landmass situated in the Rodiniasupercontinent at approximately 573.89-1,701.50 million years ago during the Proterozoic era. Although Compsopogonhad evolved for a rather long time, genetic conservation had limited its variability and rate of evolution, resulting in thecurrent monospecific global distribution. Additional global specimens and sequence information were required to increaseour understanding of the evolutionary history of this ancient red algal lineage.

Evolutionary history of the monospecific Compsopogon genus (Compsopogonales, Rhodophyta)

Nan, Fangru,Feng, Jia,Lv, Junping,Liu, Qi,Xie, Shulian The Korean Society of Phycology 2016 ALGAE Vol.31 No.4

Compsopogon specimens collected in China were examined based on morphology and DNA sequences. Five molecular markers from different genome compartments including rbcL, COI, 18S rDNA, psbA, and UPA were identified and used to construct a phylogenetic relationship. Phylogenetic analyses indicated that two different morphological types from China clustered into an independent clade with Compsopogon specimens when compared to other global samples. The Compsopogon clade exhibited robust support values, revealing the affiliation of the samples to Compsopogon caeruleus. Although the samples were distributed in a close geographical area, unexpected sequence divergences between the Chinese samples implied that they were introduced by different dispersal events and from varied origins. It was speculated that Compsopogon originated in North America, a portion of the Laurentia landmass situated in the Rodinia supercontinent at approximately 573.89-1,701.50 million years ago during the Proterozoic era.Although Compsopogonhad evolved for a rather long time, genetic conservation had limited its variability and rate of evolution, resulting in the current monospecific global distribution. Additional global specimens and sequence information were required to increase our understanding of the evolutionary history of this ancient red algal lineage.

Molecular Vibration-Activity Relationship in the Agonism of Adenosine Receptors

Chee, Hyun Keun,Oh, S. June Korea Genome Organization 2013 Genomics & informatics Vol.11 No.4

The molecular vibration-activity relationship in the receptor-ligand interaction of adenosine receptors was investigated by structure similarity, molecular vibration, and hierarchical clustering in a dataset of 46 ligands of adenosine receptors. The resulting dendrogram was compared with those of another kind of fingerprint or descriptor. The dendrogram result produced by corralled intensity of molecular vibrational frequency outperformed four other analyses in the current study of adenosine receptor agonism and antagonism. The tree that was produced by clustering analysis of molecular vibration patterns showed its potential for the functional classification of adenosine receptor ligands.

Molecular Vibration-Activity Relationship in the Agonism of Adenosine Receptors

지현근,오석준 한국유전체학회 2013 Genomics & informatics Vol.11 No.4

The molecular vibration-activity relationship in the receptor-ligand interaction of adenosine receptors was investigated bystructure similarity, molecular vibration, and hierarchical clustering in a dataset of 46 ligands of adenosine receptors. Theresulting dendrogram was compared with those of another kind of fingerprint or descriptor. The dendrogram resultproduced by corralled intensity of molecular vibrational frequency outperformed four other analyses in the current study ofadenosine receptor agonism and antagonism. The tree that was produced by clustering analysis of molecular vibrationpatterns showed its potential for the functional classification of adenosine receptor ligands.

Quantitation of relationship and development of nutrient prediction with vibrational molecular structure spectral profiles of feedstocks and co-products from canola bio-oil processing

Alessandra M.R.C.B. de Oliveira,Peiqiang Yu Asian Australasian Association of Animal Productio 2023 Animal Bioscience Vol.36 No.3

Objective: This program aimed to reveal the association of feed intrinsic molecular structure with nutrient supply to animals from canola feedstocks and co-products from bio-oil processing. The special objective of this study was to quantify the relationship between molecular spectral feature and nutrient availability and develop nutrient prediction equation with vibrational molecular structure spectral profiles. Methods: The samples of feedstock (canola oil seeds) and co-products (meals and pellets) from different bio-oil processing plants in Canada (CA) and China (CH) were submitted to this molecular spectroscopic technique and their protein and carbohydrate related molecular spectral features were associated with the nutritional results obtained through the conventional methods of analyses for chemical and nutrient profiles, rumen degradable and intestinal digestible parameters. Results: The results showed that the spectral structural carbohydrates spectral peak area (ca. 1,487.8 to 1,190.8 cm^-1) was the carbohydrate structure that was most significant when related to various carbohydrate parameters of canola meals (p<0.05, r>0.50). And spectral total carbohydrate area (ca. 1,198.5 to 934.3 cm^-1) was most significant when studying the various carbohydrate parameters of canola seeds (p<0.05, r>0.50). The spectral amide structures (ca. 1,721.2 to 1,480.1 cm^-1) were related to a few chemical and nutrient profiles, Cornell Net Carbohydrate and Protein System (CNCPS) fractions, truly absorbable nutrient supply based on the Dutch protein system (DVE/OEB), and NRC systems, and intestinal in vitro protein-related parameters in co-products (canola meals). Besides the spectral amide structures, α-helix height (ca. 1,650.8 to 1,643.1 cm^-1) and β-sheet height (ca. 1,633.4 to 1,625.7 cm^-1), and the ratio between them have shown to be related to many protein-related parameters in feedstock (canola oil seeds). Multi-regression analysis resulted in moderate to high R² values for some protein related equations for feedstock (canola seeds). Protein related equations for canola meals and carbohydrate related equations for canola meals and seeds resulted in weak R² and low p values (p<0.05). Conclusion: In conclusion, the attenuated total reflectance Fourier transform infrared spectroscopy vibrational molecular spectroscopy can be a useful resource to predict carbohydrate and protein-relates nutritional aspects of canola seeds and meals.

