Publications by authors named "Michael Witting"

106 Publications

HLH-30-dependent rewiring of metabolism during starvation in C. elegans.

Aging Cell 2021 Mar 16:e13342. Epub 2021 Mar 16.

Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark.

One of the most fundamental challenges for all living organisms is to sense and respond to alternating nutritional conditions in order to adapt their metabolism and physiology to promote survival and achieve balanced growth. Here, we applied metabolomics and lipidomics to examine temporal regulation of metabolism during starvation in wild-type Caenorhabditis elegans and in animals lacking the transcription factor HLH-30. Our findings show for the first time that starvation alters the abundance of hundreds of metabolites and lipid species in a temporal- and HLH-30-dependent manner. We demonstrate that premature death of hlh-30 animals under starvation can be prevented by supplementation of exogenous fatty acids, and that HLH-30 is required for complete oxidation of long-chain fatty acids. We further show that RNAi-mediated knockdown of the gene encoding carnitine palmitoyl transferase I (cpt-1) only impairs survival of wild-type animals and not of hlh-30 animals. Strikingly, we also find that compromised generation of peroxisomes by prx-5 knockdown renders hlh-30 animals hypersensitive to starvation, which cannot be rescued by supplementation of exogenous fatty acids. Collectively, our observations show that mitochondrial functions are compromised in hlh-30 animals and that hlh-30 animals rewire their metabolism to largely depend on functional peroxisomes during starvation, underlining the importance of metabolic plasticity to maintain survival.
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http://dx.doi.org/10.1111/acel.13342DOI Listing
March 2021

Correction to: Comparison of lipidome profiles of Caenorhabditis elegans-results from an inter-laboratory ring trial.

Metabolomics 2021 Mar 12;17(3):33. Epub 2021 Mar 12.

Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany.

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http://dx.doi.org/10.1007/s11306-021-01784-5DOI Listing
March 2021

Comparison of lipidome profiles of Caenorhabditis elegans-results from an inter-laboratory ring trial.

Metabolomics 2021 02 17;17(3):25. Epub 2021 Feb 17.

Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany.

Introduction: Lipidomic profiling allows 100s if not 1000s of lipids in a sample to be detected and quantified. Modern lipidomics techniques are ultra-sensitive assays that enable the discovery of novel biomarkers in a variety of fields and provide new insight in mechanistic investigations. Despite much progress in lipidomics, there remains, as for all high throughput "omics" strategies, the need to develop strategies to standardize and integrate quality control into studies in order to enhance robustness, reproducibility, and usability of studies within specific fields and beyond.

Objectives: We aimed to understand how much results from lipid profiling in the model organism Caenorhabditis elegans are influenced by different culture conditions in different laboratories.

Methods: In this work we have undertaken an inter-laboratory study, comparing the lipid profiles of N2 wild type C. elegans and daf-2(e1370) mutants lacking a functional insulin receptor. Sample were collected from worms grown in four separate laboratories under standardized growth conditions. We used an UPLC-UHR-ToF-MS system allowing chromatographic separation before MS analysis.

Results: We found common qualitative changes in several marker lipids in samples from the individual laboratories. On the other hand, even in this controlled experimental system, the exact fold-changes for each marker varied between laboratories.

Conclusion: Our results thus reveal a serious limitation to the reproducibility of current lipid profiling experiments and reveal challenges to the integration of such data from different laboratories.
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http://dx.doi.org/10.1007/s11306-021-01775-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7886748PMC
February 2021

UHPLC-IM-Q-ToFMS analysis of maradolipids, found exclusively in Caenorhabditis elegans dauer larvae.

Anal Bioanal Chem 2021 Mar 11;413(8):2091-2102. Epub 2021 Feb 11.

Faculty of Chemistry, Technische Universität Dresden, Bergstraße 66, 01069, Dresden, Germany.

Lipid identification is one of the current bottlenecks in lipidomics and lipid profiling, especially for novel lipid classes, and requires multidimensional data for correct annotation. We used the combination of chromatographic and ion mobility separation together with data-independent acquisition (DIA) of tandem mass spectrometric data for the analysis of lipids in the biomedical model organism Caenorhabditis elegans. C. elegans reacts to harsh environmental conditions by interrupting its normal life cycle and entering an alternative developmental stage called dauer stage. Dauer larvae show distinct changes in metabolism and morphology to survive unfavorable environmental conditions and are able to survive for a long time without feeding. Only at this developmental stage, dauer larvae produce a specific class of glycolipids called maradolipids. We performed an analysis of maradolipids using ultrahigh performance liquid chromatography-ion mobility spectrometry-quadrupole-time of flight-mass spectrometry (UHPLC-IM-Q-ToFMS) using drift tube ion mobility to showcase how the integration of retention times, collisional cross sections, and DIA fragmentation data can be used for lipid identification. The obtained results show that combination of UHPLC and IM separation together with DIA represents a valuable tool for initial lipid identification. Using this analytical tool, a total of 45 marado- and lysomaradolipids have been putatively identified and 10 confirmed by authentic standards directly from C. elegans dauer larvae lipid extracts without the further need for further purification of glycolipids. Furthermore, we putatively identified two isomers of a lysomaradolipid not known so far.
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http://dx.doi.org/10.1007/s00216-021-03172-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7943524PMC
March 2021

