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Find video protocols related to scientific articles indexed in Pubmed.
[Timing of nasojejunal feeding tube placement and enteral nutrition in children with acute pancreatitis.]
Zhongguo Dang Dai Er Ke Za Zhi
PUBLISHED: 11-20-2014
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To investigate the impact of timing of nasojejunal feeding tube placement and enteral nutrition on clinical outcomes in children with acute pancreatitis.
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Molecular and functional interactions among monocytes/macrophages and smooth muscle cells and their relevance for atherosclerosis.
Crit. Rev. Eukaryot. Gene Expr.
PUBLISHED: 11-19-2014
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Macrophages, smooth muscle cells (SMCs), and their interactions have key roles in the pathogenesis of atherosclerotic vascular diseases. In atheroma development, the phenotype of macrophages and SMCs change, which may influence the disease progression. Accumulating data on the phenotypes exhibited by these cells within atherosclerotic lesions raise many questions regarding the mechanisms and factors that might control the transition of cell phenotype. SMCs often reside in vascular lesions in close proximity to macrophage clusters and are most likely influenced by factors released from these proinflammatory phagocytes. Moreover, macrophages may be influenced by direct contact with SMCs or soluble factors released by these cells. Macrophages may promote activation and induce proatherogenic functions of SMCs, and SMCs may modulate macrophage phenotype. Addressing the mechanisms involved in SMC-macrophage crosstalk that lead to phenotypic modulation of both cell types may provide new insight into atherogenesis and new targets for therapies of various vascular diseases.
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Proposal for fabrication-tolerant SOI polarization splitter-rotator based on cascaded MMI couplers and an assisted bi-level taper.
Opt Express
PUBLISHED: 11-18-2014
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A novel silicon-on-insulator (SOI) polarization splitter-rotator (PSR) with a large fabrication tolerance is proposed based on cascaded multimode interference (MMI) couplers and an assisted mode-evolution taper. The tapers are designed to adiabatically convert the input TM0 mode into the TE1 mode, which will output as the TE0 mode after processed by the subsequent MMI mode converter, 90-degree phase shifter (PS) and MMI 3 dB coupler. The numerical simulation results show that the proposed device has a < 0.5 dB insertion loss with < -17 dB crosstalk in C optical communication band. Fabrication tolerance analysis is also performed with respect to the deviations of MMI coupler width, PS width, slab height and upper-cladding refractive index, showing that this device could work well even when affected by considerable fabrication errors. With such a robust performance with a large bandwidth, this device offers potential applications for CMOS-compatible polarization diversity, especially in the booming 100 Gb/s coherent optical communications based on silicon photonics technology.
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[Efficacies of gefitinib versus paclitaxel/carboplatin for patients with advanced pulmonary adenocarcinoma].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 11-18-2014
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To compare the clinical efficacies of gefitinib versus paclitaxel/carboplatin in patients with advanced pulmonary adenocarcinoma.
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Spata7 is a retinal ciliopathy gene critical for correct RPGRIP1 localization and protein trafficking in the retina.
Hum. Mol. Genet.
PUBLISHED: 11-16-2014
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Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are severe hereditary diseases that causes visual impairment in infants and children. SPATA7 has recently been identified as the LCA3 and juvenile RP gene in humans, whose function in the retina remains elusive. Here, we show that SPATA7 localizes at the primary cilium of cells and at the connecting cilium (CC) of photoreceptor cells, indicating that SPATA7 is a ciliary protein. In addition, SPATA7 directly interacts with the retinitis pigmentosa GTPase regulator interacting protein 1 (RPGRIP1), a key connecting cilium protein that has also been linked to LCA. In the retina of Spata7 null mutant mice, a substantial reduction of RPGRIP1 levels at the CC of photoreceptor cells is observed, suggesting that SPATA7 is required for the stable assembly and localization of the ciliary RPGRIP1 protein complex. Furthermore, our results pinpoint a role of this complex in protein trafficking across the CC to the outer segments, as we identified that rhodopsin accumulates in the inner segments and around the nucleus of photoreceptors. This accumulation then likely triggers the apoptosis of rod photoreceptors that was observed. Loss of Spata7 function in mice indeed results in a juvenile RP-like phenotype, characterized by progressive degeneration of photoreceptor cells and a strongly decreased light response. Together, these results indicate that SPATA7 functions as a key member of a retinal ciliopathy-associated protein complex, and that apoptosis of rod photoreceptor cells triggered by protein mislocalization is likely the mechanism of disease progression in LCA3/ juvenile RP patients.
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Complete Genome Sequence of Dyella japonica Strain A8 Isolated from Malaysian Tropical Soil.
Genome Announc
PUBLISHED: 11-15-2014
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We previously identified and presented the draft genome of a Xanthomonadaceae bacterial strain Dyella japonica A8 which shows quorum-quenching activity. Here, we report the complete, closed genome sequence of this bacterium. This complete genome may help to further investigate the comparative quorum-quenching activity among D. japonica strains.
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Common Variants in the MKL1 Gene Confer Risk of Schizophrenia.
Schizophr Bull
PUBLISHED: 11-09-2014
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Genome-wide association studies (GWAS) of schizophrenia have identified multiple risk variants with robust association signals for schizophrenia. However, these variants could explain only a small proportion of schizophrenia heritability. Furthermore, the effect size of these risk variants is relatively small (eg, most of them had an OR less than 1.2), suggesting that additional risk variants may be detected when increasing sample size in analysis. Here, we report the identification of a genome-wide significant schizophrenia risk locus at 22q13.1 by combining 2 large-scale schizophrenia cohort studies. Our meta-analysis revealed that 7 single nucleotide polymorphism (SNPs) on chromosome 22q13.1 reached the genome-wide significance level (P < 5.0×10(-8)) in the combined samples (a total of 38441 individuals). Among them, SNP rs6001946 had the most significant association with schizophrenia (P = 2.04×10(-8)). Interestingly, all 7 SNPs are in high linkage disequilibrium and located in the MKL1 gene. Expression analysis showed that MKL1 is highly expressed in human and mouse brains. We further investigated functional links between MKL1 and proteins encoded by other schizophrenia susceptibility genes in the whole human protein interaction network. We found that MKL1 physically interacts with GSK3B, a protein encoded by a well-characterized schizophrenia susceptibility gene. Collectively, our results revealed that genetic variants in MKL1 might confer risk to schizophrenia. Further investigation of the roles of MKL1 in the pathogenesis of schizophrenia is warranted.
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Whole-Genome Sequences of Five Oligotrophic Bacteria Isolated from Deep within Lechuguilla Cave, New Mexico.
Genome Announc
PUBLISHED: 11-08-2014
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Here, we report the whole-genome sequences and annotation of five oligotrophic bacteria from two sites within the Lechuguilla Cave in the Carlsbad Caverns National Park, NM. Three of the five genomes contain an acyl-homoserine lactone signal synthase ortholog (luxI) that is involved in cell-to-cell communication via quorum sensing.
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Electrocatalysis: Controllable Synthesis and Enhanced Electrocatalysis of Iron-based Catalysts Derived From Electrospun Nanofibers (Small 20/2014).
