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Find video protocols related to scientific articles indexed in Pubmed.
Probing riboswitch binding sites with molecular docking, focused libraries, and in-line probing assays.
Methods Mol. Biol.
PUBLISHED: 07-22-2014
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Molecular docking calculations combined with chemically focused libraries can bring insight in the exploration of the structure-activity relationships for a series of related compounds against an RNA target. Yet, the in silico engine must be fueled by experimental observations to drive the research into a more effective ligand-discovery path. Here we show how molecular docking predictions can be coupled with in-line probing assays to explore the available chemical and configurational space in a riboswitch binding pocket.
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Altered functionality of anti-bacterial antibodies in patients with chronic hepatitis C virus infection.
PLoS ONE
PUBLISHED: 01-01-2013
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Using comparative glycoproteomics, we have previously identified a glycoprotein that is altered in both amount and glycosylation as a function of liver cirrhosis. The altered glycoprotein is an agalactosylated (G0) immunoglobulin G molecule (IgG) that recognizes the heterophilic alpha-gal epitope. Since the alpha gal epitope is found on gut enterobacteria, it has been hypothesized that anti-gal antibodies are generated as a result of increased bacterial exposure in patients with liver disease.
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Development of recombinant Aleuria aurantia lectins with altered binding specificities to fucosylated glycans.
Biochem. Biophys. Res. Commun.
PUBLISHED: 08-18-2011
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Changes in glycosylation have long been associated with disease. While there are many methods to detect changes in glycosylation, plant derived lectins are often used to determine changes on specific proteins or molecules of interest. One change in glycosylation that has been observed by us and by others is a disease or antigen associated increase in fucosylation on N-linked glycans. To measure this change, the fucose binding Aleuria aurantia lectin (AAL) is often utilized in plate and solution based assays. AAL is a mushroom derived lectin that contains five fucose binding sites that preferentially bind fucose linked (?-1,3, ?-1,2, ?-,4, and ?-1,6) to N-acetyllactosamine related structures. Recently, several reports by us and by others have indicated that specific fucose linkages found on certain serum biomarker glycoproteins are more associated with disease than others. Taking a site-directed mutagenesis approach, we have created a set of recombinant AAL proteins that display altered binding affinities to different analytes containing various fucose linkages.
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Novel changes in glycosylation of serum Apo-J in patients with hepatocellular carcinoma.
Cancer Epidemiol. Biomarkers Prev.
PUBLISHED: 04-05-2011
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Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide and the occurrence of HCC has more than doubled in the United States in the past decade. Early detection is considered key to reducing the mortality of HCC.
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Genetic diversity of porcine Norovirus and Sapovirus: Canada, 2005-2007.
Arch. Virol.
PUBLISHED: 02-23-2009
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Noroviruses and sapoviruses are members of the family Caliciviridae and emerging enteric pathogens of humans and animals. Since their discovery and characterization in swine, relatively few strains have been described in detail. In order to investigate their genetic diversity, a total of 266 fecal samples collected in the province of Quebec, Canada, between 2005 and 2007 were screened for the presence of caliciviruses by RT-PCR using broadly reactive primers. Genetically heterogeneous caliciviruses were detected on the majority of farms. Typical noroviruses related to known swine genotypes were present on 20% of the farms. Sapoviruses were detected on 75% of the farms and were the most heterogeneous group. Further characterization of selected strains in their 3 end parts was carried out for their classification and unveiled possibly new clusters of sapoviruses. No human-like noroviruses or sapoviruses were detected in the present study.
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Structure-function relationships of the outer membrane translocon Wza investigated by cryo-electron microscopy and mutagenesis.
J. Struct. Biol.
PUBLISHED: 01-23-2009
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The outer membrane protein Wza, from Escherichia coli K30, forms an octameric complex that is essential for capsular polysaccharide export. Homologs of Wza are widespread in gram-negative bacterial pathogens where capsules are critical virulence determinants. Wza is unusual in that it spans the outer membrane using a barrel composed of amphipathic alpha-helices, rather than being a beta-barrel like almost all other outer membrane channels. The transmembrane helical barrel of Wza also forms the external opening to a hydrophilic translocation pathway that spans the periplasm. Here, we have probed the structure and function of the Wza complex using both cryo-electron microscopy and mutagenesis. The helical barrel structure is stable in detergent micelles under mildly acidic conditions but is destabilized at basic pH, although the overall quaternary structure is retained. Truncation of the C-terminal region that forms the helical barrel by 4 residues has no effect on the ability of Wza to oligomerize and support capsule export, but larger truncations of 18, 24 or 35 amino acids abolish its function. The bulk of the C-terminal domain is essential for the stability and assembly of the E. coli Wza complex.
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Genomic characterization of swine caliciviruses representing a new genus of Caliciviridae.
Virus Genes
PUBLISHED: 01-02-2009
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This study reports the molecular characterization of novel caliciviruses, the St-Valérien-like viruses, which were isolated from pig feces in the province of Quebec, Canada between 2005 and 2007. The genomes of St-Valérien-like viruses contain 6409 nucleotides and include two main open reading frames (ORFs). ORF1 encodes the non structural (NS) polyprotein and the major capsid protein (VP1) while ORF2 encodes the putative basic minor capsid protein. Typical conserved amino acid motifs predict a gene order reminiscent of calicivirus genomes. Phylogenetic, pairwise homology, and distance analyses performed on complete genomic sequences and partial amino acid sequences from the NTPase, polymerase, and major capsid protein segregated the St-Valérien-like viruses in a unique cluster sharing a common root with the Tulane virus and the noroviruses. Based on the genomic analyses presented, the St-Valérien-like viruses are members of a new genus of Caliciviridae for which we propose the name Valovirus.
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Dendritic cell CNS recruitment correlates with disease severity in EAE via CCL2 chemotaxis at the blood-brain barrier through paracellular transmigration and ERK activation.
J Neuroinflammation
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Transmigration of circulating dendritic cells (DCs) into the central nervous system (CNS) across the blood-brain barrier (BBB) has not thus far been investigated. An increase in immune cell infiltration across the BBB, uncontrolled activation and antigen presentation are influenced by chemokines. Chemokine ligand 2 (CCL2) is a potent chemoattractant known to be secreted by the BBB but has not been implicated in the recruitment of DCs specifically at the BBB.
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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.