Cross-Platform Comparison of Untargeted and Targeted Lipidomics Approaches on Aging Mouse Plasma.

Lipidomics - the global assessment of lipids - can be performed using a variety of mass spectrometry (MS)-based approaches. However, choosing the optimal approach in terms of lipid coverage, robustness and throughput can be a challenging task. Here, we compare a novel targeted quantitative lipidomics platform known as the Lipidyzer to a conventional untargeted liquid chromatography (LC)-MS approach. We find that both platforms are efficient in profiling more than 300 lipids across 11 lipid classes in mouse plasma with precision and accuracy below 20% for most lipids. While the untargeted and targeted platforms detect similar numbers of lipids, the former identifies a broader range of lipid classes and can unambiguously identify all three fatty acids in triacylglycerols (TAG). Quantitative measurements from both approaches exhibit a median correlation coefficient (r) of 0.99 using a dilution series of deuterated internal standards and 0.71 using endogenous plasma lipids in the context of aging. Application of both platforms to plasma from aging mouse reveals similar changes in total lipid levels across all major lipid classes and in specific lipid species. Interestingly, TAG is the lipid class that exhibits the most changes with age, suggesting that TAG metabolism is particularly sensitive to the aging process in mice. Collectively, our data show that the Lipidyzer platform provides comprehensive profiling of the most prevalent lipids in plasma in a simple and automated manner

In-depth triacylglycerol profiling using MS3 Q-Trap mass spectrometry

Total triacylglycerol (TAG) level is a key clinical marker of metabolic and cardiovascular diseases. However, the roles of individual TAGs have not been thoroughly explored in part due to their extreme structural complexity. We present a targeted mass spectrometry-based method combining multiple reaction monitoring (MRM) and multiple stage mass spectrometry (MS3) for the comprehensive qualitative and semiquantitative profiling of TAGs. This method referred as TriP-MS3 – triacylglycerol profiling using MS3 – screens for more than 6,700 TAG species in a fully automated fashion. TriP-MS3 demonstrated excellent reproducibility (median interday CV ∼ 0.15) and linearity (median R2 = 0.978) and detected 285 individual TAG species in human plasma. The semiquantitative accuracy of the method was validated by comparison with a state-of-the-art reverse phase liquid chromatography (RPLC)-MS (R2 = 0.83), which is the most commonly used approach for TAGs profiling. Finally, we demonstrate the utility and the versatility of the method by characterizing the effects of a fatty acid desaturase inhibitor on TAG profiles in vitro and by profiling TAGs in Caenorhabditis elegans.Fil: Cabruja, Matias Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; Argentina. University of Stanford; Estados UnidosFil: Priotti, Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; Argentina. University of California; Estados UnidosFil: Domizi, Pablo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; Argentina. University of Stanford; Estados UnidosFil: Papsdorf, Katharina. University of Stanford; Estados UnidosFil: Kroetz, Deanna L.. University of California; Estados UnidosFil: Brunet, Anne. University of Stanford; Estados UnidosFil: Contrepois, Kévin. University of Stanford; Estados UnidosFil: Snyder, Michael P.. University of Stanford; Estados Unido

'Where is the child I used to be?' Childhood remembered - Günter Grass’s The Tin Drum, Christa Wolf’s A Model Childhood and W.G. Sebald’s Austerlitz

Genes with reduced expression in Q 30 -YFP colonies versus Q 0 -YFP colonies. The table summarizes the expression differences of two data sets (Q0_3d, Q30_3d). Standard deviation and p-values were obtained as described above. Hits with a p-value greater than 0.05 are indicated in grey. (DOCX 16 kb

Patients' preference between two competing treatments: Carotid stenting and carotid surgery

There are two competing treatments for atherosclerotic stenosis of the carotid artery, a major cause of stroke carotid endarterectomy (CEA) and carotid artery stenting (CAS). There have been various studies of the comparative medical merits of both methods. However, there is a lack of research on factors affecting patients' preference, and the aim of this pilot- study was to attempt to determine the factors contributing to this. 15 patients, including International Carotid Stenting Study participants, and those from the Stroke unit ward and outpatients clinic, were given a standard questionnaire, covering safety, side- effects, personal fears and willingness to pay. After reading an information sheet, the patients were asked to fill in the questionnaire without intervention from myself. A 2 to 1 majority of interviewees stated a preference for stenting over surgery. The strongest factors in patients' choice appeared to be perceived risk, concern over side effects, and anxiety in regard to type of anaesthesia. It is clear that a larger study is required, perhaps with some modification to the questionnaire and a more representative sample of interviewees

