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Find video protocols related to scientific articles indexed in Pubmed.
Deep-sea Rhodococcus sp. BS-15, lacking the phytopathogenic fas genes, produces a novel glucotriose lipid biosurfactant.
Mar. Biotechnol.
PUBLISHED: 01-21-2014
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Glycolipid biosurfactant-producing bacteria were isolated from deep-sea sediment collected from the Okinawa Trough. Isolate BS15 produced the largest amount of the glycolipid, generating up to 6.31?±?1.15 g l(-1) after 4 days at 20 °C. Glucose was identified in the hydrolysate of the purified major component of the biosurfactant glycolipid. According to gas chromatography/mass spectrometry analysis, the hydrophobic moieties in the major component were hexadecanoate, octadecanoate, 3-hydroxyhexadecanoate, 2-hydroxyoctanoate, and succinate. The molecular weight of the purified major glycolipid was calculated to be 1,211, while (1)H and (13)C nuclear magnetic resonance spectra confirmed that the major component consisted of 2 mol of ?-glucoside and 1 mol of ?-glucoside. The molecular structure was assigned as novel trisaccharide-type glycolipid biosurfactant, glucotriose lipids. The critical micelle concentration of the purified major glycolipid was 2.3?×?10(-6) M, with a surface tension of 29.5 mN m(-1). Phylogenetic analysis showed isolate BS15 was closely related to a Rhodococcus strains isolated from Antarctica, and to Rhodococcus fascians, a phytopathogen. PCR analysis showed that the fasA, fasB, fasC, fasD, fasE, and fasF genes, which are involved in phytohormone-like cytokinin production, were not present in the genome of BS15; however, analysis of a draft genome sequence of BS15 (5.5 Mb) identified regions with 31 %, 53 %, 46 %, 30 %, and 31 % DNA sequence identity to the fasA, fasB, fasC, and fasD genes, respectively.
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High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes.
Front Microbiol
PUBLISHED: 01-01-2014
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Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.
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Draft Genome Sequence of Loktanella cinnabarina LL-001T, Isolated from Deep-Sea Floor Sediment.
Genome Announc
PUBLISHED: 11-16-2013
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This report describes the draft genome sequence of Loktanella cinnabarina LL-001(T), which was the first isolated strain from deep-sea floor sediment of the genus Loktanella. The draft genome sequence contains 3,896,245 bp, with a G+C content of 66.7%.
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Draft Genome Sequence of Sphingobium sp. Strain KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Isolated from Cattle Pasture Soil.
Genome Announc
PUBLISHED: 11-09-2013
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Sphingobium sp. strain KK22 was isolated from a bacterial consortium that originated from cattle pasture soil from Texas. Strain KK22 grows on phenanthrene and has been shown to biotransform the high-molecular-weight (HMW) polycyclic aromatic hydrocarbon (PAH) benz[a]anthracene. The genome of strain KK22 was sequenced to investigate the genes involved in aromatic pollutant biotransformation.
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Draft Genome Sequence of the Dimorphic Prosthecate Bacterium Brevundimonas abyssalis TAR-001T.
Genome Announc
PUBLISHED: 10-19-2013
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We report the 3.0-Mb draft genome sequence of Brevundimonas abyssalis strain TAR-001(T), isolated from deep-sea floor sediment. The draft genome sequence of strain TAR-001(T) consists of 2,979,700 bp in 128 contigs, with a G+C content of 68.2%, 2,946 potential coding sequences (CDS), 3 rRNAs, and 41 tRNAs.
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Biotransformation of the high-molecular weight polycyclic aromatic hydrocarbon (PAH) benzo[k]fluoranthene by Sphingobium sp. strain KK22 and identification of new products of non-alternant PAH biodegradation by liquid chromatography electrospray ionizatio
Microb Biotechnol
PUBLISHED: 09-09-2013
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A pathway for the biotransformation of the environmental pollutant and high-molecular weight polycyclic aromatic hydrocarbon (PAH) benzo[k]fluoranthene by a soil bacterium was constructed through analyses of results from liquid chromatography negative electrospray ionization tandem mass spectrometry (LC/ESI(-)-MS/MS). Exposure of Sphingobium sp. strain KK22 to benzo[k]fluoranthene resulted in transformation to four-, three- and two-aromatic ring products. The structurally similar four- and three-ring non-alternant PAHs fluoranthene and acenaphthylene were also biotransformed by strain KK22, and LC/ESI(-)-MS/MS analyses of these products confirmed the lower biotransformation pathway proposed for benzo[k]fluoranthene. In all, seven products from benzo[k]fluoranthene and seven products from fluoranthene were revealed and included previously unreported products from both PAHs. Benzo[k]fluoranthene biotransformation proceeded through ortho-cleavage of 8,9-dihydroxy-benzo[k]fluoranthene to 8-carboxyfluoranthenyl-9-propenic acid and 9-hydroxy-fluoranthene-8-carboxylic acid, and was followed by meta-cleavage to produce 3-(2-formylacenaphthylen-1-yl)-2-hydroxy-prop-2-enoic acid. The fluoranthene pathway converged with the benzo[k]fluoranthene pathway through detection of the three-ring product, 2-formylacenaphthylene-1-carboxylic acid. Production of key downstream metabolites, 1,8-naphthalic anhydride and 1-naphthoic acid from benzo[k]fluoranthene, fluoranthene and acenaphthylene biotransformations provided evidence for a common pathway by strain KK22 for all three PAHs through acenaphthoquinone. Quantitative analysis of benzo[k]fluoranthene biotransformation by strain KK22 confirmed biodegradation. This is the first pathway proposed for the biotransformation of benzo[k]fluoranthene by a bacterium.