The Calculation of Physical Properties of Amino Acids Using Molecular Modeling Techniques (II)

Lee, Myung-Jae,Kim, Ui-Rak Korean Chemical Society 2004 Bulletin of the Korean Chemical Society Vol.25 No.7

Six physical properties (enthalpy, density, decomposition temperature, solubility in water, pKa values, and hydronium potential) were examined by molecular modeling techniques. The molecular connectivity index, Wiener distance index, and Ad hoc descriptor are employed as structural parameters to encode information about branching, size, cyclization, unsaturation, heteroatom content, and polarizability. This paper examines the correlation of the molecular modeling techniques parameters and the physicochemical properties of amino acids. As a results, calculated values were in agreement with experimental data in the above six physical properties of amino acids and the molecular connectivity index was superior to the other indices in fitting the calculated data.

PCBs 독성 예측을 위한 주요 분자표현자 선택 기법 및 계산독성학 기반 QSAR 모델 개발

김동우 ( Dongwoo Kim ),이승철 ( Seungchel Lee ),김민정 ( Minjeong Kim ),이은지 ( Eunji Lee ),유창규 ( Changkyoo Yoo ) 한국화학공학회 2016 Korean Chemical Engineering Research(HWAHAK KONGHA Vol.54 No.5

EU의 REACH 제도 도입에 따라 각종 화학물질에 대한 독성 및 활성 정보 확보를 위해 화학물질의 분자구조 정보를 기반으로 화학물질의 독성 및 활성을 예측하는 정량적구조활성관계(QSAR)에 대한 연구가 최근 활발히 진행되고 있다. QSAR 모델에 사용되는 분자표현자는 매우 다양하기 때문에 화학물질의 물성 및 활성을 잘 표현할 수 있는 주요한 분자표현자를 선택하는 과정은 QSAR 모델 개발에 있어 중요한 부분이다. 본 연구에서는 화학물질의 분자구조 정보를 나타내는 주요 분자표현자의 통계적 선택 방법과 부분최소자승법(Partial least square: PLS) 기반의 새로운 QSAR 모델을 제안하였다. 제안된 QSAR 모델은 130종의 폴리염화바이페닐(Polychlorinated biphenyl: PCB)에 대한 분배계수(log P)와 14종의 PCBs에 대한 반수 치사 농도(Lethal concentration 50%: LC50) 예측에 사용되고, 제안된 QSAR 모델 예측 정확도는 기존의 OECD QSAR Toolbox에서 제공하는 QSAR 모델과 비교하였다. 관심 화학물질의 분자표현자와 활성정보 간의 높은 상관관계를 갖는 주요 분자표현자를 선별하기 위해서, 상관계수(r)와 variable importance on projections (VIP)기법을 적용하였으며, 화학물질의 독성 및 활성정보를 예측하기 위해 선별된 분자표현자와 활성정보를 이용해 부분최소자승법(PLS)를 사용하였다. 회귀계수(R2)와 prediction residual error sum of square (PRESS)을 이용한 성능평가결과, 제안된 QSAR 모델은 OECD QSAR Toolbox의 QSAR 모델보다 PCBs의 log P와 LC50에 대하여 각각 26%, 91% 향상된 예측력을 나타내었다. 본 연구에서 제안된 계산독성학 기반의 QSAR 모델은 화학물질의 독성 및 활성정보에 대한 예측력을 향상시킬 수 있고 이러한 방법은 유독 화학물질의 인체 및 환경 위해성 평가에 기여할 것으로 판단된다. Recently, the researches on quantitative structure activity relationship (QSAR) for describing toxicities or activities of chemicals based on chemical structural characteristics have been widely carried out in order to estimate the toxicity of chemicals in multiuse facilities. Because the toxicity of chemicals are explained by various kinds of molecular descriptors, an important step for QSAR model development is how to select significant molecular descriptors. This research proposes a statistical selection of significant molecular descriptors and a new QSAR model based on partial least square (PLS). The proposed QSAR model is applied to estimate the logarithm of partition coefficients (log P) of 130 polychlorinated biphenyls (PCBs) and lethal concentration (LC50) of 14 PCBs, where the prediction accuracies of the proposed QSAR model are compared to a conventional QSAR model provided by OECD QSAR toolbox. For the selection of significant molecular descriptors that have high correlation with molecular descriptors and activity information of the chemicals of interest, correlation coefficient (r) and variable importance of projection (VIP) are applied and then PLS model of the selected molecular descriptors and activity information is used to predict toxicities and activity information of chemicals. In the prediction results of coefficient of regression (R2) and prediction residual error sum of square (PRESS), the proposed QSAR model showed improved prediction performances of log P and LC50 by 26% and 91% than the conventional QSAR model, respectively. The proposed QSAR method based on computational toxicology can improve the prediction performance of the toxicities and the activity information of chemicals, which can contribute to the health and environmental risk assessment of toxic chemicals.