National Institute of Biological Resources

Incheon, South Korea

National Institute of Biological Resources

Incheon, South Korea
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Leyva-Lopez N.,Research Center En Alimentacion sarrollo Ac | Nair V.,Texas A&M University | Bang W.Y.,Texas A&M University | Bang W.Y.,National Institute of Biological Resources | And 2 more authors.
Journal of Ethnopharmacology | Year: 2016

Ethnopharmacological relevance Mexican oregano infusions have been traditionally used in México for the treatment of inflammation-related diseases, such as respiratory and digestive disorders, headaches and rheumatism, among others. Nevertheless, there is limited information regarding the phenolic compounds, terpenes and composition as well as biological activity of Mexican oregano. Aim of the study To determine the phenolic and terpene composition and to evaluate the anti-inflammatory potential of three species of Mexican oregano (Lippia graveolens (LG), Lippia palmeri (LP) and Hedeoma patens (HP)) in order to provide a scientific basis for their use. Materials and methods We obtained methanol and chloroform extracts from dried oregano leaves of each species. We used LC-DAD-ESI-MS/MS and GC-MS to determine the phenolic and terpene profiles of the leaves, respectively. We evaluated anti-inflammatory potential by measuring the effect of Mexican oregano extracts on some pro-inflammatory mediators, such as nitric oxide (NO) and reactive oxygen species (ROS) using lipopolysaccharide(LPS)-stimulated RAW 264.7 macrophage cells and evaluating cyclooxygenase activity (COX-1, COX-2). Results Nine phenolic compounds (phenolic acids and flavonoids) and 22 terpenes (monoterpenes and sesquiterpenes) were detected in LG, LP and HP. We studied extracts from LG, LP and HP, and fractions from LG and LP in order to know their effect on some pro-inflammatory mediators. The phenolic and terpene extracts from LG, LP and HP exhibited significant inhibitory effect on ROS and NO production and mitochondrial activity in LPS-induced inflammation in RAW 264.7 macrophage cells. Nitric oxide production was also diminished by the terpene LG fraction LGF2 and the LP fractions LPF1, LPF2 and LPF3, confirming that both monoterpenes and sesquiterpenes are active compounds of oregano. Furthermore, the total extracts of LG, LP and HP exhibited non-selective inhibitions against the activity of the cyclooxygenases COX-1 and COX-2. Conclusions Our results suggest that Lippia graveolens, Lippia palmeri and Hedeoma patens extracts have the potential to treat inflammatory diseases; their activity is mediated by polyphenols and terpenes. These findings support the claim for their traditional use in the treatment of inflammation-related diseases. © 2016 Elsevier Ireland Ltd. All rights reserved.


Repinski S.L.,University of California at Davis | Kwak M.,University of California at Davis | Kwak M.,National Institute of Biological Resources | Gepts P.,University of California at Davis
Theoretical and Applied Genetics | Year: 2012

In a common bean plant exhibiting determinate growth, the terminal shoot meristem switches from a vegetative to reproductive state, resulting in a terminal inflorescence. Contrary to this, indeterminate growth habit results in a terminal meristem that remains vegetative where it further regulates the production of lateral vegetative and reproductive growth. In the last century, breeders have selected determinate growth habit, in combination with photoperiod insensitivity, to obtain varieties with a shorter flowering period, earlier maturation and ease of mechanized harvest. Previous work has identified TFL1 as a gene controlling determinate growth habit in Arabidopsis thaliana. In this work, we have validated that the Phaseolus vulgaris candidate gene, PvTFL1y, is the functional homolog of TFL1 using three independent lines of evidence. First, in a population of ~1,500 plants, PvTFL1y was found to co-segregate with the phenotypic locus for determinate growth habit (fin) on chromosome 01. Second, using quantitative PCR, we found that two unique haplotypes associated with determinacy at the PvTFL1y locus, a 4. 1-kb retrotransposon and a splice-site mutation, cause mRNA abundance to decrease 20-133 fold, consistent with the recessive nature of fin. Finally, using a functional complementation approach, through Agrobacterium-mediated transformation of determinate Arabidopsis, we rescued tfl1-1 mutants with the wild-type PvTFL1y gene. Together, these three lines of evidence lead to the conclusion that PvTFL1y is the functional homolog of the Arabidopsis gene, TFL1, and is the gene responsible for naturally occurring variation for determinacy in common bean. Further work exploring the different haplotypes at the PvTFL1y locus may lead to improved plant architecture and phenology of common bean cultivars. © 2012 Springer-Verlag.


