3,930 research outputs found
Rapid identification of Rhodococcus equi by a PCR assay targeting the choE gene
No full textThe actinomycete Rhodococcus equi is an important pathogen of horses and an emerging opportunistic pathogen of humans. Identification of R. equi by classical bacteriological techniques is sometimes difficult, and misclassification of an isolate is not uncommon. We report here on a specific PCR assay for the rapid and reliable identification of R. equi. It is based on the amplification of a fragment of the choE gene encoding cholesterol oxidase. The choE-based PCR was assessed by using a panel of strains comprising 132 isolates from different sources and of different geographical origins, all initially identified biochemically as R. equi, and 30 isolates of representative non-R. equi actinomycete species, including cholesterol oxidase producers. The expected 959-bp amplicon was observed only with R. equi isolates, as confirmed by sequencing of a variable region of the 16S RNA gene from a random sample of 20 PCR-positive isolates. All R. equi isolates gave a positive choE-based PCR result, which correlated with a high degree of conservation of the choE gene. Three of the 132 strains originally identified as R. equi were negative for the choE gene, and subsequent analysis of their 16S RNA gene sequences confirmed that they belonged to other bacterial species (Dietzia maris, Mycobacterium peregrinum, and Staphylococcus epidermidis). All non-R. equi isolates were negative by the choE-based PCR. ATCC 21387, the only known isolate of Brevibacterium sterolicum, gave a 959-bp amplicon whose DNA sequence was virtually identical to that of R. equi choE. Comparison of the 16S RNA genes indicated that ATCC 21387 should be considered an R. equi isolate
Internally controlled real-time PCR method for quantitative species-specific detection and vapA genotyping of Rhodococcus equi
No full textWe developed a novel quantitative real-time PCR (Q-PCR) method for the soil actinomycete Rhodococcus equi, an important horse pathogen and emerging human pathogen. Species-specific quantification was achieved by targeting the chromosomal monocopy gene choE, universally conserved in R. equi. The choE Q-PCR included an internal amplification control (IAC) for identification of false negatives. A second Q-PCR targeted the virulence plasmid gene vapA, carried by most horse isolates but infrequently found in isolates from other sources. The choE-IAC and vapA assays were 100% sensitive and specific as determined using 178 R. equi isolates, 77 nontarget bacteria, and a panel of 60 R. equi isolates with known vapA+ and vapA-negative (including vapB+) plasmid genotypes. The vapA+ frequency among isolate types was as follows: horse, 85%; human, 20%; bovine and pig, 0%; others, 27%. The choE-IAC Q-PCR could detect up to one genome equivalent using R. equi DNA or 100 bacteria/ml using DNA extracted from artificially contaminated horse bronchoalveolar lavage (BAL) fluid. Quantification was linear over a 6-log dynamic range down to approximately 10 target molecules (or 1,000 CFU/ml BAL fluid) with PCR efficiency E of >0.94. The vapA assay had similar performance but appeared unsuitable for accurate (vapA+) R. equi quantification due to variability in target gene or plasmid copy number (1 to 9). The dual-reaction Q-PCR system here reported offers a useful tool to both medical and veterinary diagnostic laboratories for the quantitative detection of R. equi and (optional) vapA+ "horse-pathogenic" genotype determination
Sexual selection and mating system in Zorotypus gurneyi Choe (Insecta : Zoraptera)
No full textSocial behavior of a species in the little-known insect order Zoraptera is described for the first time. Zorotypus gurneyi Choe (Insecta: Zoraptera) is a wing-dimorphic species that lives colonially under the bark of rotting logs in central Panama. Males are larger than females in total body size and fight each other to gain access to females. Highly linear and stable dominance hierarchies exist among males. Higher-ranking males show such agonistic behavior as jerking, chasing, head-butting, hindleg-kicking, and grappling, whereas subordinates often try to avoid contacts. Higher-ranking males, the dominant males in particular, are well recognized by others and relatively free of injuries. Although the dominant males are often the largest, the correlation between body size and dominance rank is not always significant. The mating system of Z. gurneyi is an example of female defense polygyny in which the dominant males obtain the majority of matings (75% on average). Mating success among Z. gurneyi males is much more variable than that of some lekking species.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46900/1/265_2004_Article_BF00164179.pd
1921 and C. spinosus Yamaguti, 1939 (Copepoda: Siphonostomatoida: Caligidae) parasitic on amberjacks (Seriola spp.) from Korea
No full textChoe, Mi-Kyung, Kim, Il-Hoi (2010): 1921 and C. spinosus Yamaguti, 1939 (Copepoda: Siphonostomatoida: Caligidae) parasitic on amberjacks (Seriola spp.) from Korea. Zootaxa 2483: 23-34, DOI: 10.5281/zenodo.19548