Small
PUBLISHED: 10-22-2014
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Porous carbon nanofibers containing iron and nitrogen, represented by the cubes containing the nanofibers in the image, are developed by J. Luo, J. Zhu, and co-workers to efficiently catalyze the oxygen reduction reaction in fuel cells. As described on page 4072, the nanofibers are produced from electrospun polymer fibers that are denoted by the flower-like fiber bundle with an open end in the image. When the oxygen bubbles meet the nanofibers, energies ('lightning' from the bubble centers) can be generated.
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The complete mitogenome of the river blackfish, Gadopsis marmoratus (Richardson, 1848) (Teleostei: Percichthyidae).
Mitochondrial DNA
PUBLISHED: 10-21-2014
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Abstract The mitogenome of the Australian freshwater blackfish, Gadopsis marmoratus was recovered coverage by genome skimming using the MiSeq sequencer (GenBank Accession Number: NC_024436). The blackfish mitogenome has 16,407 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819?bp non-coding AT-rich region. This is the 5th mitogenome sequence to be reported for the family Percichthyidae.
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The complete mitogenome of the Australian tadpole shrimp Triops australiensis (Spencer & Hall, 1895) (Crustacea: Branchiopoda: Notostraca).
Mitochondrial DNA
PUBLISHED: 10-21-2014
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Abstract The mitochondrial genome sequence of the Australian tadpole shrimp, Triops australiensis is presented (GenBank Accession Number: NC_024439) and compared with other Triops species. Triops australiensis has a mitochondrial genome of 15,125 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The T. australiensis mitogenome is composed of 36.4% A, 16.1% C, 12.3% G and 35.1% T. The mitogenome gene order conforms to the primitive arrangement for Branchiopod crustaceans, which is also conserved within the Pancrustacean.
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Draft Genome Sequences of Two Antimicrobial-Producing Burkholderia sp. Strains, MSh1 and MSh2, Isolated from Malaysian Tropical Peat Swamp Forest Soil.
Genome Announc
PUBLISHED: 10-11-2014
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We report the draft genome sequences of two antimicrobial-producing isolates, Burkholderia sp. strains MSh1 and MSh2, which were isolated from tropical peat swamp forest soil. Putative genes related to different antimicrobial production have been annotated in both genome sequences.
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Draft Genome Sequence of Paenibacillus sp. Strain MSt1 with Broad Antimicrobial Activity, Isolated from Malaysian Tropical Peat Swamp Soil.
Genome Announc
PUBLISHED: 10-11-2014
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We report the draft genome sequence of Paenibacillus sp. strain MSt1, which has broad-range antimicrobial activity, isolated from tropical peat swamp soil. Genes involved in antimicrobial biosynthesis are found to be present in this genome.
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Genome Sequence of Nitratireductor basaltis Strain UMTGB225, a Marine Bacterium Isolated from a Green Barrel Tunicate in Bidong Island, Malaysia.
Genome Announc
PUBLISHED: 10-11-2014
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Nitratireductor basaltis strain UMTGB225 is a Gram-negative bacterium isolated from a marine tunicate found in Bidong Island, Terengganu, Malaysia. In this study, the genome of Nitratireductor basaltis UMTGB225 was sequenced to gain insight into the role of this bacterium and its association with tunicate hosts in a coral reef habitat.
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[A clinicopathologic and prognosis study of Epstein-Barr virus positive diffuse large B-cell lymphoma in west-southern China].
Sichuan Da Xue Xue Bao Yi Xue Ban
PUBLISHED: 10-08-2014
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To investigate the clinicopathologic features, immunophenotype, and the prognosis related factors of Epstein-Barr virus (EBV) positive diffuse large B-cell lymphoma (DLBCL) in west-southern China.
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Development of Retinal Amacrine Cells and Their Dendritic Stratification.
Curr Ophthalmol Rep
PUBLISHED: 08-30-2014
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Themammalian retina containsmultiple neurons, each of which contributes differentially to visual processing. Of these retinal neurons, amacrine cells have recently come to prime light since they facilitate majority of visual processing that takes place in the retina. Amacrine cells are also the most diverse group of neurons in the retina, classified majorly based on the neurotransmitter type they express and morphology of their dendritic arbors. Currently, little is known about the molecular basis contributing to this diversity during development. Amacrine cells also contribute to most of the synapses in the inner plexiform layer and mediate visual information input from bipolar cells onto retinal ganglion cells. In this review, we will describe the current understanding of amacrine cell and cell subtype development. Furthermore, we will address the molecular basis of retinal lamination at the inner plexiform layer. Overall, our review will provide a developmental perspective of amacrine cell subtype classification and their dendritic stratification.
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The complete mitogenome of the Morton Bay bug Thenus orientalis (Lund, 1793) (Crustacea: Decapoda: Scyllaridae) from a cooked sample and a new mitogenome order for the Decapoda.
Mitochondrial DNA
PUBLISHED: 08-08-2014
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Abstract The mitochondrial genome sequence of the Morton Bay bug, Thenus orientalis, is documented, which makes it the second mitogenome for species of the family Scyllaridae and the ninth for members of the superfamily Palinuroidae. Thenus orientalis has a mitogenome of 16,826 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of the T. orientalis mitogenome is 31.31% for T, 23.77% for C, 31.05% for A, and 13.87% for G, with an AT bias of 62.36%. In addition to a duplicated trnS1 and several other tRNA gene rearrangements, the mitogenome gene order has novel protein coding gene order with the nad6 and cob genes translocated as a block to a location downstream of the nad3 gene.
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The complete mitogenome of the cow tail ray Pastinachus atrus (Macleay, 1883) (Elasmobranchii; Myliobatiformes; Dasyatidae).
Mitochondrial DNA
PUBLISHED: 08-08-2014
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Abstract The complete mitogenome of the ray Pastinachus atrus was recovered from a partial genome scan using the HiSeq sequencing system. The P. atrus mitogenome has 18,162 base pairs (61% A?+?T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 2516?bp non-coding AT-rich region. This mitogenome sequence is the first for a ray from Australian waters, the first for the Genus Pastinachus, and the 6th for the family Dasyatidae.
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The complete mitogenome of the stone crab Myomenippe fornasinii (Bianconi, 1851) (Crustacea: Decapoda: Menippidae).
Mitochondrial DNA
PUBLISHED: 08-08-2014
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Abstract The mitochondrial genome sequence of the stone crab, Myomenippe fornasinii, second of the superfamily Eriphioidea is documented. Myomenippe fornasinii has a mitogenome of 15,658 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the M. fornasinii mitogenome is 36.10% for T, 18.52% for C, 35.48% for A, and 9.90% for G, with an AT bias of 71.58%. The mitogenome gene order conforms to what is the standard arrangement for brachyuran crabs.
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Quorum sensing activity of Mesorhizobium sp. F7 isolated from potable water.
ScientificWorldJournal
PUBLISHED: 08-06-2014
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We isolated a bacterial isolate (F7) from potable water. The strain was identified as Mesorhizobium sp. by 16S rDNA gene phylogenetic analysis and screened for N-acyl homoserine lactone (AHL) production by an AHL biosensor. The AHL profile of the isolate was further analyzed using high resolution triple quadrupole liquid chromatography mass spectrometry (LC/MS) which confirmed the production of multiple AHLs, namely, N-3-oxo-octanoyl-L-homoserine lactone (3-oxo-C8-HSL) and N-3-oxo-decanoyl-L-homoserine lactone (3-oxo-C10-HSL). These findings will open the perspective to study the function of these AHLs in plant-microbe interactions.
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Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia.