IL-17 controls central nervous system autoimmunity through the intestinal microbiome.

Sci Immunol 2021 Feb;6(56)

Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.

Interleukin-17A- (IL-17A) and IL-17F-producing CD4 T helper cells (T17 cells) are implicated in the development of chronic inflammatory diseases, such as multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE). T17 cells also orchestrate leukocyte invasion of the central nervous system (CNS) and subsequent tissue damage. However, the role of IL-17A and IL-17F as effector cytokines is still confused with the encephalitogenic function of the cells that produce these cytokines, namely, T17 cells, fueling a long-standing debate in the neuroimmunology field. Here, we demonstrated that mice deficient for IL-17A/F lose their susceptibility to EAE, which correlated with an altered composition of their gut microbiota. However, loss of IL-17A/F in T cells did not diminish their encephalitogenic capacity. Reconstitution of a wild-type-like intestinal microbiota or reintroduction of IL-17A specifically into the gut epithelium of IL-17A/F-deficient mice reestablished their susceptibility to EAE. Thus, our data demonstrated that IL-17A and IL-17F are not encephalitogenic mediators but rather modulators of intestinal homeostasis that indirectly alter CNS-directed autoimmunity.
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http://dx.doi.org/10.1126/sciimmunol.aaz6563DOI Listing
February 2021

Reduced peroxisomal import triggers peroxisomal retrograde signaling.

Cell Rep 2021 Jan;34(3):108653

Faculty of Biology, Ludwig Maximilian University of Munich, 82152 Martinsried, Germany. Electronic address:

Maintaining organelle function in the face of stress is known to involve organelle-specific retrograde signaling. Using Caenorhabditis elegans, we present evidence of the existence of such retrograde signaling for peroxisomes, which we define as the peroxisomal retrograde signaling (PRS). Specifically, we show that peroxisomal import stress caused by knockdown of the peroxisomal matrix import receptor prx-5/PEX5 triggers NHR-49/peroxisome proliferator activated receptor alpha (PPARα)- and MDT-15/MED15-dependent upregulation of the peroxisomal Lon protease lonp-2/LONP2 and the peroxisomal catalase ctl-2/CAT. Using proteomic and transcriptomic analyses, we show that proteins involved in peroxisomal lipid metabolism and immunity are also upregulated upon prx-5(RNAi). While the PRS can be triggered by perturbation of peroxisomal β-oxidation, we also observed hallmarks of PRS activation upon infection with Pseudomonas aeruginosa. We propose that the PRS, in addition to a role in lipid metabolism homeostasis, may act as a surveillance mechanism to protect against pathogens.
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http://dx.doi.org/10.1016/j.celrep.2020.108653DOI Listing
January 2021

Emergency Department Asthma "Spacing Trials": Institutional Variability and Time Cost.

J Emerg Med 2020 Dec 7. Epub 2020 Dec 7.

Department of Emergency Medicine, University of Maryland School of Medicine, Baltimore, Maryland.

Background: Some admitting physicians request a medication-free interval ("spacing trial") in the emergency department (ED) to determine whether a patient with an acute exacerbation of asthma can be safely admitted to a hospital ward bed, where bronchodilators are only available every 4 h.

Objective: Our objectives were to estimate the frequency of ED spacing trials in different hospitals and their associated time cost.

Methods: This multicenter retrospective cohort study examined patients admitted for asthma from 2015 to 2018. We included all university records and a random sample of records from two community hospitals in the same urban area. Two team members abstracted data from each record using recommended methods, with group consensus to resolve differences. Proportion confidence intervals were calculated using normal binomial approximation. We calculated mean differences in ED stay associated with spacing trials, using multivariable linear regression to adjust for age, hospital type, history of intubation, initial pulse, initial respiratory rate, initial signs of distress.