Structural and functional studies of the acetylcholinesterase ChoE from Pseudomonas aeruginosa
No full textL'acétylcholine (ACh), bien connue comme neurotransmetteur chez les animaux, est le substrat des acétylcholinestérases eucaryotes et procaryotes (AChE). La structure et la fonction des AChE de mammifères ont été bien étudiées en raison de leur importance à la fois dans les synapses cérébrales cholinergiques, dans le système nerveux périphérique et également comme une cible médicamenteuse clé pour de nombreuses maladies telles que la maladie d'Alzheimer chez les humains. En revanche, les acétylcholinestérases procaryotes restent mal comprises malgré une longue historique d'études. La bactérie Pseudomonas aeruginosa possède le système d'acquisition de la choline comprenant l'enzyme ChoE, qui aide à importer la choline comme source de nutriments. Fait intéressant, ChoE a été identifiée comme une acétylcholinestérase putative qui présente des propriétés enzymatiques similaires aux AChE de mammifères malgré sa taille beaucoup plus petite. Dans ce travail, pour mieux comprendre l'acétylcholinestérase d'origine procaryote, nous avons effectué la caractérisation structurale et biochimique de ChoE en utilisant la cristallographie aux rayons X et l'enzymologie comme approches primaires. Nous avons démontré que ChoE est indispensable à la croissance de P. aeruginosa lorsque l'acétylcholine est utilisée comme seule source de carbone et d'azote. Un ensemble complet de structures à haute résolution de ChoE a été obtenu, y compris des complexes avec des substrats, des produits, un intermédiaire acyle ainsi qu'un inhibiteur. Ces structures ont révélé les déterminants moléculaires de la reconnaissance du substrat, des instantanés des différentes étapes catalytiques et la base moléculaire de l'inhibition du substrat à des concentrations élevées de substrat. D'après ces résultats, la libération retardée du produit acétate facilite la liaison non productive du substrat, provoquant l'inhibition du substrat. En utilisant une série de mutants, nous avons étudié le rôle des résidus critiques dans la triade catalytique, le trou oxyanion et la poche de liaison de la choline, tels que Ser38, Tyr106, Asn147, Asp285, Trp287 et His288. Ces résultats ont révélé que Ser38 et His288 dans la triade catalytique sont essentiels pour l'activité ChoE tandis que Asp285 n'est pas essentiel. Conformément au mécanisme moléculaire déduit de ces structures, l'inhibition du substrat est abolie ou considérablement atténuée chez les mutants N147A, Y106A, D285N et W287A. Par-dessus tout, nous avons identifié trois conformations distinctes de Ser38 catalytique, dont la plasticité conformationnelle contrôle vraisemblablement la géométrie du site actif et donc les états fonctionnels de ChoE, ce qui est également corroboré par notre analyse structurale d'autres hydrolases SGNH. En résumé, ces travaux ont fourni des informations moléculaires sans précédent sur les acétylcholinestérases bactériennes et la famille des hydrolases SGNH.Acetylcholine (ACh), a well-known neurotransmitter in animals, is the substrate of both eukaryotic and prokaryotic acetylcholinesterases (AChE). The structure and the function of mammalian AChEs have been well studied due to their importance in both cholinergic brain synapses and the peripheral nervous systems. They are also a key drug target for many diseases such as Alzheimer's disease in humans. In contrast, prokaryotic acetylcholinesterases remain poorly understood despite a long history of studies. Pseudomonas aeruginosa bacterium possesses the choline acquisition system including the enzyme ChoE, helping it to import choline as a nutrient source. ChoE has been identified as a putative acetylcholinesterase which exhibits similar enzymatic properties to mammalian AChEs despite its much smaller size. In this work, to better understand the acetylcholinesterase of prokaryotic sources, we performed the structural and biochemical characterization of ChoE using X-ray crystallography and enzymology as the primary approaches. We have demonstrated that ChoE is indispensable for P. aeruginosa growth when acetylcholine is used as the sole carbon and nitrogen source. A comprehensive set of high-resolution structures of ChoE have been obtained including the complexes of enzyme with substrates, products, acyl intermediate and inhibitor. These structures have revealed the molecular determinants for substrate recognition, snapshots of the various catalytic steps, and the molecular basis of substrate inhibition at high substrate concentrations. From these results, the retarded release of the acetate product facilitates the nonproductive binding of substrate causing substrate inhibition. Using a series of mutants, we have studied the role of critical residues in the catalytic triad, the oxyanion hole and the choline-binding pocket, such as Ser38, Tyr106, Asn147, Asp285, Trp287 and His288. These results indicated that both Ser38 and His288 in the catalytic triad are strictly required for ChoE activity while Asp285 is not essential. Consistent with the molecular mechanism deduced from our structures, substrate inhibition is abolished or significantly alleviated in the N147A, Y106A, D285N and W287A mutants. Importantly, we have identified three distinct conformations of catalytic Ser38, whose conformational plasticity presumably controls the active site geometry and thus the functional states of ChoE, which is also substantiated by our structural analysis of other SGNH hydrolases. In summary, this work has provided unprecedented molecular insights into both bacterial acetylcholinesterases and the SGNH hydrolase family
