• Title/Summary/Keyword: Species affinity

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Computer-aided drug design of Azadirachta indica compounds against nervous necrosis virus by targeting grouper heat shock cognate protein 70 (GHSC70): quantum mechanics calculations and molecular dynamic simulation approaches

  • Islam, Sk Injamamul;Saloa, Saloa;Mahfuj, Sarower;Islam, Md Jakiul;Jahan Mou, Moslema
    • Genomics & Informatics
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    • v.20 no.3
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    • pp.33.1-33.17
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    • 2022
  • Nervous necrosis virus (NNV) is a deadly infectious disease that affects several fish species. It has been found that the NNV utilizes grouper heat shock cognate protein 70 (GHSC70) to enter the host cell. Thus, blocking the virus entry by targeting the responsible protein can protect the fishes from disease. The main objective of the study was to evaluate the inhibitory potentiality of 70 compounds of Azadirachta indica (Neem plant) which has been reported to show potential antiviral activity against various pathogens, but activity against the NNV has not yet been reported. The binding affinity of 70 compounds was calculated against the GHSC70 with the docking and molecular dynamics (MD) simulation approaches. Both the docking and MD methods predict 4 (PubChem CID: 14492795, 10134, 5280863, and 11119228) inhibitory compounds that bind strongly with the GHSC70 protein with a binding affinity of -9.7, -9.5, -9.1, and -9.0 kcal/mol, respectively. Also, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the compounds confirmed the drug-likeness properties. As a result of the investigation, it may be inferred that Neem plant compounds may act as significant inhibitors of viral entry into the host cell. More in-vitro testing is needed to establish their effectiveness.

Habitats Environmental Characteristics of Polypodium vulgare L. in Ulleung-do (울릉도 미역고사리(Polypodium vulgare L.) 자생지의 입지환경특성)

  • Cheon, Kyeong-Sik;Han, Jun-Soo;Kim, Kyung-Ah;Ok, Kil-Hwan;Yoo, Ki-Oug
    • Korean Journal of Environment and Ecology
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    • v.26 no.1
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    • pp.1-10
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    • 2012
  • The habitats characteristics of Polypodium vulgare L. in Ulleung-do were investigated to compile basic data for conservation and restoration. Natural habitats were located at altitudes of 410~748m with inclinations of $12{\sim}80^{\circ}$. Sixty six vascular plants were identified from 10 quadrats in 4 habitats. Dominant species among the woody plants, based on importance value, were Acer pictum subsp. mono(49.52%) in the tree (T1) layer, Sorbus amurensis(28.99%) in the subtree (T2) and Schizophragma hydrangeoides(51.99%), Ligustrum foliosum(8.82%), Fagus engleriana(7.25%) in the shrub (S) layer. Importance value for members of the herb (H) layer were as follows: Polypodium vulgare 23.23%; Maianthemum dilatatum 9.65%; Phryma leptostachya var. asiatica 9.23%; Dryopteris crassirhizoma 8.40%; Carex shimidzensis 6.75% and Dystaenia takesimana 5.42%. The importance value of the last five species were high, so they were at affinity with Polypodium vulgare in their habitats. Species diversity was 1.18, and dominance and evenness were found to be 0.11 and 0.84, respectively. The soil types were sandy loam. Average field capacity was 30.42%, and the organic matter and pH were 17.95%, and 4.70. Correlation coefficients based on environmental factors, vegetation and soil analysis were showed that positive correlations between species diversity and species richness, whereas between species diversity and dominance, coverage of Polypodium vulgare and species richness were showed negative correlations.