News Article | November 2, 2016
Site: www.eurekalert.org

The first whole genome sequence of the Far Eastern Amur leopard is published in the open access journal Genome Biology, providing new insight into carnivory and how it impacts on genetic diversity and population size. Mr. Yunsung Cho, lead author from Ulsan National Institute of Science and Technology, said: "Using the Amur leopard genome and comparing it to that of other mammalian genomes we found that carnivory seems to be a strong selection force for genes involved in dietary adaptation - something not as apparent in mammals that are omnivores or herbivores. For example, cows could eat meat without it having a major impact on their health, but leopards eating grass would quickly die as they have evolved to survive on meat." Specialized diets result in physiological, biochemical and morphological adaptations and carnivory is considered to be an evolutionary instable diet. Current research shows that animals in the cat family, Felidae, have relatively low genetic diversity and small population sizes. This could be due to the inflexible nature of their strict diet and explains their vulnerability and critical conservation status. Mr. Cho explained: "Carnivory related genetic adaptations such as extreme agility, muscle power and specialized diet make leopards such successful predators, but these lifestyle traits also make them genetically vulnerable." An international team of researchers sequenced the Amur leopard genome using a muscle sample of a female from Korea. They then analyzed a further 18 mammalian genomes including eight carnivores (domestic cat, tiger, cheetah, lion, leopard, polar bear, killer whale and Tasmanian devil), five omnivores (human, mouse, dog, pig, and opossum) and five herbivores (giant panda, cow, horse, rabbit, and elephant). Comparing the genomes they found that carnivores share two genes that are not present in other genomes that play an important role in bone development and repair, which could drive selection for a diet specialized towards meat. Professor Steve O'Brien, who has been researching rare endangered cat species for decades emphasizes that "Leopards are the most widespread species of the big cats, found in Africa to the Russian Far East, and thrive in a variety of environments. However, populations are fast declining, especially the Amur leopard, which is now critically endangered and perhaps the most endangered animal species on Earth." This is the first de novo genome assembly and the second leopard genome to be sequenced following the snow leopard published in 2013. The researchers hope that this Amur leopard reference genome will serve as a useful tool for understanding Felidae evolution and aid conservation. Dr. Soonok Kim, who initiated and led the project as the PI of National Institute of Biological Resources of Korea adds: "Cats are also a good model for studying health issues, such as human diabetes, and this new leopard genome reference is an environmental treasure that could help us understand these conditions further." 1. Images are available. Please contact Alanna Orpen. 2. Comparison of three dietary groups in mammals: carnivore, omnivore, and herbivore genome analyses with a new leopard assembly Soonok Kim, Yun Sung Cho, Hak-Min Kim et al. Genome Biology 2016 During the embargo period, please contact Alanna Orpen for a copy of the article. After the embargo lifts, the article will be available at the journal website here: https:/ Please name the journal in any story you write. If you are writing for the web, please link to the article. All articles are available free of charge, according to BioMed Central's open access policy. 3. Genome Biology covers all areas of biology and biomedicine studied from a genomic and post-genomic perspective. Content includes research, new methods and software tools, and reviews, opinions and commentaries. Areas covered include, but are not limited to: sequence analysis; bioinformatics; insights into molecular, cellular and organismal biology; functional genomics; epigenomics; population genomics; proteomics; comparative biology and evolution; systems and network biology; genomics of disease; and clinical genomics. All content is open access immediately on publication. 4. BioMed Central is an STM (Science, Technology and Medicine) publisher which has pioneered the open access publishing model. All peer-reviewed research articles published by BioMed Central are made immediately and freely accessible online, and are licensed to allow redistribution and reuse. BioMed Central is part of Springer Nature, a major new force in scientific, scholarly, professional and educational publishing, created in May 2015 through the combination of Nature Publishing Group, Palgrave Macmillan, Macmillan Education and Springer Science+Business Media. http://www.