ScientificWorldJournal
PUBLISHED: 08-05-2014
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The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135(T) that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS) and nonribosomal polyketide synthetase (NRPS) genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%), PKS-II (42.5%), and NRPS (5.7%) genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites.
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The complete mitogenome of the swimming crab Thalamita crenata (Rüppell, 1830) (Crustacea; Decapoda; Portunidae).
Mitochondrial DNA
PUBLISHED: 08-05-2014
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Abstract The complete mitochondrial genome of the swimming crab Thalamita crenata was obtained from a partial genome scan using the MiSeq sequencing system. The Thalamita crenata mitogenome has 15,787 base pairs (70% A+T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 897?bp non-coding AT-rich region. This Thalamita mitogenome sequence is the first for the genus and the eighth for the family Portunidae.
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The complete mitogenome of the moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae).
Mitochondrial DNA
PUBLISHED: 08-05-2014
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Abstract The complete mitochondrial genome of the moon crab Ashtoret lunaris was obtained from a partial genome scan using the MiSeq sequencing system. The Ashtoret lunaris mitogenome is 15,807 base pairs in length (70% A?+?T content) and made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 956?bp non-coding AT-rich region. This A. lunaris mitogenome sequence is the first for the genus, as well as the family Matutidae and superfamily Calappoidea.
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Microbacterium mangrovi sp. nov., an amylolytic actinobacterium isolated from mangrove forest soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-23-2014
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Strain MUSC 115(T) was isolated from mangrove soil of the Tanjung Lumpur river in the state of Pahang, Peninsular Malaysia. Cells of this strain stained Gram-positive and were non-spore-forming, short rods that formed yellowish-white colonies on different agar media. The taxonomy of strain MUSC 115(T) was studied by a polyphasic approach, and the organism showed a range of phylogenetic and chemotaxonomic properties consistent with those of the genus Microbacterium. The cell-wall peptidoglycan was of type B2?, containing the amino acids ornithine, alanine, glycine, glutamic acid and homoserine. The muramic acid was of the N-glycolyl form. The predominant menaquinones detected were MK-12, MK-13 and MK-11. The polar lipids consisted of phosphatidylglycerol, phosphoglycolipid, diphosphatidylglycerol, two unidentified lipids, three unidentified phospholipids and four unidentified glycolipids. The major fatty acids of the cell membrane were anteiso-C15:0 and anteiso-C17:0. The whole-cell sugars detected were ribose, glucose, mannose and galactose. Based on the 16S rRNA gene sequence, strain MUSC 115(T) showed the highest sequence similarity to Microbacterium immunditiarum SK 18(T) (98.1%), M. ulmi XIL02(T) (97.8%) and M. arborescens DSM 20754(T) (97.5%) and lower sequence similarity to strains of other species of the genus Microbacterium. DNA-DNA hybridization experiments revealed a low level of DNA-DNA relatedness (less than 24%) between strain MUSC 115(T) and the type strains of closely related species. Furthermore, BOX-PCR fingerprint comparison also indicated that strain MUSC 115(T) represented a unique DNA profile. The DNA G+C content determined was 70.9 ± 0.7 mol%, which is lower than that of M. immunditiarum SK 18(T). Based on the combination of genotypic and phenotypic data, it is proposed that strain MUSC 115(T) represents a novel species of the genus Microbacterium, for which the name Microbacterium mangrovi sp. nov. is proposed. The type strain is MUSC 115(T) ( = MCCC 1K00251(T) = DSM 28240(T) = NBRC 110089(T)).
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Some evidences on the mode of action of Cinnamomum verum bark essential oil, alone and in combination with piperacillin against a multi-drug resistant Escherichia coli strain.
J. Microbiol. Biotechnol.
PUBLISHED: 07-21-2014
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The purpose of this study was to investigate the mode of action of the cinnamon bark essential oil (CB) when use singly and in combination with piperacillin on its antimicrobial and synergistic activity against plasmid-conferred multi-drug resistant Escherichia coli J53 R1. Viable count of this combination showed a complete killing profile at 20 h and further confirmed its synergistic effect by reducing the bacteria cell numbers. Analysis of the membrane permeabilizing effects of CB on treated cultures through their stability against sodium dodecyl sulfate (SDS) revealed that the essential oils played a role in disrupting the bacterial cell membrane. Scanning electron microscopy analysis and zeta potential measurement also revealed that CB causes irreversible membrane damage and reduces the bacterial surface charge. In addition, reduction in bioluminescence expression of Escherichia coli [pSB1075] and E. coli [pSB401] by CB showed the presence of potential quorum sensing (QS) inhibitors. Gas-chromatography and mass spectrometry (GC-MS) of the essential oil of Cinnamomum verum showed that trans-cinnamaldehyde (72.81%), benzyl alcohol (12.5%) and eugenol (6.57%) were found to be the major components in the essential oil. These findings suggest that CB has the potential to reverse bacteria resistance to piperacillin in E. coli J53 R1 and may operate via two mechanisms: alteration of outer membrane permeability and inhibition of bacterial QS.
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Streptomyces pluripotens sp. nov., a bacteriocin-producing streptomycete that inhibits meticillin-resistant Staphylococcus aureus.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-03-2014
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Two novel actinobacteria, strains MUSC 135(T) and MUSC 137, were isolated from mangrove soil at Tanjung Lumpur, Malaysia. The 16S rRNA gene sequence similarity and DNA-DNA relatedness between strains MUSC 135(T) and MUSC 137 were 100?% and 83±3.2?%, confirming that these two strains should be classified in the same species. Strain MUSC 135(T) exhibited a broad-spectrum bacteriocin against the pathogens meticillin-resistant Staphylococcus aureus (MRSA) strain ATCC BAA-44, Salmonella typhi ATCC 19430(T) and Aeromonas hydrophila ATCC 7966(T). A polyphasic approach was used to study the taxonomy of MUSC 135(T), and it showed a range of phylogenetic and chemotaxonomic properties consistent with those of the genus Streptomyces. The diamino acid of the cell-wall peptidoglycan was ll-diaminopimelic acid. The predominant menaquinones were MK-9(H6), MK-9(H4) and MK-9(H8). Polar lipids detected were a lipid, an aminolipid, a phospholipid, phosphatidylinositol, phosphatidylethanolamine and two glycolipids. The predominant cellular fatty acids (>10.0?%) were anteiso-C15?:?0 (20.8?%), iso-C16?:?0 (18.0?%), iso-C15?:?0 (12.2?%) and anteiso-C17?:?0 (11.6?%). The whole-cell sugars were ribose, glucose and mannose. These results suggested that MUSC 135(T) should be placed within the genus Streptomyces. Phylogenetic analysis based on the 16S rRNA gene sequence exhibited that the most closely related strains were Streptomyces cinereospinus NBRC 15397(T) (99.18?% similarity), Streptomyces mexicanus NBRC 100915(T) (99.17?%) and Streptomyces coeruleofuscus NBRC 12757(T) (98.97?%). DNA-DNA relatedness between MUSC 135(T) and closely related type strains ranged from 26.3±2.1 to 49.6±2.5?%. BOX-PCR fingerprint comparisons showed that MUSC 135(T) exhibited a unique DNA profile. The DNA G+C content determined was 70.7±0.3 mol%. Based on our polyphasic study of MUSC 135(T), the strain merits assignment to a novel species, for which the name Streptomyces pluripotens sp. nov. is proposed. The type strain is MUSC 135(T) (?=?MCCC 1K00252(T)?=?DSM 42140(T)).