Population Structure and Fine-scale Habitat Affinity of Cymbidium kanran Protected Area as a Natural Monument (천연기념물 한란 보호구역의 개체군 구조 및 미세 서식처 선호성)

  • Shin, Jae-Kwon;Koo, Bon-Youl;Kim, Han-Gyeoul;Kwon, He-Jin;Son, Sung-Won;Lee, Jong-Seok;Cho, Hyun-Je;Bae, Kwan-Ho;Cho, Young-Chan
    • Korean Journal of Ecology and Environment
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    • v.47 no.3
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    • pp.176-185
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    • 2014
  • There are no population ecological research on the natural monument (No. 191) Jeju Cymbidium kanran in South Korea. In this study, we analyzed the population structure and fine-scale habitat affinity of C. kanran in Sanghyo-dong, Jejudo Island from Oct. 2013 to Feb. 2014. We observed total of 1,237 individuals (4,341 pseudobulbs) of C. kanran (989.6 population $ha^{-1}$) within (1.25 ha) and only 17 (1.4%) individuals were inflorescent. In 60.9% of the entire populations, disease symptoms such as spots and blight leaves were observed. C. kanran populaton exhibited reverse-J shaped size distribution based on leaf area classes as individual size parameter. The three size related attributes of C. kanran (no. of pseudobulb $r_s$=-0.159, no. of leaves $r_s$=-0.148 and leaf arera $r_s$=-0.114) and soil temperature revealed a negative relationship (p<0.0001). Most of C. kanran (95.4%) were grown under Castamopsis cuspidata and spatially, C. kanran were strongly clumped at all distances. Population characteristics of C. kanran in the study area were likely originated from species habitat affinity and successional environment. Through this study, base line data for C. kanran's habitat monitoring was established and conservation measures based on population characteristics were discussed.

Metal Biosorption by Surface-Layer Proteins from Bacillus Species

  • Allievi, Mariana Claudia;Florencia, Sabbione;Mariano, Prado-Acosta;Mercedes, Palomino Maria;Ruzal, Sandra M.;Carmen, Sanchez-Rivas
    • Journal of Microbiology and Biotechnology
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    • v.21 no.2
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    • pp.147-153
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    • 2011
  • Bacillus species have been involved in metal association as biosorbents, but there is not a clear understanding of this chelating property. In order to evaluate this metal chelating capacity, cultures and spores from Grampositive bacteria of species either able or unable to produce surface layer proteins (S-layers) were analyzed for their capacity of copper biosorption. Only those endowed of S-layers, like Bacillus sphaericus and B. thuringiensis, showed a significant biosorption capacity. This capacity (nearly 50%) was retained after heating of cultures, thus supporting that structural elements of the envelopes are responsible for such activity. Purified S-layers from two Bacillus sphaericus strains had the ability to biosorb copper. Copper biosorption parameters were determined for strain B. sphaericus 2362, and after analyses by means of the Langmuir model, the affinity and capacity were shown to be comparable to other bacterial biosorbents. A competitive effect of $Ca^{2+}$ and $Zn^{2+}$, but not of $Cd^{2+}$, was also observed, thus indicating that other cations may be biosorbed by this protein. Spores that have been shown to be proficient for copper biosorption were further analyzed for the presence of S-layer content. The retention of S-layers by these spores was clearly observed, and after extensive treatment to eliminate the S-layers, the biosorption capacity of these spores was significantly reduced. For the first time, a direct correlation between S-layer protein content and metal biosorption capacity is shown. This capacity is linked to the retention of S-layer proteins attached to Bacillus spores and cells.

Quantitative Speciation of Selenium in Human Blood Serum and Urine with AE- RP- and AF-HPLC-ICP/MS

  • Jeong, Ji-Sun;Lee, Jonghae;Pak, Yong-Nam
    • Bulletin of the Korean Chemical Society
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    • v.34 no.12
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    • pp.3817-3824
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    • 2013
  • Various separation modes in HPLC, such as anion exchange (AE), reversed-phase (RP), and affinity (AF) chromatography were examined for the separation of selenium species in human blood serum and urine. While RP- and AE-HPLC were mainly used for the separation of small molecular selenium species, double column AF-HPLC achieved the separation of selenoproteins in blood serum efficiently. Further, the effluent of AF-HPLC was enzymatically hydrolyzed and then analyzed with RP HPLC for selenoamino acid study. The versatility of the hybrid technique makes the in-depth study of selenium species possible. For quantification, post column isotope dilution (ID) with $^{78}Se$ spike was performed. ORC ICP/MS (octapole reaction cell inductively coupled plasma/mass spectrometry) was used with 4 mL $min^{-1}$ Hydrogen as reaction gas. In urine sample, inorganic selenium and SeCys were identified. In blood serum, selenoproteins GPx, SelP and SeAlb were detected and quantified. The concentration for GPx, SelP and SeAlb was $22.8{\pm}3.4\;ng\;g^{-1}$, $45.2{\pm}1.7\;ng\;g^{-1}$, and $16.1{\pm}2.2\;ng\;g^{-1}$, respectively when $^{80}Se/^{78}Se$ was used. The sum of these selenoproteins ($84.1{\pm}4.4\;ng\;g^{-1}$) agrees well with the total selenium concentration measured with the ID method of $87.0{\pm}3.0\;ng\;g^{-1}$. Enzymatic hydrolysis of each selenium proteins revealed that SeCys is the major amino acid for all three proteins and SeMet is contained in SeAlb only.

