JoVE Visualize What is visualize?
Stop Reading. Start Watching.
Advanced Search
Stop Reading. Start Watching.
Regular Search
Find video protocols related to scientific articles indexed in Pubmed.
The effect of perhexiline on myocardial protection during coronary artery surgery: a two-centre, randomized, double-blind, placebo-controlled trial.
Eur J Cardiothorac Surg
PUBLISHED: 06-21-2014
Show Abstract
Hide Abstract
Perhexiline is thought to modulate metabolism by inhibiting mitochondrial carnitine palmitoyltransferase-1, reducing fatty acid uptake and increasing carbohydrate utilization. This study assessed whether preoperative perhexiline improves markers of myocardial protection in patients undergoing coronary artery bypass graft surgery and analysed its effect on the myocardial metabolome.
Related JoVE Video
Exo-metabolome of Pseudovibrio sp. FO-BEG1 analyzed by ultra-high resolution mass spectrometry and the effect of phosphate limitation.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
Oceanic dissolved organic matter (DOM) is an assemblage of reduced carbon compounds, which results from biotic and abiotic processes. The biotic processes consist in either release or uptake of specific molecules by marine organisms. Heterotrophic bacteria have been mostly considered to influence the DOM composition by preferential uptake of certain compounds. However, they also secrete a variety of molecules depending on physiological state, environmental and growth conditions, but so far the full set of compounds secreted by these bacteria has never been investigated. In this study, we analyzed the exo-metabolome, metabolites secreted into the environment, of the heterotrophic marine bacterium Pseudovibrio sp. FO-BEG1 via ultra-high resolution mass spectrometry, comparing phosphate limited with phosphate surplus growth conditions. Bacteria belonging to the Pseudovibrio genus have been isolated worldwide, mainly from marine invertebrates and were described as metabolically versatile Alphaproteobacteria. We show that the exo-metabolome is unexpectedly large and diverse, consisting of hundreds of compounds that differ by their molecular formulae. It is characterized by a dynamic recycling of molecules, and it is drastically affected by the physiological state of the strain. Moreover, we show that phosphate limitation greatly influences both the amount and the composition of the secreted molecules. By assigning the detected masses to general chemical categories, we observed that under phosphate surplus conditions the secreted molecules were mainly peptides and highly unsaturated compounds. In contrast, under phosphate limitation the composition of the exo-metabolome changed during bacterial growth, showing an increase in highly unsaturated, phenolic, and polyphenolic compounds. Finally, we annotated the detected masses using multiple metabolite databases. These analyses suggested the presence of several masses analogue to masses of known bioactive compounds. However, the annotation was successful only for a minor part of the detected molecules, underlining the current gap in knowledge concerning the biosynthetic ability of marine heterotrophic bacteria.
Related JoVE Video
HAMMER: Automated operation of Mass Frontier to construct in-silico mass spectral fragmentation libraries.
Bioinformatics
PUBLISHED: 12-11-2013
Show Abstract
Hide Abstract
Experimental MS(n) mass spectral libraries currently do not adequately cover chemical space. This limits the robust annotation of metabolites in metabolomics studies of complex biological samples. In-silico fragmentation libraries would improve the identification of compounds from experimental multi-stage fragmentation data when experimental reference data is unavailable. Here we present a freely-available software package to automatically control Mass Frontier software to construct in-silico mass spectral libraries, and to perform spectral matching. Based on two case studies we have demonstrated that HAMMER allows researchers to generate in-silico mass spectral libraries in an automated and high-throughput fashion with little or no human intervention required.
Related JoVE Video
A stable-isotope mass spectrometry-based metabolic footprinting approach to analyze exudates from phytoplankton.
Mar Drugs
PUBLISHED: 08-12-2013
Show Abstract
Hide Abstract
Phytoplankton exudates play an important role in pelagic ecology and biogeochemical cycles of elements. Exuded compounds fuel the microbial food web and often encompass bioactive secondary metabolites like sex pheromones, allelochemicals, antibiotics, or feeding attractants that mediate biological interactions. Despite this importance, little is known about the bioactive compounds present in phytoplankton exudates. We report a stable-isotope metabolic footprinting method to characterise exudates from aquatic autotrophs. Exudates from (13)C-enriched alga were concentrated by solid phase extraction and analysed by high-resolution Fourier transform ion cyclotron resonance mass spectrometry. We used the harmful algal bloom forming dinoflagellate Alexandrium tamarense to prove the method. An algorithm was developed to automatically pinpoint just those metabolites with highly (13)C-enriched isotope signatures, allowing us to discover algal exudates from the complex seawater background. The stable-isotope pattern (SIP) of the detected metabolites then allowed for more accurate assignment to an empirical formula, a critical first step in their identification. This automated workflow provides an effective way to explore the chemical nature of the solutes exuded from phytoplankton cells and will facilitate the discovery of novel dissolved bioactive compounds.