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The complete mitogenome of the Australian spiny crayfish Euastacus yarraensis (McCoy, 1888) (Crustacea: Decapoda: Parastacidae).
Mitochondrial DNA
PUBLISHED: 06-19-2014
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Abstract The mitochondrial genome sequence of the Australian crayfish, Euastacus yarraensis, is documented and compared with other Australian crayfish genera. Euastacus yarraensis has a mitogenome of 15,548 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The base composition of E. yarraensis mitogenome is 32.39% for T, 22.45% for C, 34.43% for A, and 10.73% for G, with an AT bias of 66.82%. The mitogenome gene order conforms to what is considered the primitive arrangement for parastacid crayfish.
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The complete mitochondrial genome of the invasive house crow Corvus splendens (Passeriformes: Corvidae).
Mitochondrial DNA
PUBLISHED: 06-19-2014
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Abstract The complete mitochondrial genome of the invasive house crow (Corvus splendens) was sequenced (GenBank accession number: KJ766304) using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitochondrial genome is 16,962?bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal subunit genes and a non-coding control region. The mitogenome structural organization is identical to that of the other Corvus species and related genera. The overall base composition of C. splendens is 30.65% for A, 29.71% for C, 14.84% for G and 24.80% for T, with an AT content of 55.45%. We propose to use full mitochondrial genome to address taxonomic issues and to study the population genetics of crows.
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Novel ultra-broadband polarization splitter-rotator based on mode-evolution tapers and a mode-sorting asymmetric Y-junction.
Opt Express
PUBLISHED: 06-13-2014
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A novel silicon-on-insulator (SOI) polarization splitter-rotator is proposed based on mode-evolution tapers and a mode-sorting asymmetric Y-junction. The tapers are designed to adiabatically convert the input TM0 mode into the TE1 mode, which will evolve into the TE0 mode in the wide output arm while the input TE0 mode excites the TE0 mode in the narrow arm. The numerical simulation results show that the mode conversion efficiency increases with the lengths of the tapers and the Y-junction for the output waveguide widths in a large range. This proposed device has < 0.4 dB insertion loss with > 12 dB extinction ratio in an ultra-broad wavelength range from 1350 nm to 1750 nm. With such a broad operating bandwidth, this device offers potential applications for polarization diversity operating across every communication bands. Fabrication tolerance analysis is also performed in terms of the device width variation, the slab height variation and the variation of the upper-cladding refractive index.
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Pseudomonas cremoricolorata strain ND07 produces N-acyl homoserine lactones as quorum sensing molecules.
Sensors (Basel)
PUBLISHED: 05-28-2014
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Quorum sensing (QS) is a bacterial cell-to-cell communication system controlling QS-mediated genes which is synchronized with the population density. The regulation of specific gene activity is dependent on the signaling molecules produced, namely N-acyl homoserine lactones (AHLs). We report here the identification and characterization of AHLs produced by bacterial strain ND07 isolated from a Malaysian fresh water sample. Molecular identification showed that strain ND07 is clustered closely to Pseudomonas cremoricolorata. Spent culture supernatant extract of P. cremoricolorata strain ND07 activated the AHL biosensor Chromobacterium violaceum CV026. Using high resolution triple quadrupole liquid chromatography-mass spectrometry, it was confirmed that P. cremoricolorata strain ND07 produced N-octanoyl-L-homoserine lactone (C8-HSL) and N-decanoyl-L-homoserine lactone (C10-HSL). To the best of our knowledge, this is the first documentation on the production of C10-HSL in P. cremoricolorata strain ND07.
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Enterobacter asburiae strain L1: complete genome and whole genome optical mapping analysis of a quorum sensing bacterium.
Sensors (Basel)
PUBLISHED: 05-26-2014
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Enterobacter asburiae L1 is a quorum sensing bacterium isolated from lettuce leaves. In this study, for the first time, the complete genome of E. asburiae L1 was sequenced using the single molecule real time sequencer (PacBio RSII) and the whole genome sequence was verified by using optical genome mapping (OpGen) technology. In our previous study, E. asburiae L1 has been reported to produce AHLs, suggesting the possibility of virulence factor regulation which is quorum sensing dependent. This evoked our interest to study the genome of this bacterium and here we present the complete genome of E. asburiae L1, which carries the virulence factor gene virK, the N-acyl homoserine lactone-based QS transcriptional regulator gene luxR and the N-acyl homoserine lactone synthase gene which we firstly named easI. The availability of the whole genome sequence of E. asburiae L1 will pave the way for the study of the QS-mediated gene expression in this bacterium. Hence, the importance and functions of these signaling molecules can be further studied in the hope of elucidating the mechanisms of QS-regulation in E. asburiae. To the best of our knowledge, this is the first documentation of both a complete genome sequence and the establishment of the molecular basis of QS properties of E. asburiae.
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The complete mitogenome of the Australian crayfish Geocharax gracilis Clark 1936 (Crustacea: Decapoda: Parastacidae).
Mitochondrial DNA
PUBLISHED: 05-22-2014
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Abstract The mitogenome of the black yabby, Geocharax gracilis, was sequenced using the MiSeq Personal Sequencer. It has 15,924 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of G. gracilis mitogenome is 32.18% for T, 22.32% for C, 34.83% for A, and 10.68% for G, with an AT bias of 67.01%. The mitogenome gene order is typical for that of parastacid crayfish with the exception of some minor rearrangements involving tRNA genes.
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Complete Genome Sequence of Pandoraea pnomenusa 3kgm, a Quorum-Sensing Strain Isolated from a Former Landfill Site.
Genome Announc
PUBLISHED: 05-10-2014
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Pandoraea pnomenusa strain 3kgm has been identified as a quorum-sensing strain isolated from soil. Here, we report the complete genome sequence of P. pnomenusa strain 3kgm by using the Pacific Biosciences single-molecule real-time (PacBio RS SMRT) sequencer high-resolution technology.
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Prevalence of unclassified bacteria in tropical coastal waters of malaysia revealed by metagenomic approach.
Genome Announc
PUBLISHED: 05-10-2014
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The metagenomes of marine prokaryotes from coastal seawaters in Malaysia are reported in this study. The investigation of the microbial communities using 16S rRNA gene amplicon metagenomic sequencing revealed that majority of the bacteria in the seawater samples remain unclassified.
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Whole-genome sequences of 13 endophytic bacteria isolated from shrub willow (salix) grown in geneva, new york.
Genome Announc
PUBLISHED: 05-10-2014
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Shrub willow, Salix spp. and hybrids, is an important bioenergy crop. Here we report the whole-genome sequences and annotation of 13 endophytic bacteria from stem tissues of Salix purpurea grown in nature and from commercial cultivars and Salix viminalis × Salix miyabeana grown in bioenergy fields in Geneva, New York.
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Improving farming practices reduces the carbon footprint of spring wheat production.