Molecular dynamics studies of interactions between Arg9(nona-arginine) and a DOPC/DOPG(4:1) membrane
No full textIt has been known that the uptake mechanisms of cell-penetrating peptides (CPPs) depend on the experimental conditions such as the concentration of peptides, lipid composition, and temperature. In this study, we investigate the temperature dependence of the penetration of Arg 9 s into a DOPC/DOPG(4:1) membrane using molecular dynamics (MD) simulations at two different temperatures, T = 310 K and T = 288 K. Although it is difficult to identify the temperature dependence because of having only one single simulation at each temperature and no evidence of translocation of Arg 9 s across the membrane at both temperatures, our simulations suggest that following are strongly correlated with the penetration of Arg 9 s: a number of water molecules coordinated by Arg 9 s and the electrostatic energy between Arg 9 s and the lipid molecules. We also present how Arg 9 s change a bending rigidity of the membrane and how a collective behavior between Arg 9 s enhances the penetration and the membrane bending. Our analyses can be applicable to any CPPs to investigate their interactions with various membranes using MD simulations. © 2020 Author(s).1
Optimal managerial hedging and contracting with self-esteem concerns
No full textAbstract not availableChongwoo Choe, Donald Lien, Chia-Feng (Jeffrey) Y
Global trends in raw materials consumption
No full textThis paper reviews movements in raw materials consumption over the past 30 years. Included in this review are all base metals and steel, and important agricultural raw materials. These primary commodities share the common characteristic that they are used as inputs in manufacturing and construction. Some metals and minerals, energy commodities, and timber products are not included in this review for various reasons. The period reviewed is from 1961 to 1988. A prominent characteristic of the metals market during the past 15 years has been its very slow growth. In some years consumption of several raw materials has even declined. Explaining the causes of this slowdown, in the face of moderate economic growth, has become a topical issue. The slowdown has important implications for a number of developing countries that rely heavily on exports of these materials. The severity and persistence of post-1973 declines in metals intensity per unit of GNP, prompted the conjecture that it may have been structural. This paper reviews the debate on this issue, including results of statistical tests. It also summarizes the trends in raw materials consumption and reviews the technological developments relating to raw materials consumption.Mining&Extractive Industry (Non-Energy),Montreal Protocol,Sanitation and Sewerage,Primary Metals,Environmental Economics&Policies
GENOMIC STRUCTURE OF C-KI-RAS PROTOONCOGENE OF THE HERMAPHRODITIC FISH RIVULUS-MARMORATUS (TELEOSTEI, RIVULIDAE)
No full textThe ras homologue of the rivulid fish Rivulus marmoratus was isolated and characterized by screening about 3.0 x 10(5) genomic clones from a Rivulus genomic library using human c-Ha-ras probe. When this clone was partially sequenced focusing on the region coding exons, it showed 97.5% amino acid homology to the human c-Ki-ras gene. The Rivulus c-Ki-ras gene spans about 6.3 kb and consists of five exons including the alternative splicing exon 4a/4b. The exon-intron boundaries of Rivulus c-Ki-ras gene coincided with the GT/AG rule of consensus splice acceptor and donor sequences as in mammalian c-Ki-ras genes. Amino acid sequence analysis of some domain regions of the Rivulus c-Ki-ras gene revealed 100% identity to mammalian c-Ki-ras gene. This report is the first that elucidate the entire structure of c-Ki-ras in a fish
FIGURE 2. Caligus spinosus Yamaguti, 1939, female. A in 1921 and C. spinosus Yamaguti, 1939 (Copepoda: Siphonostomatoida: Caligidae) parasitic on amberjacks (Seriola spp.) from Korea
No full textFIGURE 2. Caligus spinosus Yamaguti, 1939, female. A, sternal furca; B, leg 1; C, leg 2; D, leg 3; E, first exopodal segment of leg 3; F, leg 4. Scale bars: 0.05 mm for A and E; 0.1 mm for B–D, and F.Published as part of Choe, Mi-Kyung & Kim, Il-Hoi, 2010, 1921 and C. spinosus Yamaguti, 1939 (Copepoda: Siphonostomatoida: Caligidae) parasitic on amberjacks (Seriola spp.) from Korea, pp. 23-34 in Zootaxa 2483 on page 26, DOI: 10.5281/zenodo.19548
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