Related JoVE Video
Characterization of isotopic abundance measurements in high resolution FT-ICR and Orbitrap mass spectra for improved confidence of metabolite identification.
Anal. Chem.
PUBLISHED: 04-19-2011
Show Abstract
Hide Abstract
Currently there is limited information available on the accuracy and precision of relative isotopic abundance (RIA) measurements using high-resolution direct-infusion mass spectrometry (HR DIMS), and it is unclear if this information can benefit automated peak annotation in metabolomics. Here we characterize the accuracy of RIA measurements on the Thermo LTQ FT Ultra (resolution of 100,000-750,000) and LTQ Orbitrap (R = 100,000) mass spectrometers. This first involved reoptimizing the SIM-stitching method (Southam, A. D. Anal. Chem. 2007, 79, 4595-4602) for the LTQ FT Ultra, which achieved a ca. 3-fold sensitivity increase compared to the original method while maintaining a root-mean-squared mass error of 0.16 ppm. Using this method, we show the quality of RIA measurements is highly dependent on signal-to-noise ratio (SNR), with RIA accuracy increasing with higher SNR. Furthermore, a negative offset between the theoretical and empirically calculated numbers of carbon atoms was observed for both mass spectrometers. Increasing the resolution of the LTQ FT Ultra lowered both the sensitivity and the quality of RIA measurements. Overall, although the errors in the empirically calculated number of carbons can be large (e.g., 10 carbons), we demonstrate that RIA measurements do improve automated peak annotation, increasing the number of single empirical formula assignments by >3-fold compared to using accurate mass alone.
Related JoVE Video
Discriminating between different acute chemical toxicities via changes in the daphnid metabolome.
Toxicol. Sci.
PUBLISHED: 08-18-2010
Show Abstract
Hide Abstract
Currently, there is widespread interest in exploiting "omics" approaches to screen the toxicity of chemicals, potentially enabling their rapid categorization into classes of defined mode of action (MOA). Direct infusion Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) metabolomics provides a sensitive and nontargeted analysis of potentially a thousand endogenous metabolites. Our previous work has shown that mass spectra can be recorded from whole-organism homogenate or hemolymph of single adult Daphnia magna. Here we develop multivariate models and discover perturbations to specific metabolic pathways that can discriminate between the acute toxicities of four chemicals to D. magna using FT-ICR MS metabolomics. We focus on model toxicants (cadmium, fenvalerate, dinitrophenol, and propranolol) with different MOAs. First, we confirmed that a toxicant-induced metabolic effect could be determined for each chemical in both the hemolymph and the whole-organism metabolome, with between 9 and 660 mass spectral peaks changing intensities significantly, dependent upon toxicant and sample type. Subsequently, supervised multivariate models were built that discriminated significantly all four acute metabolic toxicities, yielding mean classification error rates (across all classes) of 3.9 and 6.9% for whole-organism homogenates and hemolymph, respectively. Following extensive peak annotation, we discovered toxicant-specific perturbations to putatively identified metabolic pathways, including propranolol-induced disruption of fatty acid metabolism and eicosanoid biosynthesis and fenvalerate-induced disruption of amino sugar metabolism. We conclude that the metabolic profiles of whole-daphnid homogenates are more discriminatory for toxicant action than hemolymph. Furthermore, our findings highlight the capability of metabolomics to discover early-event metabolic responses that can discriminate between the acute toxicities of chemicals.
Related JoVE Video
MaConDa: a publicly accessible mass spectrometry contaminants database.
Bioinformatics
Show Abstract
Hide Abstract
Mass spectrometry is widely used in bioanalysis, including the fields of metabolomics and proteomics, to simultaneously measure large numbers of molecules in complex biological samples. Contaminants routinely occur within these samples, for example, originating from the solvents or plasticware. Identification of these contaminants is crucial to enable their removal before data analysis, in particular to maintain the validity of conclusions drawn from uni- and multivariate statistical analyses. Although efforts have been made to report contaminants within mass spectra, this information is fragmented and its accessibility is relatively limited. In response to the needs of the bioanalytical community, here we report the creation of an extensive manually well-annotated database of currently known small molecule contaminants.
Related JoVE Video

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.