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Find video protocols related to scientific articles indexed in Pubmed.
Phylotranscriptomic analysis of the origin and early diversification of land plants.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 10-29-2014
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Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
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Recovering metallic fractions from waste electrical and electronic equipment by a novel vibration system.
Waste Manag
PUBLISHED: 01-08-2013
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The need to recover and recycle valuable resources from Waste Electrical and Electronic Equipment (WEEE) is of growing importance as increasing amounts are generated due to shorter product life cycles, market expansions, new product developments and, higher consumption and production rates. The European Commission (EC) directive, 2002/96/EC, on WEEE became law in UK in January 2007 setting targets to recover up to 80% of all WEEE generated. Printed Wire Board (PWB) and/or Printed Circuit Board (PCB) is an important component of WEEE with an ever increasing tonnage being generated. However, the lack of an accurate estimate for PCB production, future supply and uncertain demands of its recycled materials in international markets has provided the motivation to explore different approaches to recycle PCBs. The work contained in this paper focuses on a novel, dry separation methodology in which vertical vibration is used to separate the metallic and non-metallic fractions of PCBs. When PCBs were comminuted to less than 1mm in size, metallic grades as high as 95% (measured by heavy liquid analysis) could be achieved in the recovered products.
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Surgical infection prophylaxis for left ventricular assist device implantation.
J Card Surg
PUBLISHED: 05-09-2011
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Antimicrobial prophylaxis is commonly administered to patients undergoing left ventricular assist device (LVAD) surgeries to prevent infectious complications. However, optimal surgical infection prophylaxis (SIP) for LVAD surgeries is not well defined.
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Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant.
Curr. Biol.
PUBLISHED: 01-06-2011
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New hybrid species might be expected to show patterns of gene expression intermediate to those shown by parental species. "Transcriptomic shock" may also occur, in which gene expression is disrupted; this may be further modified by whole genome duplication (causing allopolyploidy). "Shock" can include instantaneous partitioning of gene expression between parental copies of genes among tissues. These effects have not previously been studied at a population level in a natural allopolyploid plant species. Here, we survey tissue-specific expression of 144 duplicated gene pairs derived from different parental species (homeologs) in two natural populations of 40-generation-old allotetraploid Tragopogon miscellus (Asteraceae) plants. We compare these results with patterns of allelic expression in both in vitro "hybrids" and hand-crossed F(1) hybrids between the parental diploids T. dubius and T. pratensis, and with patterns of homeolog expression in synthetic (S(1)) allotetraploids. Partitioning of expression was frequent in natural allopolyploids, but F(1) hybrids and S(1) allopolyploids showed less partitioning of expression than the natural allopolyploids and the in vitro "hybrids" of diploid parents. Our results suggest that regulation of gene expression is relaxed in a concerted manner upon hybridization, and new patterns of partitioned expression subsequently emerge over the generations following allopolyploidization.
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The effects of behavioral skills training on caregiver implementation of guided compliance.
J Appl Behav Anal
PUBLISHED: 12-02-2009
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The effectiveness of a behavioral skills training package that consisted of modeling, rehearsal, and feedback was evaluated to increase correct implementation of guided compliance by caregivers of 3 children who exhibited noncompliance. Results showed that the training package improved performance of guided compliance. Generalization probes indicated that the skills learned were exhibited in different settings 3 to 6 weeks after training ended.
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Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes.
PLoS ONE
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Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ? 1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.
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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.