• 제목/요약/키워드: Species affinity

검색결과 161건 처리시간 0.018초

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
    • /
    • 제20권3호
    • /
    • pp.33.1-33.17
    • /
    • 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.

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

  • 신재권;구본열;김한결;권혜진;손성원;이종석;조현제;배관호;조용찬
    • 생태와환경
    • /
    • 제47권3호
    • /
    • pp.176-185
    • /
    • 2014
  • 멸종위기종이며 식물지리학적으로 중요 종임에도 불구하고, 천연기념물 제191호 한란의 개체군 생태에 관한 연구는 우리나라에서 수행된 바 없다. 본 연구는 2013년 10월부터 2014년 2월까지 제주특별자치도 서귀포시 상효동 돈내코 계곡과 접한 한란 자생지의 환경 개체군 구조 및 미세 석시처 선호성을 분석하였다. 조사지역 (1.25 ha)에서 총 1,237 (989.6개체 $ha^{-1}$)개체의 한란을 관찰하였으며, 위인경 (pseudobulb)은 모두 4,341개, 그리고 17개체 (1.4%)에서 개화를 확인하였다. 전체 개체 중 60.9%에서 잎마름 및 반점 등의 병징이 관찰되었다. 엽면적의 경우 전체적으로 소형 개체가 가장 많고, 준중형, 중형, 준대형 및 대형의 순으로 많은 역-J자 형태로 나타났다. 한란의 크기 (위인경 수 $r_s$=-0.159, 잎 수 $r_s$=-0.148, 그리고 엽면적 $r_s$=-0.114)는 토양온도와 약하지만 유의한(p<0.0001) 음의상관을 나타내었다. 한란은 거의 모든 개체 (95.4%)가 구실잣밤나무 아래에서 자라고 있었으며, 공간적으로 모여서 자라는 특성을 나타내었다. 연구 지역에 나타난 한란 개체군 특성은 종의 서식처 선호성과 자생지의 천이 진행에 의한 것으로 생각된다. 본 연구를 통하여 한란 자생지 모니터링 기반을 마련하였으며, 개체군 특성에 기초한 보전방안을 논의 하였다.

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

  • 천경식;한준수;김경아;옥길환;유기억
    • 한국환경생태학회지
    • /
    • 제26권1호
    • /
    • pp.1-10
    • /
    • 2012
  • 본 연구는 희귀식물로 지정되어 있는 울릉도 미역고사리의 자생지 환경을 조사하여 보전 및 복원 시 기초자료를 제공하고자 하였다. 조사결과 미역고사리의 자생지는 해발고도 410~748m 범위와 경사 $12{\sim}80^{\circ}$의 암석지에 주로 생육하는 것으로 조사되었다. 식생분석결과 4개 지역의 10개 방형구내에서 조사된 관속식물은 총 66분류군이었다. 자생지 상층수목 중 교목층의 중요치는 고로쇠나무(49.52%)가 아교목층은 당마가목(28.99%)이 가장 높았으며, 관목층은 바위수국(51.99%), 섬쥐똥나무(8.82%), 너도밤나무(7.25%)가 높은 값을 보였다. 초본층은 미역고사리가 23.23%로 가장 높았으며, 다음으로는 큰두루미꽃(9.65%), 파리풀(9.23%), 관중(8.40%), 산꼬리사초(6.75%), 섬바디(5.42%) 등이 높은 값을 보여 이 종류들이 친화도가 높은 것으로 판단된다. 종다양도는 1.18로 산출되었으며, 우점도와 균등도는 각각 0.11와 0.84로 확인되었다. 토양분석 결과 토성은 사양토로 나타났으며, 포장용수량은 30.42%, 유기물함량은 17.95%, pH는 4.70으로 측정되었다. 환경특성과 식생 및 토양분석 결과에 기초한 상관분석에서는 종다양도와 종풍부도는 정의 상관관계를 보였고, 종다양도와 우점도 그리고 미역고사리의 피도와 종풍부도는 부의상관관계를 형성하였다.

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
    • /
    • 제21권2호
    • /
    • pp.147-153
    • /
    • 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
    • /
    • 제34권12호
    • /
    • pp.3817-3824
    • /
    • 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
    • /
    • 제15권3호
    • /
    • pp.98-107
    • /
    • 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.

