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Find video protocols related to scientific articles indexed in Pubmed.
A systematic analysis of Acanthamoeba genotype frequency correlated with source and pathogenicity: T4 is confirmed as a pathogen-rich genotype.
Eur. J. Protistol.
PUBLISHED: 01-03-2013
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Acanthamoeba is a genus of facultative human parasites that is currently classified into 17 genotypes (T1-T17) each of which arguably represents a species. These amoebae cause Acanthamoeba Keratitis (AK) a disease of the eye, and a rare but usually fatal Granulatomous Acanthamoeba Encephalitis (GAE). A database of strains derived from the literature and a number of fresh isolates has been constructed to detect trends of pathogenic and other associations with these genotypes. One genotype in particular, T4, was found to be over represented in human disease. The prevalence of this genotype has been commented upon previously, however T4 is also the most common type isolated from the environment. Our statistical analysis of the database allows us to claim that T4 is in fact the genotype most often associated with human disease, even after its abundance in the general environment is taken into account. T3 and T11 are closest relatives to T4 and they are the second and third most often associated with AK. A number of other more subtle correlations also emerge from this analysis.
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Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6) before the radiation of Viridiplantae.
BMC Evol. Biol.
PUBLISHED: 03-11-2011
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The drug/metabolite transporter superfamily comprises a diversity of protein domain families with multiple functions including transport of nucleotide sugars. Drug/metabolite transporter domains are contained in both solute carrier families 30, 35 and 39 proteins as well as in acyl-malonyl condensing enzyme proteins. In this paper, we present an evolutionary analysis of nucleotide sugar transporters in relation to the entire superfamily of drug/metabolite transporters that considers crucial intra-protein duplication events that have shaped the transporters. We use a method that combines the strengths of hidden Markov models and maximum likelihood to find relationships between drug/metabolite transporter families, and branches within families.
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High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA.
J. Mol. Biol.
PUBLISHED: 02-10-2009
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We have mapped in vitro nucleosome positioning on the sheep beta-lactoglobulin gene using high-throughput sequencing to characterise the DNA sequences recovered from reconstituted nucleosomes. This methodology surpasses previous approaches for coverage, accuracy and resolution and, most importantly, offers a simple yet rapid and relatively inexpensive method to characterise genomic DNA sequences in terms of nucleosome positioning capacity. We demonstrate an unambiguous correspondence between in vitro and in vivo nucleosome positioning around the promoter of the gene; identify discrete, sequence-specific nucleosomal structures above the level of the canonical core particle-a feature that has implications for regulatory protein access and higher-order chromatin packing; and reveal new insights into the involvement of periodically organised dinucleotide sequence motifs of the type GG and CC and not AA and TT, as determinants of nucleosome positioning-an observation that supports the idea that the core histone octamer can exploit different patterns of sequence organisation, or structural potential, in the DNA to bring about nucleosome positioning.
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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.