Nat Commun
PUBLISHED: 05-09-2014
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Wheat is one of the world's most favoured food sources, reaching millions of people on a daily basis. However, its production has climatic consequences. Fuel, inorganic fertilizers and pesticides used in wheat production emit greenhouse gases that can contribute negatively to climate change. It is unknown whether adopting alternative farming practices will increase crop yield while reducing carbon emissions. Here we quantify the carbon footprint of alternative wheat production systems suited to semiarid environments. We find that integrating improved farming practices (that is, fertilizing crops based on soil tests, reducing summerfallow frequencies and rotating cereals with grain legumes) lowers wheat carbon footprint effectively, averaging -256?kg CO2 eq?ha(-1) per year. For each kg of wheat grain produced, a net 0.027-0.377?kg CO2 eq is sequestered into the soil. With the suite of improved farming practices, wheat takes up more CO2 from the atmosphere than is actually emitted during its production.
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Short chain N-acyl homoserine lactone production in tropical marine Vibrio sinaloensis strain T47.
Sensors (Basel)
PUBLISHED: 05-08-2014
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Quorum sensing (QS), acts as one of the gene regulatory systems that allow bacteria to regulate their physiological activities by sensing the population density with synchronization of the signaling molecules that they produce. Here, we report a marine isolate, namely strain T47, and its unique AHL profile. Strain T47 was identified using 16S rRNA sequence analysis confirming that it is a member of Vibrio closely clustered to Vibrio sinaloensis. The isolated V. sinaloensis strain T47 was confirmed to produce N-butanoyl-L-homoserine lactone (C4-HSL) by using high resolution liquid chromatography tandem mass spectrometry. V. sinaloensis strain T47 also formed biofilms and its biofilm formation could be affected by anti-QS compound (cathechin) suggesting this is a QS-regulated trait in V. sinaloensis strain T47. To our knowledge, this is the first documentation of AHL and biofilm production in V. sinaloensis strain T47.
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Detection of quorum sensing activity in the multidrug-resistant clinical isolate Pseudomonas aeruginosa strain GB11.
Sensors (Basel)
PUBLISHED: 05-07-2014
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A multidrug-resistant clinical bacteria strain GB11 was isolated from a wound swab on the leg of a patient. Identity of stain GB11 as Pseudomonas aeruginosa was validated by using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Detection of the production of signaling molecules, N-acylhomoserine lactones (AHLs), was conducted using three different bacterial biosensors. A total of four different AHLs were found to be produced by strain GB11, namely N-butyryl homoserine lactone (C4-HSL), N-hexanoylhomoserine lactone (C6-HSL), N-octanoyl homoserine lactone (C8-HSL) and N-3-oxo-dodecanoylhomoserine lactone (3-oxo-C12-HSL) using high resolution liquid chromatography tandem mass spectrometry (LC-MS/MS). Of these detected AHLs, 3-oxo-C12-HSL was found to be the most abundant AHL produced by P. aeruginosa GB11.
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Low-loss and low-crosstalk 8 × 8 silicon nanowire AWG routers fabricated with CMOS technology.
Opt Express
PUBLISHED: 05-03-2014
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Low-loss and low-crosstalk 8 × 8 arrayed waveguide grating (AWG) routers based on silicon nanowire waveguides are reported. A comparative study of the measurement results of the 3.2 nm-channel-spacing AWGs with three different designs is performed to evaluate the effect of each optimal technique, showing that a comprehensive optimization technique is more effective to improve the device performance than a single optimization. Based on the comprehensive optimal design, we further design and experimentally demonstrate a new 8-channel 0.8 nm-channel-spacing silicon AWG router for dense wavelength division multiplexing (DWDM) application with 130 nm CMOS technology. The AWG router with a channel spacing of 3.2 nm (resp. 0.8 nm) exhibits low insertion loss of 2.32 dB (resp. 2.92 dB) and low crosstalk of -20.5~-24.5 dB (resp. -16.9~-17.8 dB). In addition, sophisticated measurements are presented including all-input transmission testing and high-speed WDM system demonstrations for these routers. The functionality of the Si nanowire AWG as a router is characterized and a good cyclic rotation property is demonstrated. Moreover, we test the optical eye diagrams and bit-error-rates (BER) of the de-multiplexed signal when the multi-wavelength high-speed signals are launched into the AWG routers in a system experiment. Clear optical eye diagrams and low power penalty from the system point of view are achieved thanks to the low crosstalk of the AWG devices.
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The complete mitogenome of the whale shark parasitic copepod Pandarus rhincodonicus norman, Newbound & Knott (Crustacea; Siphonostomatoida; Pandaridae) - a new gene order for the copepoda.
Mitochondrial DNA
PUBLISHED: 05-01-2014
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Abstract The complete mitochondrial genome of the parasitic copepod Pandarus rhincodonicus was obtained from a partial genome scan using the HiSeq sequencing system. The Pandarus rhincodonicus mitogenome has 14,480 base pairs (62% A+T content) made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 384?bp non-coding AT-rich region. This Pandarus mitogenome sequence is the first for the family Pandaridae, the second for the order Siphonostomatoida and the sixth for the Copepoda.
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The complete mitogenome of the Murray Cod, Maccullochella peelii (Mitchell, 1838) (Teleostei: Percichthyidae).
Mitochondrial DNA
PUBLISHED: 05-01-2014
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Abstract The complete mitochondrial genome of the iconic Australian freshwater fish, the Murray Cod, Maccullochella peelii, was recovered from partial genome sequencing data using the HiSeq platform (Illumina, San Diego, CA). The mitogenome consists of 16,442?bp (58% A?+?T content) containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 768?bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Maccullochella, and the fourth for the family Percichthyidae.
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Protein engineering of selected residues from conserved sequence regions of a novel Anoxybacillus ?-amylase.
Sci Rep
PUBLISHED: 04-29-2014
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The ?-amylases from Anoxybacillus species (ASKA and ADTA), Bacillus aquimaris (BaqA) and Geobacillus thermoleovorans (GTA, Pizzo and GtamyII) were proposed as a novel group of the ?-amylase family GH13. An ASKA yielding a high percentage of maltose upon its reaction on starch was chosen as a model to study the residues responsible for the biochemical properties. Four residues from conserved sequence regions (CSRs) were thus selected, and the mutants F113V (CSR-I), Y187F and L189I (CSR-II) and A161D (CSR-V) were characterised. Few changes in the optimum reaction temperature and pH were observed for all mutants. Whereas the Y187F (t1/2 43?h) and L189I (t1/2 36?h) mutants had a lower thermostability at 65°C than the native ASKA (t1/2 48?h), the mutants F113V and A161D exhibited an improved t1/2 of 51?h and 53?h, respectively. Among the mutants, only the A161D had a specific activity, k(cat) and k(cat)/K(m) higher (1.23-, 1.17- and 2.88-times, respectively) than the values determined for the ASKA. The replacement of the Ala-161 in the CSR-V with an aspartic acid also caused a significant reduction in the ratio of maltose formed. This finding suggests the Ala-161 may contribute to the high maltose production of the ASKA.
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Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma.
Nat. Med.
PUBLISHED: 04-24-2014
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Pediatric brainstem gliomas often harbor oncogenic K27M mutation of histone H3.3. Here we show that GSKJ4 pharmacologic inhibition of K27 demethylase JMJD3 increases cellular H3K27 methylation in K27M tumor cells and demonstrate potent antitumor activity both in vitro against K27M cells and in vivo against K27M xenografts. Our results demonstrate that increasing H3K27 methylation by inhibiting K27 demethylase is a valid therapeutic strategy for treating K27M-expressing brainstem glioma.
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Draft Genome Sequence of Quorum-Sensing and Quorum-Quenching Pseudomonas aeruginosa Strain MW3a.