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

  • 박경화;김진태;이병훈
    • Animal Systematics, Evolution and Diversity
    • /
    • 제12권2호
    • /
    • pp.121-136
    • /
    • 1996
  • 톡토기목 가운데 털보톡토기상과에 속하는 3개 과의 종들간의 유연관계를 조사하기 위하여 이들 과에 속하는 3종 및 인접 상과에 속하는 3과 4종에 대해 유전자분석을 실시하 였다. 이를 위해서 전기영동을 실시하고 대립유전자빈도를 구한 후 유전적차이치(D)를 이용 하여 UPGMA 방법으로 dendrogram을 작성하였다. 그 결과 분절아목 중 털보톡토기상과에 속하는 마디톡토기과, 털보톡토기과 및 가시톡토기과의 종들이 함께 유집되었고, 인접상과인 보라톡토기과, 어리톡토기과 및 혹무늬톡토기과의 종들이 함께 유집되었다. 한편 가시톡토기 과의 종은 털보톡토기과의 종과 그리고 혹무늬톡토기과의 종은 보라톡토기과의 종과 가깝게 유집이 되기는 하나, 이들 종간의 유전적 차이값이 매우 높아 일부 학자의 견해대로 한 과 에 속하는 두 아과로 놓기보다는 별개의 과로 두는 것이 타당하다고 판단되었다. 아울러 굴 톡토기는 어리톡토기과와 유집되기는 하나 유전적차이가 크므로 독립된 과로서의 성격이 인 정된다. 이 결과는 형태형질 및 18S rDNA 염기서열을 분석한 결과와도 대체로 일치하였다.

  • PDF

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

  • Lee, Ho-Joon;Heung-Lak Choung;Byung-Ho Bae
    • The Korean Journal of Ecology
    • /
    • 제18권1호
    • /
    • pp.121-136
    • /
    • 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.

  • PDF

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

  • Zheng, Wei
    • 한국환경성돌연변이발암원학회:학술대회논문집
    • /
    • 한국환경성돌연변이발암원학회 2003년도 추계학술대회
    • /
    • pp.34-63
    • /
    • 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.

  • PDF

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

  • 장수길;천경식;정지희;김진수;유기억
    • 환경생물
    • /
    • 제27권3호
    • /
    • pp.314-322
    • /
    • 2009
  • 특산속 식물인 모데미풀의 자생지 식생을 비롯해 환경 및 토양 특성을 조사하여 보존 및 복원 시 기초자료를 제공하고자 하였다. 모데미풀의 자생지는 770~1,440m에 위치하고, 경사는 $0{\sim}20^{\circ}$로 완만하였으며, 주로 계곡부 북사면에 불연속적인 군락을 형성하고 있었다. 식생분석결과 78개 방형구 내에서 조사된 분류군은 총 111종류였다. 중요치는 모데미풀이 27.05%로 가장 높았으며, 모데미풀과 비슷한 환경을 선호하는 분류군으로는 박새 (5.67%), 현호색 (5.32%), 눈개승마 (4.35%), 벌깨덩굴(4.06%), 홀아비바람꽃(3.91%) 등으로 나타났다. 자생지 상층 수목 중 교목층은 층층나무, 가래나무, 신갈나무, 당단풍나무, 고로쇠나무 등이 우점종으로 나타났고, 아교목층은 당단풍나무와 까치박달이 높은 빈도를 보였으며, 관목층은 물참대와 귀룽나무가 우점하였다. 종다양도는 평균 1.16이었고, 우점도와 균등도는 각각 0.12와 0.81로 나타났다. 토양의 포장용수량은 평균 26.41%이었으며, 유기물 함량은 7.83%로 나타났고, pH는 5.83으로 확인되었다. 환경특성과 식생 및 토양 분석 결과에 기초한 상관분석에서는 경사와 pH, 경사와 유기물함량, 우점도와 중요치, 종다양도와 종풍부도가 정의 상관관계를, 우점도와 종다양도, 종다양도와 중요치는 부의 상관관계를 보였다.