Genomic Analysis of miR-21-3p and Expression Pattern with Target Gene in Olive Flounder

  • Jo, Ara;Lee, Hee-Eun;Kim, Heui-Soo
    • Genomics & Informatics
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    • v.15 no.3
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    • pp.98-107
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    • 2017
  • MicroRNAs (miRNAs) act as regulators of gene expression by binding to the 3' untranslated region (UTR) of target genes. They perform important biological functions in the various species. Among many miRNAs, miR-21-3p is known to serve vital functions in development and apoptosis in olive flounder. Using genomic and bioinformatic tools, evolutionary conservation of miR-21-3p was examined in various species, and expression pattern was analyzed in olive flounder. Conserved sequences (5'-CAGUCG-3') in numerous species were detected through the stem-loop structure of miR-21-3p. Thus, we analyzed target genes of miR-21-3p. Among them, 3' UTR region of PPIL2 gene indicated the highest binding affinity with miR-21-3p based on the minimum free energy value. The PPIL2 gene showed high expression levels in testis tissue of the olive flounder, whereas miR-21-3p showed rather ubiquitous expression patterns except in testis tissue, indicating that miR-21-3p seems to control the PPIL2 gene expression in a complementary repression manner in various tissues of olive flounder. Taken together, this current study contributes to infer the target gene candidates for the miR-21-3p using bioinformatics tools. Furthermore, our data offers important information on the relationship between miR-21-3p and target gene for further functional study.

Phylogeny and Speciation of Entomobryoidea (Collembola, Insecta) from Korea (한국산 털보톡토기상과 (톡토기목, 곤충강)의 계통과 종분화)

  • 박경화;김진태;이병훈
    • Animal Systematics, Evolution and Diversity
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    • v.12 no.2
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    • pp.121-136
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    • 1996
  • In order to understand affinities and phylogeny of three families of the Superfamily Entomobryoidea allozyme analysis was performed with three species presumably representing each family, in addition to four species belonging to the neighboring Superfamily Poduroidea together. Electrophoresis for this purpose produced data for calculating allele frequency and enabled to obtain genetic distance and to depict dendrograms as well. The species of Isotomidae, Entomobryidae and Tomoceridae were clustered together whereas those of Hypogastruridae, Onychiuridae and Neanuridae were grouped as monophylies, respectively. Even though Tomoceridae and Entomobryidae were brought together they are considered complete families by showing high genetic distance value between them, thus supporting the hypothesis on their affinity among others. Gulgastrura reticulosa has been revealed to be separated from Hypogastruridae by being clustered rather with Onychiuridae. However, its high genetic distance value suggests the status as an independent family. The present result agreed with the phylogeny of Suborder Arthropleona divided into two Superfamilies mentioned above as in conventional systematics and also when compared with analysis of data of their morphological characters as well as 18S rDNA performed and published elsewhere by the present writers.