The Korean flying fish, Cheilopogon doederleinii, is a marine fish species belonging to the family Exocoetidae. In this study, I report for the first time the sequencing and assembly of the complete mitochondrial genome of C. doederleinii. The complete mitochondrial genome is 16,525 bp long and includes 13 protein-coding, 22 tRNA, and 2 rRNA genes. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 10 species showed that C. doederleinii is clustered with C. arcticeps and grouped with the other Exocoetidae species. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution. © 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.


Lee S.,National Institute of Biological Resources
Mitochondrial DNA Part B: Resources | Year: 2016

The mud loach (Misgurnus mizolepis) is a small benthic species belonging to the family Cobitidae. In this study, I report the first sequencing and assembly of the complete mitochondrial genome of M. mizolepis. The complete mitochondrial genome is 16,647 bp long, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 20 species showed that M. mizolepis is clustered with M. anguillicaudatus and M. bipartitus. This mitochondrial genome provides potentially important resources for studying molecular evolution and biogeography. © 2016 The Author(s).


Mr. Yunsung Cho, lead author from Ulsan National Institute of Science and Technology, said: "Using the Amur leopard genome and comparing it to that of other mammalian genomes we found that carnivory seems to be a strong selection force for genes involved in dietary adaptation - something not as apparent in mammals that are omnivores or herbivores. For example, cows could eat meat without it having a major impact on their health, but leopards eating grass would quickly die as they have evolved to survive on meat." Specialized diets result in physiological, biochemical and morphological adaptations and carnivory is considered to be an evolutionary instable diet. Current research shows that animals in the cat family, Felidae, have relatively low genetic diversity and small population sizes. This could be due to the inflexible nature of their strict diet and explains their vulnerability and critical conservation status. Mr. Cho explained: "Carnivory related genetic adaptations such as extreme agility, muscle power and specialized diet make leopards such successful predators, but these lifestyle traits also make them genetically vulnerable." An international team of researchers sequenced the Amur leopard genome using a muscle sample of a female from Korea. They then analyzed a further 18 mammalian genomes including eight carnivores (domestic cat, tiger, cheetah, lion, leopard, polar bear, killer whale and Tasmanian devil), five omnivores (human, mouse, dog, pig, and opossum) and five herbivores (giant panda, cow, horse, rabbit, and elephant). Comparing the genomes they found that carnivores share two genes that are not present in other genomes that play an important role in bone development and repair, which could drive selection for a diet specialized towards meat. Professor Steve O'Brien, who has been researching rare endangered cat species for decades emphasizes that "Leopards are the most widespread species of the big cats, found in Africa to the Russian Far East, and thrive in a variety of environments. However, populations are fast declining, especially the Amur leopard, which is now critically endangered and perhaps the most endangered animal species on Earth." This is the first de novo genome assembly and the second leopard genome to be sequenced following the snow leopard published in 2013. The researchers hope that this Amur leopard reference genome will serve as a useful tool for understanding Felidae evolution and aid conservation. Dr. Soonok Kim, who initiated and led the project as the PI of National Institute of Biological Resources of Korea adds: "Cats are also a good model for studying health issues, such as human diabetes, and this new leopard genome reference is an environmental treasure that could help us understand these conditions further." More information: Soonok Kim et al. Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly, Genome Biology (2016). DOI: 10.1186/s13059-016-1071-4