Results: We collected data from 274 patients in the university hospital, and 71 and 70 cases from the community hospitals. An explicit spacing trial was noted in 52 of 274 (19%) university hospital records vs. 3 of 141 (2%) community hospital records, with a difference of 17% (95% confidence interval [CI] 11-23%). Delayed patient decompensation occurred in 3%, with no difference between hospitals. Spacing trials were associated with an adjusted mean of 159 min (95% CI 102-217 min) increase in ED stay.

Conclusions: The practice of spacing varies widely between hospitals and is associated with substantial delay without an apparent benefit.
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http://dx.doi.org/10.1016/j.jemermed.2020.10.036DOI Listing
December 2020

Clinically relevant adverse cardiovascular events in intermediate heart score patients admitted to the hospital following a negative emergency department evaluation.

Am J Emerg Med 2020 Nov 3. Epub 2020 Nov 3.

University of Maryland School of Medicine, Department of Emergency Medicine, United States of America.

Study Hypothesis: Study objective: To estimate the frequency of clinically relevant adverse cardiac events (CRACE) in patients admitted to the hospital for chest pain with an intermediate HEART score (4, 5, 6), non-diagnostic EKG, and a negative initial troponin.

Methods: We conducted a retrospective analysis of all patients admitted to the University of Maryland Medical Center (UMMC) from May 2016 to May 2019 with an intermediate HEART score (4, 5, or 6), a non-diagnostic EKG, and a negative initial troponin. Our primary outcome was the rate of inpatient clinically relevant adverse cardiac events (CRACE), composite of life-threatening dysrhythmia, inpatient STEMI, cardiac or respiratory arrest, and all-cause mortality during hospitalization.

Results: A total of 1118 patients met our inclusion criteria, 6 of whom had CRACE. Overall the rate of CRACE was 0.5% (95% CI, 0.2-1.2%). Six patients (0.5%, 95% CI, 0.2%-1.2%) experienced inpatient NSTEMIs, 212 patients (19%, 95% CI, 17-21%) underwent provocative testing during their inpatient stay, 5 patients received a stent or CABG, and 5 patients had false positive non-invasive testing and underwent a negative cardiac catheterization.

Conclusions: In this cohort of admitted patients with a documented intermediate-risk HEART score, nonischemic EKG, and negative initial troponin, the occurrence of CRACE during the index hospitalization was 0.5%.
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http://dx.doi.org/10.1016/j.ajem.2020.10.065DOI Listing
November 2020

Feature-based molecular networking in the GNPS analysis environment.

Nat Methods 2020 09 24;17(9):905-908. Epub 2020 Aug 24.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.

Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.
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http://dx.doi.org/10.1038/s41592-020-0933-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7885687PMC
September 2020

Comprehensive Vitamer Profiling of Folate Mono- and Polyglutamates in Baker's Yeast () as a Function of Different Sample Preparation Procedures.

Metabolites 2020 Jul 23;10(8). Epub 2020 Jul 23.

Chair of Analytical Food Chemistry, Technical University of Munich, 85354 Freising-Weihenstephan, Germany.

Folates are a group of B vitamins playing an important role in many metabolic processes such as methylation reactions, nucleotide synthesis or oxidation and reduction processes. However, humans are not able to synthesize folates de novo and thus rely on external sources thereof. Baker's yeast () has been shown to produce high amounts of this vitamin but extensive identification of its folate metabolism is still lacking. Therefore, we optimized and compared different sample preparation and purification procedures applying solid phase extraction (SPE). Strong anion exchange (SAX), C18 and hydrophilic-lipophilic-balanced (HLB) materials were tested for their applicability in future metabolomics studies. SAX turned out to be the preferred material for the quantitative purification of folates. Qualification of several folate vitamers was achieved by ultra-high pressure liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-Q-ToF-MS) measurements and quantification was performed by liquid chromatography tandem mass spectrometry (LC-MS/MS) applying stable isotope dilution assays (SIDAs). The oxidation product -pyrazino-triazine (MeFox) was included into the SIDA method for total folate determination and validation. Applying the best protocol (SAX) in regard to folate recovery, we analyzed 32 different vitamers in different polyglutamate states up to nonaglutamates, of which we could further identify 26 vitamers based on tandem-MS (MS) spectra. Total folate quantification revealed differences in formyl folate contents depending on the cartridge chemistry used for purification. These are supposedly a result of interconversion reactions occurring during sample preparation due to variation in pH adjustments for the different purification protocols. The occurrence of interconversion and oxidation reactions should be taken into consideration in sample preparation procedures for metabolomics analyses with a focus on folates.
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http://dx.doi.org/10.3390/metabo10080301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464241PMC
July 2020

Metabolomic adjustments in the orchid mycorrhizal fungus Tulasnella calospora during symbiosis with Serapias vomeracea.

