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Find video protocols related to scientific articles indexed in Pubmed.
Comparative transcriptome analysis of aboveground and underground tissues of Rhodiola algida, an important ethno-medicinal herb endemic to the Qinghai-Tibetan Plateau.
Gene
PUBLISHED: 06-16-2014
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Transcriptome sequencing is a powerful tool for the assessment of gene expression and the identification and characterization of molecular markers in non-model organisms. Rhodiola algida L. (Crassulaceae), endemic to the Qinghai-Tibetan Plateau, has long been used in traditional Chinese medicine to prevent altitude sickness and eliminate fatigue. Illumina-based high-throughput transcriptome sequencing of aboveground and underground tissues of R. algida respectively yielded 5.40 million and 5.18 million clean reads. A total of 82,664 unigenes averaging 577bp in length were generated from the aboveground clean reads, with 86,237 unigenes of 502-bp mean length obtained from the underground tissues. Of 55,028 unigenes compared with sequences in UniProt databases, 20,413 unigenes had significant similarities with existing sequences in NR, NT, Swiss-Prot, GO, KEGG, and COG databases. Single nucleotide polymorphism (SNP) analysis identified 237,294 SNPs from 154,636 contigs of aboveground tissues and 197,540 SNPs from 144,963 underground-derived contigs. The information uncovered in this study should serve as a valuable resource for the characterization of important traits related to secondary metabolite formation and for the identification of associated molecular mechanisms.
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Isolation and characterization of a Chinese strain of Tembusu virus from Hy-Line Brown layers with acute egg-drop syndrome in Fujian, China.
Arch. Virol.
PUBLISHED: 06-09-2013
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Tembusu virus (TMUV) has been a causative agent of an acute egg-drop syndrome found in Chinese duck populations since at least 2010. In this paper, we report the characterization of a TMUV-like flavivirus (named CJD05) isolated from naturally infected egg-laying fowl. The virus was identified and then isolated from hens suffering from severe egg drop and fever in Fujian Province, China. The virus replicated well in MDEF and CEF cells, and its cytopathogenic effect (CPE) was apparent. Hemagglutinating activity (HA) was negative for this virus using erythrocytes from both chickens and pigeons. Viral particles were enveloped and approximately 45 nm in diameter, as observed by electron microscopy. Phylogenetic analysis of the full-length nucleotide sequence of CJD05 indicated that this virus is closely related to the duck-origin TMUV, belonging to Ntaya group of flavivirus. Most importantly, pathogenicity studies showed that CJD05 is highly virulent in 1-day-old chicks, 1-day-old Muscovy ducks, egg-laying chickens and shelducks. Our research highlights the increase in epidemic disease caused by avian TMUV, and subsequent outbreaks are becoming more complicated to treat. The pathogenic mechanisms of the virus are still not fully understood, further research is needed.
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Spatial variation profiling of four phytochemical constituents in Gentiana straminea (Gentianaceae).
J Nat Med
PUBLISHED: 03-05-2013
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Gentiana straminea is the famous Tibetan folk medicine thought to cure various diseases. Historically, the Qinghai-Tibetan region has been considered as the geo-authentic production area of "Mahua Jiao," where large quantities of the medicine are grown. However, there is still little known about the phytochemical constituent spatial variation of this species. In order to find the differences between the main phytochemical constituents of G. straminea and to provide comprehensive information for quality evaluation, four main bioactive compounds (loganic acid, swertiamarin, gentiopicroside and sweroside) were analysed in 26 populations grown in areas with elevations ranging from 2320 to 4720 m across the Qinghai-Tibetan Plateau. The results showed that the four phytochemical constitutes concentrations varied greatly in the spatial profiling of the Qinghai-Tibetan region. Throughout the range of distribution of this species, no altitudinal, latitudinal or longitudinal trends have proven to be significant in any of the four constitutes concentrations or their summation. Furthermore, hierarchical clustering analysis and statistical tests showed that four populations (Liu0609-18, Liu0609-15, Liu2006-13-9 and Liu0609-22) had total constitute contents that were higher than other populations. The spatial profiling of the four phytochemical constituents suggests that the geo-authentic producing area of this species exists at a few regions within the Qinghai province, which could be attributed to specific environmental or genetic factors.
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Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data.
PLoS ONE
PUBLISHED: 01-01-2013
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Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems.
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[Immunosuppression effect of co-infection with MDRV and H9 AIV on thymus in muscovy ducks].
Wei Sheng Wu Xue Bao
PUBLISHED: 02-01-2011
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To study the immunosuppression effect on the thymus of muscovy ducks after infected with muscovy duck reovirus (MDRV) and H9 influenza virus (AIV).
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Reverse transcription loop-mediated isothermal amplification for rapid detection of the newly emerged poultry Flavivirus.
Folia Microbiol. (Praha)
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Poultry Flavivirus (PF) was a recently emerged virus with high morbidity rates and mortality rates in China. It is the causative agent of egg drop syndrome at present. Development of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was the most efficient way to prevent and control the PF disease. The assay was performed at 64 °C for 45 min, using six specific primers that recognized eight targets of the PF E gene. The RT-LAMP assay, compared to conventional reverse transcription polymerase chain reaction, has 100-fold-greater sensitivity, with a detection limit of 1?×?10(-3) copies per ?L RNA and no cross-reaction with poultry other viruses. The RT-LAMP assay is a valuable tool for detected PF without requiring any sophisticated equipment, and the detection has potential usefulness for clinical diagnosis in the field.
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Adapted Tembusu-like virus in chickens and geese in China.
J. Clin. Microbiol.
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An outbreak of egg drop disease occurred in many chicken and goose farms in China in 2011. By using an NS5-specific reverse transcriptase PCR (RT-PCR), we found that 56% of chicken and 38% of goose samples were positive for Tembusu-like virus (TMUV). Isolates showed high sequence homology to duck TMUVs, and chickens and geese showed signs of egg drop disease after experimental infection with duck TMUV. Our data suggest TMUV has adapted in domestic birds.
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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.

How does it work?

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

Video X seems to be unrelated to Abstract Y...

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.