Genome Announc
PUBLISHED: 04-19-2014
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Pseudomonas aeruginosa has a broad range of habitation, from aquatic environments to human lungs. The coexistence of quorum-sensing and quorum-quenching activities occurs in P. aeruginosa strain MW3a. In this work, we present the draft genome sequence of P. aeruginosa MW3a, an interesting bacterium isolated from a marine environment.
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Unusual multiple production of N-acylhomoserine lactones a by Burkholderia sp. strain C10B isolated from dentine caries.
Sensors (Basel)
PUBLISHED: 04-18-2014
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Bacteria realize the ability to communicate by production of quorum sensing (QS) molecules called autoinducers, which regulate the physiological activities in their ecological niches. The oral cavity could be a potential area for the presence of QS bacteria. In this study, we report the isolation of a QS bacterial isolate C10B from dentine caries. Preliminary screening using Chromobacterium violaceum CV026 biosensor showed that isolate C10B was able to produce N-acylhomoserine lactones (AHLs). This bacterium was further identified as a member of Burkholderia, an opportunistic pathogen. The isolated Burkholderia sp. was confirmed to produce N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL), N-decanoyl-L-homoserine lactone (C10-HSL) and N-dodecanoyl-L-homoserine lactone (C12-HSL).
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The complete mitogenome of the Australian land crayfish Engaeus lyelli (Clark 1936) (Crustacea: Decapoda: Parastacidae).
Mitochondrial DNA
PUBLISHED: 04-16-2014
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Abstract The complete mitochondrial genome of the enigmatic freshwater crayfish Engaeus lyelli was sequenced using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitogenome has 16,027?bp consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of E. lyelli is 29.01% for T, 27.13% for C, 31.43% for A, and 12.44% for G, with an AT bias of 60.44%. The species has the distinctive gene order characteristic of parastacid crayfish with the exception of some minor rearrangements involving the tRNA genes.
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Freshwater-borne bacteria isolated from a Malaysian rainforest waterfall exhibiting quorum sensing properties.
Sensors (Basel)
PUBLISHED: 04-08-2014
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One obvious requirement for concerted action by a bacterial population is for an individual to be aware of and respond to the other individuals of the same species in order to form a response in unison. The term "quorum sensing" (QS) was coined to describe bacterial communication that is able to stimulate expression of a series of genes when the concentration of the signaling molecules has reached a threshold level. Here we report the isolation from aquatic environment of a bacterium that was later identified as Enterobacter sp.. Chromobacterium violaceum CV026 and Escherichia coli [pSB401] were used for preliminary screening of N-acyl homoserine lactone (AHL) production. The Enterobacter sp. isolated was shown to produce two types of AHLs as confirmed by analysis using high resolution tandem mass spectrometry. To the best of our knowledge, this is the first documentation of an Enterobacter sp. that produced both 3-oxo-C6-HSL and 3-oxo-C8-HSL as QS signaling molecules.
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Discovery of Pantoea rodasii strain ND03 that produces N-(3-Oxo-hexanoyl)-L-homoserine lactone.
Sensors (Basel)
PUBLISHED: 04-08-2014
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Proteobacteria use quorum sensing to regulate target gene expression in response to population density. Quorum sensing (QS) is achieved via so-called signalling molecules and the best-studied QS signalling system uses N-acyl homoserine lactones (AHLs). This study aimed to identify and characterize the production of AHLs by a bacterium ND03 isolated from a Malaysian tropical rainforest waterfall. Molecular identification showed that ND03 is a Pantoea sp. closely related to Pantoea rodasii. We used Chromobacterium violaceum CV026, an AHL biosensor for preliminary AHL production screening and then used high resolution triple quadrupole liquid chromatography-mass spectrometry, to confirm that P. rodasii strain ND03 produced N-(3-oxo-hexanoyl)-L-homoserine lactone (3-oxo-C6-HSL). To the best of our knowledge, this is the first report for such a discovery in P. rodasii strain ND03.
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Complete Genome Sequence of Pseudomonas aeruginosa Strain YL84, a Quorum-Sensing Strain Isolated from Compost.
Genome Announc
PUBLISHED: 04-05-2014
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Here, we report the complete genome sequence of Pseudomonas aeruginosa strain YL84, which was isolated from compost. This strain was found to be a chitinase-producing quorum-sensing bacterium.
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De Novo Assembly of the Quorum-Sensing Pandoraea sp. Strain RB-44 Complete Genome Sequence Using PacBio Single-Molecule Real-Time Sequencing Technology.
Genome Announc
PUBLISHED: 04-05-2014
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We report the first complete genome sequence of Pandoraea sp. strain RB-44, which was found to possess quorum-sensing properties. To the best of our knowledge, this is the first documentation of both a complete genome sequence and quorum-sensing properties of a Pandoraea species.
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Labrenzia sp. BM1: a quorum quenching bacterium that degrades N-acyl homoserine lactones via lactonase activity.
Sensors (Basel)
PUBLISHED: 04-01-2014
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We report the degradation of quorum sensing N-acylhomoserine lactone molecules by a bacterium isolated from a Malaysian marine water sample. MALDI-TOF and phylogenetic analysis indicated this isolate BM1 clustered closely to Labrenzia sp. The quorum quenching activity of this isolate was confirmed by using a series of bioassays and rapid resolution liquid chromatography analysis. Labrenzia sp. degraded a wide range of N-acylhomoserine lactones namely N-(3-hexanoyl)-L-homoserine lactone (C6-HSL), N-(3-oxohexanoyl)-L-homoserine lactone (3-oxo-C6-HSL) and N-(3-hydroxyhexanoyl)-L-homoserine lactone (3-hydroxy-C6-HSL). Re-lactonisation bioassays confirmed Labrenzia sp. BM1 degraded these signalling molecules efficiently via lactonase activity. To the best of our knowledge, this is the first documentation of a Labrenzia sp. capable of degrading N-acylhomoserine lactones and confirmation of its lactonase-based mechanism of action.
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Quorum sensing activity of a Kluyvera sp. isolated from a Malaysian waterfall.
Sensors (Basel)
PUBLISHED: 03-31-2014
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In many species of bacteria, the quorum sensing mechanism is used as a unique communication system which allows them to regulate gene expression and behavior in accordance with their population density. N-Acylhomoserine lactones (AHLs) are known as diffusible autoinducer molecules involved in this communication network. This finding aimed to characterize the production of AHL of a bacterial strain ND04 isolated from a Malaysian waterfall. Strain ND04 was identified as Kluyvera sp. as confirmed by molecular analysis of its 16S ribosomal RNA gene sequence. Kluyvera sp. is closely related to the Enterobacteriaceae family. Chromobacterium violaceum CV026 was used as a biosensor to detect the production of AHL by strain ND04. High resolution triple quadrupole liquid chromatography-mass spectrometry analysis of strain ND04 showed our isolate produced two AHLs which are N-(3-oxohexanoyl)homoserine lactone (3-oxo-C6 HSL) and N-3-oxo-octanoyl-L-homoserine lactone (3-oxo-C8 HSL).
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Characterisation of a marine bacterium Vibrio brasiliensis T33 producing N-acyl homoserine lactone quorum sensing molecules.