The Lid Domain of Caenorhabditis elegans Hsc70 Influences ATP Turnover, Cofactor Binding and Protein Folding Activity

Hsc70 is a conserved ATP-dependent molecular chaperone, which utilizes the energy of ATP hydrolysis to alter the folding state of its client proteins. In contrast to the Hsc70 systems of bacteria, yeast and humans, the Hsc70 system of C. elegans (CeHsc70) has not been studied to date

Construction and evaluation of yeast expression networks by database-guided predictions

DNA-Microarrays are powerful tools to obtain expression data on the genome-wide scale. We performed microarray experiments to elucidate the transcriptional networks, which are up- or down-regulated in response to the expression of toxic polyglutamine proteins in yeast. Such experiments initially generate hit lists containing differentially expressed genes. To look into transcriptional responses, we constructed networks from these genes. We therefore developed an algorithm, which is capable of dealing with very small numbers of microarrays by clustering the hits based on co-regulatory relationships obtained from the SPELL database. Here, we evaluate this algorithm according to several criteria and further develop its statistical capabilities. Initially, we define how the number of SPELL-derived co-regulated genes and the number of input hits influences the quality of the networks. We then show the ability of our networks to accurately predict further differentially expressed genes. Including these predicted genes into the networks improves the network quality and allows quantifying the predictive strength of the networks based on a newly implemented scoring method. We find that this approach is useful for our own experimental data sets and also for many other data sets which we tested from the SPELL microarray database. Furthermore, the clusters obtained by the described algorithm greatly improve the assignment to biological processes and transcription factors for the individual clusters. Thus, the described clustering approach, which will be available through the ClusterEx web interface, and the evaluation parameters derived from it represent valuable tools for the fast and informative analysis of yeast microarray data

Cross-Platform Comparison of Untargeted and Targeted Lipidomics Approaches on Aging Mouse Plasma.

Lipidomics - the global assessment of lipids - can be performed using a variety of mass spectrometry (MS)-based approaches. However, choosing the optimal approach in terms of lipid coverage, robustness and throughput can be a challenging task. Here, we compare a novel targeted quantitative lipidomics platform known as the Lipidyzer to a conventional untargeted liquid chromatography (LC)-MS approach. We find that both platforms are efficient in profiling more than 300 lipids across 11 lipid classes in mouse plasma with precision and accuracy below 20% for most lipids. While the untargeted and targeted platforms detect similar numbers of lipids, the former identifies a broader range of lipid classes and can unambiguously identify all three fatty acids in triacylglycerols (TAG). Quantitative measurements from both approaches exhibit a median correlation coefficient (r) of 0.99 using a dilution series of deuterated internal standards and 0.71 using endogenous plasma lipids in the context of aging. Application of both platforms to plasma from aging mouse reveals similar changes in total lipid levels across all major lipid classes and in specific lipid species. Interestingly, TAG is the lipid class that exhibits the most changes with age, suggesting that TAG metabolism is particularly sensitive to the aging process in mice. Collectively, our data show that the Lipidyzer platform provides comprehensive profiling of the most prevalent lipids in plasma in a simple and automated manner

CeHsc70 truncation mutants show an altered ATP turnover.

<p>(<b>A</b>) Domain organization and amino acid identity (Id) and homology (Hom) of CeHsc70 towards bacterial, yeast and human homologs. The truncation mutants generated in this work are indicated by black arrows. (<b>B</b>) Structure of DnaK based on the PDB file 2KHO <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033980#pone.0033980-Bertelsen1" target="_blank">[93]</a>. The truncations are colored in red (CeHsc70-Δ384), red and blue (CeHsc70-Δ512) and red, blue and yellow (CeHsc70-Δ545). The lid region, which is missing in the CeHsc70-Δ545 mutant, is highlighted in orange. (<b>C</b>) The single-turnover experiments using 20 µM CeHsc70 variants were performed as outlined in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033980#s4" target="_blank">Materials and Methods</a> section in standard buffer at 25°C. Data for CeHsc70-Δ384 (▾), CeHsc70-Δ512 (▴), CeHsc70-Δ545 (•) and CeHsc70 (▪) were fit to single exponential functions. The inset shows the initial phase of the hydrolysis reaction within the first 200 s.</p