New Phytol 2020 12 13;228(6):1939-1952. Epub 2020 Aug 13.

Institute for Sustainable Plant Protection, National Research Council, Viale Mattioli 25, Torino, 10125, Italy.

All orchids rely on mycorrhizal fungi for organic carbon, at least during early development. In fact, orchid seed germination leads to the formation of a protocorm, a heterotrophic postembryonic structure colonized by intracellular fungal coils, thought to be the site of nutrient transfer. The molecular mechanisms underlying mycorrhizal interactions and metabolic changes induced by this symbiosis in both partners remain mostly unknown. We studied plant-fungus interactions in the mycorrhizal association between the Mediterranean orchid Serapias vomeracea and the basidiomycete Tulasnella calospora using nontargeted metabolomics. Plant and fungal metabolomes obtained from symbiotic structures were compared with those obtained under asymbiotic conditions. Symbiosis induced substantial metabolomic alterations in both partners. In particular, structural and signaling lipid compounds increased markedly in the external fungal mycelium growing near the symbiotic protocorms, whereas chito-oligosaccharides were identified uniquely in symbiotic protocorms. This work represents the first description of metabolic changes occurring in orchid mycorrhiza. These results - combined with previous transcriptomic data - provide novel insights on the mechanisms underlying the orchid mycorrhizal association and open intriguing questions on the role of fungal lipids in this symbiosis.
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http://dx.doi.org/10.1111/nph.16812DOI Listing
December 2020

Transesophageal Echocardiography Training of Emergency Physicians Through an E-Learning System.

J Emerg Med 2020 Jun 30;58(6):947-952. Epub 2020 Apr 30.

Department of Emergency Medicine, University of Maryland School of Medicine, Baltimore, Maryland.

Background: Transesophageal echocardiography (TEE) has been shown to be a powerful tool that emergency physicians can use to guide resuscitation efforts during cardiac arrest. Currently, there is no standardized curriculum to teach TEE to emergency physicians.

Objective: We hypothesized that the use of a pilot training course combining interactive e-learning and hands-on simulation would increase the percentage of students achieving a score of ≥80% on a multiple-choice test of knowledge and increase self-reported comfort using TEE.

Methods: We designed a 2.5-h TEE course for emergency physicians and medical intensive care unit fellows. Participants took a test of knowledge and a survey of comfort-both online-before, just after, and 4 weeks after taking the course. Survey responses measured participants self-reported comfort with using TEE in clinical practice. A normal binomial approximation was used to calculate the 95% confidence interval.

Results: Of the 3 tests of knowledge, 15 participants completed all tests. Of the surveys of comfort, 31 participants completed the precourse survey, 32 completed the postcourse survey, and 19 completed the 4-week follow-up survey. The proportion of students scoring ≥80% improved from 40% on the precourse test to 80% on the postcourse test (95% confidence interval 1-79). The proportion of students indicating comfort with using TEE improved from 3% precourse to 53% postcourse (95% confidence interval 28-71).

Conclusions: A TEE training course resulted in a 50% increase in surveyed participants feeling comfortable using TEE in cardiac arrest and a 40% increase in participants scoring ≥80% on a test of knowledge.
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http://dx.doi.org/10.1016/j.jemermed.2020.03.036DOI Listing
June 2020

Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Model.

Authors:
Michael Witting

Metabolites 2020 Mar 28;10(4). Epub 2020 Mar 28.

Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.

Genome scale metabolic models (GSMs) are a representation of the current knowledge on the metabolism of a given organism or superorganism. They group metabolites, genes, enzymes and reactions together to form a mathematical model and representation that can be used to analyze metabolic networks in silico or used for analysis of omics data. Beside correct mass and charge balance, correct structural annotation of metabolites represents an important factor for analysis of these metabolic networks. However, several metabolites in different GSMs have no or only partial structural information associated with them. Here, a new systematic nomenclature for acyl-based metabolites such as fatty acids, acyl-carnitines, acyl-coenzymes A or acyl-carrier proteins is presented. This nomenclature enables one to encode structural details in the metabolite identifiers and improves human readability of reactions. As proof of principle, it was applied to the fatty acid biosynthesis and degradation in the consensus model WormJam.
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http://dx.doi.org/10.3390/metabo10040130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241080PMC
March 2020

Evaluation of Spodick's Sign and Other Electrocardiographic Findings as Indicators of STEMI and Pericarditis.