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Syntaxonomy and Analysis of Interspecific Association on the Forest Vegetation of Mt.Ch분ongnyang (청량산 삼림식생의 군락분류 및 종간연관 분석)

  • Lee, Ho-Joon;Heung-Lak Choung;Byung-Ho Bae
    • The Korean Journal of Ecology
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    • v.18 no.1
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    • pp.121-136
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    • 1995
  • The forest vegetation on Mt. Ch’ongnyang was investigated for phytosociological analysis of the vegetation types and interspecific association. The forest was classified into seven vegetation units; A: Quercus Mongolica community, A-1: Group of Quercus variabilis, A-1-a: Subgroup of Pinus densiflora, A-1-b: Typical subgroup, A-2: Group of Aconitum trilobum, A-3: Group of Quercus dentata, B: Zelkova serrata communty. The group of Quercus variabilis was distributed on southeast- and southwest-facing slopes in 400~830 m above the sea level, and organic matter in the soil was 3.36~4.67%. The group of Aconitum trilobum was distributed on northeast- and northwest-facing slopes in 650~830 m above the sea level, and organic matter in the soil was 7.18%. The group of Quercus dentata was distributed on southwest-facing solpes in the vicinity of 810 m above the sea level, and organic matter in the soil was 9.7%. The Zelkova serrata community was distributed in the vicinity of ravines, and organic matter in the soil was 7.6%. The contents of Mg and Ca, and electric conductivity in the Zelkova serrata community were relatively high, 11.82 me/100mg, and 11.27 me/100mg, 102.2 μ mos/cm, respectively. In the results of polar ordination, environmental gradient of axis Ⅰ and axis Ⅱwere correlated with moisture, inclination and azimuth, respectively. Group of Quercus variabilis has occurred in xeric, group of Aconitum trilobum in submesic, and the Zelrova serrata community in mesic sites. In the meantime the interspecific association analysis based on chi-square yielded three species groupings with high positive affinity(p<0.01), i.e.group Ⅰ consisted of 18 species, including Acer pseudo-sieboldianum, Ansliaea acerifolia, Aconitum trilobum and group Ⅲ consisted of 19 species, in cluding Zelrova serrata, Oplismenus undulatifolius, Acer truncatum var. barbinerve, respectively.

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Manganese and Iron Interaction: a Mechanism of Manganese-Induced Parkinsonism

  • Zheng, Wei
    • Proceedings of the Korea Environmental Mutagen Society Conference
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    • 2003.10a
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    • pp.34-63
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    • 2003
  • Occupational and environmental exposure to manganese continue to represent a realistic public health problem in both developed and developing countries. Increased utility of MMT as a replacement for lead in gasoline creates a new source of environmental exposure to manganese. It is, therefore, imperative that further attention be directed at molecular neurotoxicology of manganese. A Need for a more complete understanding of manganese functions both in health and disease, and for a better defined role of manganese in iron metabolism is well substantiated. The in-depth studies in this area should provide novel information on the potential public health risk associated with manganese exposure. It will also explore novel mechanism(s) of manganese-induced neurotoxicity from the angle of Mn-Fe interaction at both systemic and cellular levels. More importantly, the result of these studies will offer clues to the etiology of IPD and its associated abnormal iron and energy metabolism. To achieve these goals, however, a number of outstanding questions remain to be resolved. First, one must understand what species of manganese in the biological matrices plays critical role in the induction of neurotoxicity, Mn(II) or Mn(III)? In our own studies with aconitase, Cpx-I, and Cpx-II, manganese was added to the buffers as the divalent salt, i.e., $MnCl_2$. While it is quite reasonable to suggest that the effect on aconitase and/or Cpx-I activites was associated with the divalent species of manganese, the experimental design does not preclude the possibility that a manganese species of higher oxidation state, such as Mn(III), is required for the induction of these effects. The ionic radius of Mn(III) is 65 ppm, which is similar to the ionic size to Fe(III) (65 ppm at the high spin state) in aconitase (Nieboer and Fletcher, 1996; Sneed et al., 1953). Thus it is plausible that the higher oxidation state of manganese optimally fits into the geometric space of aconitase, serving as the active species in this enzymatic reaction. In the current literature, most of the studies on manganese toxicity have used Mn(II) as $MnCl_2$ rather than Mn(III). The obvious advantage of Mn(II) is its good water solubility, which allows effortless preparation in either in vivo or in vitro investigation, whereas almost all of the Mn(III) salt products on the comparison between two valent manganese species nearly infeasible. Thus a more intimate collaboration with physiochemists to develop a better way to study Mn(III) species in biological matrices is pressingly needed. Second, In spite of the special affinity of manganese for mitochondria and its similar chemical properties to iron, there is a sound reason to postulate that manganese may act as an iron surrogate in certain iron-requiring enzymes. It is, therefore, imperative to design the physiochemical studies to determine whether manganese can indeed exchange with iron in proteins, and to understand how manganese interacts with tertiary structure of proteins. The studies on binding properties (such as affinity constant, dissociation parameter, etc.) of manganese and iron to key enzymes associated with iron and energy regulation would add additional information to our knowledge of Mn-Fe neurotoxicity. Third, manganese exposure, either in vivo or in vitro, promotes cellular overload of iron. It is still unclear, however, how exactly manganese interacts with cellular iron regulatory processes and what is the mechanism underlying this cellular iron overload. As discussed above, the binding of IRP-I to TfR mRNA leads to the expression of TfR, thereby increasing cellular iron uptake. The sequence encoding TfR mRNA, in particular IRE fragments, has been well-documented in literature. It is therefore possible to use molecular technique to elaborate whether manganese cytotoxicity influences the mRNA expression of iron regulatory proteins and how manganese exposure alters the binding activity of IPRs to TfR mRNA. Finally, the current manganese investigation has largely focused on the issues ranging from disposition/toxicity study to the characterization of clinical symptoms. Much less has been done regarding the risk assessment of environmenta/occupational exposure. One of the unsolved, pressing puzzles is the lack of reliable biomarker(s) for manganese-induced neurologic lesions in long-term, low-level exposure situation. Lack of such a diagnostic means renders it impossible to assess the human health risk and long-term social impact associated with potentially elevated manganese in environment. The biochemical interaction between manganese and iron, particularly the ensuing subtle changes of certain relevant proteins, provides the opportunity to identify and develop such a specific biomarker for manganese-induced neuronal damage. By learning the molecular mechanism of cytotoxicity, one will be able to find a better way for prediction and treatment of manganese-initiated neurodegenerative diseases.

