(1'R,3S,4'S,7'Z,8'R,9'S)-7'-Ethylidene-1-methoxy-5'-methylspiro[indole-3,2'-oxaazatricyclo[126.96.36.199]dodecan]-2(1H)-one/PS-triphenylphosphine/triphenylphosphine-polystyrene/TRIPHENYLPHOSPHINE NOVAGEL/TRIPHENYLPHOSPHINE PS/TRIPHENYLPHOSPHINE RESIN/Sarpagan-17-oic acid, 16-(hydroxymethyl)-, methyl ester, (15α,16S,19trans)-/diphenylphosphinated/polymer-supported triphenylphosphine/17-hydroxy-sarpagane-16-carboxylic acid methyl ester/DIPHENYLPHOSPHINO-POLYSTYRENE/TRIPHENYLPHOSPHINE PS RESIN/triphenyl phosphine on polymer/Polyneuridin/PL-TPP MP-RESIN/polymer-bound triphenylphosphine/triphenylphosphine on polystyrene/Methyl (15α,16S,19Z)-16-(hydroxymethyl)sarpagan-17-oate/PL-TPP RESIN/POLYSTYRENE-PPH2/(Z)-Akuammidine
ambient temperature, bacteria, bioremediation, culturability, petroleum degradation
480.1±55.0 °C at 760 mmHg
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In this study, we compared the culturability of aerobic bacteria isolated from long-term oil-contaminated soils via enrichment and direct-plating methods; bacteria were cultured at 30°C or ambient temperatures. Two soil samples were collected from two sites in the Shengli oilfield located in Dongying, China. One sample (S0) was close to the outlet of an oil-production water treatment plant, and the other sample (S1) was located 500 m downstream of the outlet. In total, 595 bacterial isolates belonging to 56 genera were isolated, distributed in Actinobacteria, Firmicutes, Bacterioidetes, and Proteobacteria. It was interesting that Actinobacteria and Firmicutes were not detected from the 16S rRNA gene clone library. The results suggested the activation of rare species during culture. Using the enrichment method, 239 isolates (31 genera) and 96 (22 genera) isolates were obtained at ambient temperatures and 30°C, respectively, from S0 soil. Using the direct-plating method, 97 isolates (15 genera) and 163 isolates (20 genera) were obtained at ambient temperatures and 30°C, respectively, from two soils. Of the 595 isolates, 244 isolates (41.7% of total isolates) could degrade n-hexadecane. A greater number of alkane-degraders was isolated at ambient temperatures using the enrichment method, suggesting that this method could significantly improve bacterial culturability. Interestingly, the proportion of alkane degrading isolates was lower in the isolates obtained using enrichment method than that obtained using direct-plating methods. Considering the greater species diversity of isolates obtained via the enrichment method, this technique could be used to increase the diversity of the microbial consortia. Furthermore, phenol hydroxylase genes (pheN), medium-chain alkane monooxygenases genes (alkB and CYP153A), and long-chain alkane monooxygenase gene (almA) were detected in 60 isolates (11 genotypes), 91 isolates (27 genotypes) and 93 isolates (24 genotypes), and 34 isolates (14 genotypes), respectively. This study could provide new insights into microbial resources from oil fields or other environments, and this information will be beneficial for bioremediation of petroleum contamination and for other industrial applications.
ambient temperature, bacteria, bioremediation, culturability, petroleum degradation
Functional Genetic Diversity and Culturability of Petroleum-Degrading Bacteria Isolated From Oil-Contaminated Soils
Ji-Quan Sun,1,† Lian Xu,1,† Xue-Ying Liu,1 Gui-Fang Zhao,2 Hua Cai,2 Yong Nie,1 and Xiao-Lei Wu1,*
For a monograph based on a polythetic concept, several thousands of herbarium specimens, and several hundreds of freshly collected and cultured specimens of Daldinia and allied Xylariaceae, originating from around the world, were studied for morphological traits, including by SEM, and chemically by HPLC profiles using UV-visible and mass spectrometric detection. Emphasis was given to tropical material, and importantly, ancient specimens, including as many types as possible, were tracked and studied to review earlier taxonomic concepts. An epitype of D. eschscholtzii was selected as representative of the morphochemotype that is most widely distributed in the tropics. Six new species of Daldinia from the tropics and the southern Hemisphere are described. Daldinia asphalatum is resurrected, and D. cudonia is regarded as its synonym. In addition, the following binomials are epi-, iso-, neo- and/or lectotypified: Daldinia asphalatum, D. caldariorum, D. clavata, D. cuprea, D. durissima, D. eschscholtzii, D. grandis, D. loculata, and D. vernicosa. Annellosporium and Versiomyces are regarded as synonyms of Daldinia. Many new synonymies in Daldinia are proposed, and some previously published names are rejected. In total, 47 taxa in Daldinia are recognised and a key is provided. Their biogeography, chorology, and ecology, as well as the importance of their secondary metabolites, are also discussed. The previous definition of the genus is emended. The species concept is based mainly on morphological and other phenotype-derived characters because, despite diligent search, no molecular data or cultures of several of the accepted species could be obtained. Daldinia is segregated into five major groups, based on phenotypic characteristics. Some unnamed but aberrant specimens were not found in good condition and are therefore not formally described as new species. However, they are illustrated in detail in a hope that this will facilitate the discovery of fresh material in future. A preliminary molecular phylogeny based on 5.8S/ITS nrDNA including numerous representatives of all hitherto described taxa for which cultures are extant, was found basically in agreement with the above mentioned segregation of the genus, based on morphological and chemotaxonomic evidence. In the rDNA based phylogenetic tree, Daldinia appears clearly distinct from members of the genera Annulohypoxylon and Hypoxylon; nevertheless, representatives of small genera of predominantly tropical origin (Entonaema, Phylacia, Ruwenzoria, Rhopalostroma, Thamnomyces) appear to have evolved from daldinioid ancestors and are nested inside the Daldinia clade. Interestingly, these findings correlate with chemotaxonomic characters to a great extent, especially regarding the distribution of marker metabolites in their mycelial cultures. Hence, the current study revealed for the first time that fungal secondary metabolite profiles can have taxonomic value beyond the species rank and even coincide with phylogenetic data.
Daldinia andina sp. nov., D. australis sp. nov., D. hausknechtii sp. nov., D. rehmii sp. nov., D. starbaeckii sp. nov., D. theissenii sp. nov., D. cahuchosa comb. nov., D. nemorosa comb. nov.
Ascomycota, biodiversity, chemotaxonomy, systematics, Xylariales
A polyphasic taxonomy of Daldinia (Xylariaceae)1
Marc Stadler,1,* Thomas Læssøe,2 Jacques Fournier,3 Cony Decock,4 Beata Schmieschek,5 Hans-Volker Tichy,6 and Derek Per?oh7,8
2014 Mar 15;
Viruses from the Coronaviridae, Togaviridae, and Hepeviridae families ?all contain genes that encode a conserved protein domain, called a macrodomain; however, the role of this domain during infection has remained enigmatic. The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Here, we comprehensively review this rapidly expanding field, describing the structures and enzymatic activities of viral macrodomains, and discussing their roles in viral replication and pathogenesis.
macrodomain, ADP-ribosylation, poly-ADP-ribose polymerase (PARP), interferon (IFN), replication, pathogenesis, Coronaviridae, Togaviridae, Hepeviridae
Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis
Anthony R. Fehr,1,3,? Gytis Jankevicius,2,3 Ivan Ahel,2 and Stanley Perlman1,?