Ahn K.-J.,Chungnam National University | Jeon M.-J.,National Institute of Biological Resources | Branham M.A.,University of Florida
Cladistics | Year: 2010

A phylogenetic analysis of the tribe Liparocephalini Fenyes is presented based on morphological and molecular characters. The data set comprised 50 adult morphological characters, partial COI (907 bp), COII (366 bp) and 12S rDNA (325-355 bp), and nearly complete sequences of 18S rDNA (1768-1902 bp) for 21 species. Eighteen species of liparocephaline beetles from all eight genera and three outgroups, are included. The sequences were analysed separately and simultaneously with morphological characters by direct optimization in the program POY4 and by partitioned Bayesian analysis for the combined data. The direct optimization (DO) tree for the combined data under equal weighting, which also shows a minimum incongruence length difference value, resulted in a monophyletic Liparocephalini with the following patterns of phylogenetic relationships (outgroup ((Baeostethus, Ianmoorea) (Paramblopusa ((Amblopusa, Halorhadinus) (Liparocephalus, Diaulota))))). A sensitivity analysis using 16 different parameter sets for the combined data shows the monophyly of the liparocephalines and all its genera under all parameter sets. Bayesian analysis resulted in topological differences in comparison with the DO tree under equal weighting only in the position of the genus Paramblopusa and clade (Amblopusa + Halorhadinus), which were reversed. Historical biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini are discussed. Based on the biogeographical analyses, we hypothesize that the ancestor of the Liparocephalini occurred along the Panthallassan Ocean, the direct antecedent of the Pacific Ocean, followed by repeated dispersals to the Nearctic from the Palearctic. We also hypothesize that ancestors of the Liparocephalini appear to have arisen in the littoral zone of beaches and then colonized rocky reef areas in the low tidal zone later through high- to mid-tide zones. © The Willi Hennig Society 2009. © The Willi Hennig Society 2009.


Moon K.H.,National Institute of Biological Resources
Journal of Japanese Botany | Year: 2011

As a result of taxonomic studies of the genus Menegazzia (Parmeliaceae, Lecanorales) in Korea, four species are recognized; M. anteforata Aptroot, M. J. Lai & Sparrius, M. nipponica K. H. Moon, Kurok. & Kashiw., M. primaria Aptroot, M. J. Lai & Sparrius and M. terebrata (Hoffm.) A. Massal. Among them M. anteforata is a new addition to the present area. Menegazzia asahinae (Yasuda ex Asahina) R. Sant. is excluded from the lichen flora of Korea.


An analytical procedure is proposed for the direct simultaneous determination in a single scan of Co, Cu, Fe, Ni and V in sediment pore waters by means of adsorptive cathodic stripping voltammetry (ACSV) with mixed ligands (DMG and catechol). Optimum conditions for the determination of these five elements were studied. Detection limits of the technique depended upon the reproducibility of the procedure blank, and were found to be 0.04 nM Co, 0.09 nM Cu, 1.29 nM Fe, 0.46 nM Ni and 2,52 nM V making the method suitable for the direct simultaneous determination of these five metals in pore waters, estuarine waters and probably coastal waters. © 2011 Elsevier B.V. All rights reserved.


News Article | November 10, 2016
Site: www.nature.com

Carnivores have experienced stronger natural selection than plant-eating animals, perhaps because of their limited diet. Joo-Hong Yeo at the National Institute of Biological Resources in the Republic of Korea and his colleagues compared the genomes of 18 mammals, including carnivores such as leopards, omnivores such as humans, and herbivores such as giant pandas. They found that carnivore genomes have lost many genes for carbohydrate digestion, and share changes to genes involved in muscle strength and agility, making them good hunters. By contrast, omnivore and herbivore genomes shared fewer adaptations with others in their groups, suggesting that their diets have imposed weaker selection compared with that of carnivores. Many big cats showed recent losses in genetic diversity, suggesting that population declines may be linked to their strict diet.

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