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Environmental Characteristics and Vegetation of Megaleranthis saniculifolia Ohwi Habitats (모데미풀 자생지의 환경특성과 식생)

  • Jang, Su-Kil;Cheon, Kyoung-Sic;Jeong, Ji-Hee;Kim, Zin-Suh;Yoo, Ki-Oug
    • Korean Journal of Environmental Biology
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    • v.27 no.3
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    • pp.314-322
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    • 2009
  • Vegetation, environmental characteristics and soil analysis of Megaleranthis saniculifolia Ohwi habitats were investigated to propose the basal data for conservation and restoration. M. saniculifolia was distributed around an altitude of 770~1,440 m with an inclination of $0{\sim}20^{\circ}$, and mostly formed discontinuous populations in northern part of valley. The vascular plants from 78 quadrates of 11 habitats were identified 111 taxa. Importance value of M. saniculifolia was 27.05%, and highly ranked 5 species such as Veratrum oxysepalum (5.67%), Corydalis turtschaninovii (5.32%), Aruncus dioicus var. kamtschaticus (4.35%), Meehania urticifolia (4.06%) and Anemone koraiensis (3.91%) were considered to be an affinity with M. saniculifolia. Dominant species of woody plants in 78 quadrates were represented as Cornus controversa, Juglans mandshurica, Quercus mongolica, Acer pseudo-sieboldianum and A. mono in tree (B1) layer, A. pseudo-sieboldianum and Carpinus cordata in subtree (B2) layer, Deutzia glabrata and Prunus padus in shrub (S) layer. Average species diversity was 1.16, and dominance and evenness were found to be 0.12 and 0.81, respectively. Average field capacity was 26.41%, and the organic matter and soil pH were 7.83% and 5.83. Correlation coefficients based on environmental factors, vegetation and soil analysis were showed that the positive correlations between slope degrees and pH, slope degrees and organic matter, dominance and importance value, species diversity and richness, whereas between species diversity and dominance, and importance value and dominance were showed negative correlations.