Sensors (Basel)
PUBLISHED: 03-30-2014
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N-acylhomoserine lactones (AHL) plays roles as signal molecules in quorum sensing (QS) in most Gram-negative bacteria. QS regulates various physiological activities in relation with population density and concentration of signal molecules. With the aim of isolating marine water-borne bacteria that possess QS properties, we report here the preliminary screening of marine bacteria for AHL production using Chromobacterium violaceum CV026 as the AHL biosensor. Strain T33 was isolated based on preliminary AHL screening and further identified by using 16S rDNA sequence analysis as a member of the genus Vibrio closely related to Vibrio brasiliensis. The isolated Vibrio sp. strain T33 was confirmed to produce N-hexanoyl-L-homoserine lactone (C6-HSL) and N-(3-oxodecanoyl)-L-homoserine lactone (3-oxo-C10 HSL) through high resolution tandem mass spectrometry analysis. We demonstrated that this isolate formed biofilms which could be inhibited by catechin. To the best of our knowledge, this is the first report that documents the production of these AHLs by Vibrio brasiliensis strain T33.
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Pantoea sp. isolated from tropical fresh water exhibiting N-acyl homoserine lactone production.
ScientificWorldJournal
PUBLISHED: 03-27-2014
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N-Acyl homoserine lactone (AHL) serves as signaling molecule for quorum sensing (QS) in Gram-negative bacteria to regulate various physiological activities including pathogenicity. With the aim of isolating freshwater-borne bacteria that can cause outbreak of disease in plants and portrayed QS properties, environmental water sampling was conducted. Here we report the preliminary screening of AHL production using Chromobacterium violaceum CV026 and Escherichia coli [pSB401] as AHL biosensors. The 16S rDNA gene sequence of isolate M009 showed the highest sequence similarity to Pantoea stewartii S9-116, which is a plant pathogen. The isolated Pantoea sp. was confirmed to produce N-3-oxohexanoyl-L-HSL (3-oxo-C6-HSL) through analysis of high resolution mass tandem mass spectrometry.
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Design of a SiO? top-cladding and compact polarization splitter-rotator based on a rib directional coupler.
Opt Express
PUBLISHED: 03-26-2014
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A compact polarization splitter-rotator based on a silicon-on-insulator rib asymmetrical directional coupler with SiO2 top-cladding is proposed. Unlike previously reported PSRs which specifically required the top-cladding material to be different from the bottom cladding in order to break the symmetry of the waveguide cross-section, our proposed PSR has no such limitation on the top-cladding due to the horizontal asymmetry of the rib waveguide. In addition, the device is highly compact and has a total length as short as 24 ?m. Numerical simulation shows that a high conversion efficiency of ~97% is obtained at the wavelength of 1550 nm. With the width variation of ± 15 nm and the gap variation of ± 50 nm, the PSR still has high ER of 12 dB at the cross-port, showing large fabrication tolerance. This device can be cascaded to improve the performance at the through port and an example of a two-stage PSR is presented. The mode conversion between the strip waveguide and the rib waveguide is also discussed.
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An underlying prognosis predictor of hepatocellular carcinoma: Oncoprotein 18.
Biomed Rep
PUBLISHED: 03-21-2014
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Recent studies have reported the association between the expression of oncoprotein 18 (op18) and hepatocellular carcinoma (HCC). However, any underlying mechanistic connection between op18 expression and hepatocarcinogenesis is poorly understood. In the present study, Flag-pcDNA3.1 vector and Flag-pcDNA3.1-op18 plasmid were stably transfected in SMMC7721 cells, respectively. Stable SMMC7721 control and op18 overexpression SMMC7721 cell lines were constructed and identified by western blot analysis. Using a cell counting kit-8 (CCK8), it was shown that cell proliferation was significantly increased in the op18 overexpression SMMC7721 cell group (0.60±0.05), compared with the control group (0.29±0.03) at an absorbance of 450 nm (P<0.01). Flow cytometry was used to analyze cell apoptosis by FITC-Annexin V and propidium iodide (PI) apoptosis assay kit. The results demonstrated that the percentage of apoptotic cells was inhibited to 5.80±0.33% in the op18 overexpression group, compared with 11.79±1.09% in the control group. Using FACS, single cell analysis data showed that op18 overexpression induced cell cycle arrest by inhibiting progression from G2 to M phase. The results suggest that op18 expression is closely associated with SMMC7721 cell proliferation and apoptosis, which appears to be a potential predictor of prognosis in HCC.
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High-Quality Draft Whole-Genome Sequences of Three Strains of Enterobacter Isolated from Jamaican Dioscorea cayenensis (Yellow Yam).
Genome Announc
PUBLISHED: 03-15-2014
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Here we report the whole-genome sequences of three endophytic bacteria, Enterobacter sp. strain DC1, Enterobacter sp. strain DC3, and Enterobacter sp. strain DC4, from root tubers of the yellow yam plant, Dioscorea cayenensis. Preliminary analyses suggest that the genomes of the three bacteria contain genes involved in acetoin and indole-3-acetic acid metabolism.
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The complete mitogenome of the red claw crayfish Cherax quadricarinatus (Von Martens, 1868) (Crustacea: Decapoda: Parastacidae).
Mitochondrial DNA
PUBLISHED: 03-13-2014
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Abstract The commercial freshwater crayfish Cherax quadricarinatus complete mitochondrial genome was recovered from partial genome sequencing using the MiSeq Personal Sequencer. The mitogenome has 15,869 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The base composition of C. quadricarinatus is 32.16% for T, 23.39% for C, 33.26% for A, and 11.19% for G, with an AT bias of 65.42%.
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The complete mitogenome of the Macquarie perch, Macquaria australasica Cuvier, 1830 (Teleostei: Percichthyidae).
Mitochondrial DNA
PUBLISHED: 03-13-2014
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Abstract The complete mitochondrial genome of the conservationally significant Macquarie perch (Macquaria australasica) was obtained from low-coverage shotgun sequencing using the MiSeq sequencer. The M. australasica mitogenome has 16,496 base pairs (55% A?+?T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819?bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Macquaria, and the third to be reported for the family Percichthyidae.
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The complete mitogenome of the marine bivalve Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae).
Mitochondrial DNA
PUBLISHED: 03-13-2014
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Abstract The complete mitochondrial genome of the commercially important snout otter clam Lutraria rhynchaena was obtained from low-coverage shotgun sequencing data on the MiSeq platform. The L. rhynchaena mitogenome has 16,927 base pairs (69% A?+?T content) and made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 953?bp non-coding AT-rich region. This is the first mitogenome to be sequenced from the genus Lutraria, and the seventh to be reported for the family Mactridae.
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The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea.
Mitochondrial DNA
PUBLISHED: 03-13-2014
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Abstract The complete mitochondrial genome of a highland freshwater crayfish, Cherax monticola, was recovered by shotgun sequencing. The mitogenome consists of 15,917 base pairs containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of C. monticola is 33.46% for T, 21.48% for C, 33.71% for A and 11.35% for G, with an AT bias of 67.17%.
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Quorum sensing activity in Pandoraea pnomenusa RB38.
Sensors (Basel)
PUBLISHED: 03-05-2014
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Strain RB38 was recovered from a former dumping area in Malaysia. MALDI-TOF mass spectrometry and genomic analysis identified strain RB-38 as Pandoraea pnomenusa. Various biosensors confirmed its quorum sensing properties. High resolution triple quadrupole liquid chromatography-mass spectrometry analysis was subsequently used to characterize the N-acyl homoserine lactone production profile of P. pnomenusa strain RB38, which validated that this isolate produced N-octanoyl homoserine lactone as a quorum sensing molecule. This is the first report of the production of N-octanoyl homoserine lactone by P. pnomenusa strain RB38.