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Active bacterial flora surrounding foraminifera (xenophyophorea) living on the deep-sea floor.
Biosci. Biotechnol. Biochem.
PUBLISHED: 02-07-2013
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Bacteria form unique ecosystems by coexisting with large organisms. Here we present the first evidence of active flora surrounding xenophyophorea revealed through clone analyses of environmental ribosomal RNA gene sequences. The flora included eight phyla in the xenophyophorean cells with agglutinated test. The major operational taxonomic units were unique from that in the near-surface sediment. This flora appears to be formed by coexistence with xenophyophores.
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Microbacterium saccharophilum sp. nov., isolated from a sucrose-refining factory.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 01-11-2013
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A Gram-stain-positive, non-motile, non-spore-forming, rod-shaped bacterium, designated strain K-1(T), was isolated from soil at a sucrose refinery in Japan. The strain grew at 9-37 °C (optimum, 30 °C) and at pH 6-11 (optimum, pH 7.0). Phylogenetic analysis based on the full-length 16S rRNA gene sequence of strain K-1(T) revealed that it was a member of the genus Microbacterium. High 16S rRNA gene sequence similarities were found between strains K-1(T) and both Microbacterium pumilum NBRC 101279(T) (99.7 %) and Microbacterium deminutum NRRL B-24453(T) (99.5 %). However, the DNA-DNA hybridization values between strain K-1(T) and M. pumilum NBRC 101279(T) and M. deminutum NRRL B-24453(T) were only 12 % and 10 %, respectively. The DNA G+C content of strain K-1(T) was 73 mol%. The major fatty acids of strain K-1(T) were anteiso-C15 : 0 and anteiso-C17 : 0, and the major menaquinones were MK-12 and MK-13. The diamino acid in the cell-wall peptidoglycan was lysine. On the basis of these results, strain K-1(T) is considered to represent a novel species of the genus Microbacterium, for which the name Microbacterium saccharophilum sp. nov. is proposed. The type strain is K-1(T) (= NBRC 108778(T) = NCIMB 14782(T)).
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Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group.
Nucleic Acids Res.
PUBLISHED: 12-15-2010
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The domain Archaea has historically been divided into two phyla, the Crenarchaeota and Euryarchaeota. Although regarded as members of the Crenarchaeota based on small subunit rRNA phylogeny, environmental genomics and efforts for cultivation have recently revealed two novel phyla/divisions in the Archaea; the Thaumarchaeota and Korarchaeota. Here, we show the genome sequence of Candidatus Caldiarchaeum subterraneum that represents an uncultivated crenarchaeotic group. A composite genome was reconstructed from a metagenomic library previously prepared from a microbial mat at a geothermal water stream of a sub-surface gold mine. The genome was found to be clearly distinct from those of the known phyla/divisions, Crenarchaeota (hyperthermophiles), Euryarchaeota, Thaumarchaeota and Korarchaeota. The unique traits suggest that this crenarchaeotic group can be considered as a novel archaeal phylum/division. Moreover, C. subterraneum harbors an ubiquitin-like protein modifier system consisting of Ub, E1, E2 and small Zn RING finger family protein with structural motifs specific to eukaryotic system proteins, a system clearly distinct from the prokaryote-type system recently identified in Haloferax and Mycobacterium. The presence of such a eukaryote-type system is unprecedented in prokaryotes, and indicates that a prototype of the eukaryotic protein modifier system is present in the Archaea.
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Unique substrate specificity of a thermostable glycosyl hydrolase from an uncultured Anaerolinea, derived from bacterial mat on a subsurface geothermal water stream.
Biotechnol. Lett.
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To investigate novel extremozymes encoded by sequenced metagenes from a microbial community in an extreme environment, we have characterized a recombinant glycosyl hydrolase (rGH) from an uncultured bacterium within the order Chloroflexi. rGH formed insoluble bodies in an Escherichia coli protein expression system. The protein was partially dissolved by a surfactant and was enzymatically characterized. The MW of the monomeric peptide was ~62 kDa, and it formed a homodimers in buffer. It was optimally active at 65 °C and from pH 4 to 8. rGH showed hydrolytic activity for ?-1,1, ?-1,2 and ?-1,6 linkages, including isomaltose, but not ?-1,4 and ?-linkages.
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A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem.
PLoS ONE
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A nearly complete genome sequence of Candidatus Acetothermum autotrophicum, a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that Ca. A. autotrophicum is one of the earliest diverging bacterial lineages. It possesses a folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway of CO(2) fixation, is predicted to have an acetogenic lifestyle, and possesses the newly discovered archaeal-autotrophic type of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase. A phylogenetic analysis of the core gene cluster of the acethyl-CoA pathway, shared by acetogens, methanogens, some sulfur- and iron-reducers and dechlorinators, supports the hypothesis that the core gene cluster of Ca. A. autotrophicum is a particularly ancient bacterial pathway. The habitat, physiology and phylogenetic position of Ca. A. autotrophicum support the view that the first bacterial and archaeal lineages were H(2)-dependent acetogens and methanogenes living in hydrothermal environments.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.