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Quorum sensing activity of Aeromonas caviae strain YL12, a bacterium isolated from compost.
Sensors (Basel)
PUBLISHED: 03-04-2014
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Quorum sensing is a well-studied cell-to-cell communication method that involves a cell-density dependent regulation of genes expression mediated by signalling molecules. In this study, a bacterium isolated from a plant material compost pile was found to possess quorum sensing activity based on bioassay screening. Isolate YL12 was identified using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and molecular typing using rpoD gene which identified the isolate as Aeromonas caviae. High resolution tandem mass spectrometry was subsequently employed to identify the N-acyl homoserine lactone profile of Aeromonas caviae YL12 and confirmed that this isolate produced two short chain N-acyl homoserine lactones, namely C4-HSL and C6, and the production was observed to be cell density-dependent. Using the thin layer chromatography (TLC) bioassay, both AHLs were found to activate C. violaceum CV026, whereas only C6-HSL was revealed to induce bioluminescence expression of E. coli [pSB401]. The data presented in this study will be the leading steps in understanding the role of quorum sensing in Aeromonas caviae strain YL12.
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Quorum sensing activity of Hafnia alvei isolated from packed food.
Sensors (Basel)
PUBLISHED: 03-02-2014
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Quorum sensing (QS) is a mechanism adopted by bacteria to regulate expression of genes according to population density. N-acylhomoserine lactones (AHLs) are a type of QS signalling molecules commonly found in Gram-negative bacteria which have been reported to play a role in microbial spoilage of foods and pathogenesis. In this study, we isolated an AHL-producing Hafnia alvei strain (FB1) from spherical fish pastes. Analysis via high resolution triple quadrupole liquid chromatography/mass spectrometry (LC/MS) on extracts from the spent supernatant of H. alvei FB1 revealed the existence of two short chain AHLs: N-(3-oxohexanoyl) homoserine lactone (3-oxo-C6-HSL) and N-(3-oxo- octanoyl) homoserine lactone (3-oxo-C8-HSL). To our knowledge, this is the first report of the production of AHLs, especially 3-oxo-C8-HSL, by H. alvei.
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Immunohistochemical screening and fluorescence in situ hybridization confirmation of ALK translocation in lung adenocarcinoma and its clinicopathological significance: a single-center large-scale investigation of Chinese patients.
Hum. Pathol.
PUBLISHED: 02-17-2014
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Anaplastic lymphoma kinase (ALK) translocation-positive adenocarcinoma of the lung is a newly recognized molecular subgroup. Limited data on the clinicopathological features of this entity in the Chinese population are available. We performed immunohistochemical staining for the ALK protein and fluorescence in situ hybridization detection of the ALK translocation. We enrolled 793 Chinese patients with lung adenocarcinoma and identified 54 ALK translocation-positive patients (6.8%) in the group. Compared with the entire group of patients, ALK translocation-positive patients were younger (P < .01) and more likely to be nonsmokers (P = .017), but presented with a higher percentage of advanced-stage disease (P = .022) and lymph node metastases (P = .006). ALK translocation-positive patients more commonly exhibited poorly differentiated tumor histology and a predominantly solid tumor growth pattern relative to the ALK translocation-negative patients. Morphologically, ALK translocation was associated with extracellular mucus secretion, a mucinous cribriform structure, and signet ring cell (SRC) components. ALK translocation was present in 42.5% and 34.0% of adenocarcinomas with SRC components or wild-type EGFR, respectively. ALK translocation, occurring at a frequency of 6.8% in Chinese patients, defines a unique molecular subgroup of lung tumors. Fluorescence in situ hybridization should be performed in each case of lung adenocarcinoma with SRC components or wild-type EGFR to identify ALK translocation-positive patients.
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Tandem mass spectrometry detection of quorum sensing activity in multidrug resistant clinical isolate Acinetobacter baumannii.
ScientificWorldJournal
PUBLISHED: 02-16-2014
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Many Proteobacteria communicate via production followed by response of quorum sensing molecules, namely, N-acyl homoserine lactones (AHLs). These molecules consist of a lactone moiety with N-acyl side chain with various chain lengths and degrees of saturation at C-3 position. AHL-dependent QS is often associated with regulation of diverse bacterial phenotypes including the expression of virulence factors. With the use of biosensor and high resolution liquid chromatography tandem mass spectrometry, the AHL production of clinical isolate A. baumannii 4KT was studied. Production of short chain AHL, namely, N-hexanoyl-homoserine lactone (C6-HSL) and N-octanoyl-homoserine lactone (C8-HSL), was detected.
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Draft Genome Sequences of Two Cellulolytic Paenibacillus sp. Strains, MAEPY1 and MAEPY2, from Malaysian Landfill Leachate.
Genome Announc
PUBLISHED: 02-15-2014
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We report the draft genome sequences of two Paenibacillus species with cellulose-degrading abilities isolated from landfill leachate. An array of genes putatively involved in cellulose degradation have been identified in both genome sequences, which can benefit various biotechnological industries.
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Sparse representation for tumor classification based on feature extraction using latent low-rank representation.
Biomed Res Int
PUBLISHED: 02-11-2014
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Accurate tumor classification is crucial to the proper treatment of cancer. To now, sparse representation (SR) has shown its great performance for tumor classification. This paper conceives a new SR-based method for tumor classification by using gene expression data. In the proposed method, we firstly use latent low-rank representation for extracting salient features and removing noise from the original samples data. Then we use sparse representation classifier (SRC) to build tumor classification model. The experimental results on several real-world data sets show that our method is more efficient and more effective than the previous classification methods including SVM, SRC, and LASSO.
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Lithium chloride decreases proliferation and migration of C6 glioma cells harboring isocitrate dehydrogenase 2 mutant via GSK-3?.
Mol. Biol. Rep.
PUBLISHED: 02-08-2014
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The gene encoding isocitrate dehydrogenase (IDH) is somatically mutated predominantly in secondary glioblastoma multiforme. Mutations of IDH1 and IDH2 lead to simultaneous loss and gain of activities in the production of ?-ketoglutarate and 2-hydroxyglutarate, respectively. Lithium chloride was recently proved efficient in inhibiting glioma cell migration. The mechanism of lithium chloride on C6 glioma cells harboring IDH2 mutation has not been studied. Here, we found lithium chloride induced inhibitive effects on cell proliferation of both C6 glioma cells with and without IDH2 mutation, although IDH2 mutation increased the stability of HIF-1?. GSK-3? could be phosphorylated at Ser9 and its activity was inhibited when C6 glioma cells were treated by lithium chloride. The degree of phosphorylation in IDH2(R172G) treatment group was lower than that as compared to the control and IDH2 treatment groups. At the same time, the accumulation of ?-catenin in C6 cell nucleus was decreased. Moreover, although the ?-catenin and HIF-1? increased the secretion of metalloproteinase-2,-9 in C6 glioma cells harboring IDH2 mutation, the migration potential of lithium chloride-treated C6 glioma cells harboring the IDH2 and its mutant was uniform. These results indicated lithium chloride could decrease the proliferation and migration potential of C6 glioma cells harboring IDH2 mutation.
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