J Emerg Med 2020 Apr 25;58(4):562-569. Epub 2020 Mar 25.

Department of Emergency Medicine, University of Maryland School of Medicine, Baltimore, Maryland.

Background: Patients with ST elevation on electrocardiogram (ECG) could have ST elevation myocardial infarction (STEMI) or pericarditis. Spodick's sign, a downsloping of the ECG baseline (the T-P segment), has been described, but not validated, as a sign of pericarditis.

Objective: This study estimates the frequency of Spodick's sign and other findings in patients diagnosed with STEMI and those with pericarditis.

Methods: In this retrospective review, we selected charts that met prospective definitions of STEMI (cases) and pericarditis (controls). We excluded patients whose ECGs lacked ST elevation. An authority on electrocardiography reviewed all ECGs, noting the presence or absence of Spodick's sign, ST depression (in leads besides V and aVR), PR depression, greater ST elevation in lead III than in lead II (III > II), abrupt take-off of ST segment (the RT checkmark sign), and upward or horizontal ST convexity. We quantified strength of association using odds ratio (OR) with 95% confidence interval (CI).

Results: One hundred and sixty-five patients met criteria for STEMI and 42 met those for pericarditis. Spodick's sign occurred in 5% of patients with STEMI (95% CI 3-10%) and 29% of patients with pericarditis (95% CI 16-45%). All other findings statistically distinguished STEMI from pericarditis, but ST depression (OR 31), III > II (OR 21), and absence of PR depression (OR 12) had the greatest OR values.

Conclusions: Spodick's sign is statistically associated with pericarditis, but it is seen in 5% of patients with STEMI. Among other findings, ST depression, III > II, and absence of PR depression were the most discriminating.
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http://dx.doi.org/10.1016/j.jemermed.2020.01.017DOI Listing
April 2020

Autophagy compensates for defects in mitochondrial dynamics.

PLoS Genet 2020 03 19;16(3):e1008638. Epub 2020 Mar 19.

Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany.

Compromising mitochondrial fusion or fission disrupts cellular homeostasis; however, the underlying mechanism(s) are not fully understood. The loss of C. elegans fzo-1MFN results in mitochondrial fragmentation, decreased mitochondrial membrane potential and the induction of the mitochondrial unfolded protein response (UPRmt). We performed a genome-wide RNAi screen for genes that when knocked-down suppress fzo-1MFN(lf)-induced UPRmt. Of the 299 genes identified, 143 encode negative regulators of autophagy, many of which have previously not been implicated in this cellular quality control mechanism. We present evidence that increased autophagic flux suppresses fzo-1MFN(lf)-induced UPRmt by increasing mitochondrial membrane potential rather than restoring mitochondrial morphology. Furthermore, we demonstrate that increased autophagic flux also suppresses UPRmt induction in response to a block in mitochondrial fission, but not in response to the loss of spg-7AFG3L2, which encodes a mitochondrial metalloprotease. Finally, we found that blocking mitochondrial fusion or fission leads to increased levels of certain types of triacylglycerols and that this is at least partially reverted by the induction of autophagy. We propose that the breakdown of these triacylglycerols through autophagy leads to elevated metabolic activity, thereby increasing mitochondrial membrane potential and restoring mitochondrial and cellular homeostasis.
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http://dx.doi.org/10.1371/journal.pgen.1008638DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7135339PMC
March 2020

Current status of retention time prediction in metabolite identification.

J Sep Sci 2020 May 6;43(9-10):1746-1754. Epub 2020 Apr 6.

Chair of Bioinformatics, Friedrich-Schiller-Universität Jena, Jena, Germany.

Metabolite identification is a crucial step in nontargeted metabolomics, but also represents one of its current bottlenecks. Accurate identifications are required for correct biological interpretation. To date, annotation and identification are usually based on the use of accurate mass search or tandem mass spectrometry analysis, but neglect orthogonal information such as retention times obtained by chromatographic separation. While several tools are available for the analysis and prediction of tandem mass spectrometry data, prediction of retention times for metabolite identification are not widespread. Here, we review the current state of retention time prediction in liquid chromatography-mass spectrometry-based metabolomics, with a focus on publications published after 2010.
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http://dx.doi.org/10.1002/jssc.202000060DOI Listing
May 2020

iTAG-RNA Isolates Cell-Specific Transcriptional Responses to Environmental Stimuli and Identifies an RNA-Based Endocrine Axis.

Cell Rep 2020 03;30(9):3183-3194.e4

Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany. Electronic address:

Biofluids contain various circulating cell-free RNAs (ccfRNAs). The composition of these ccfRNAs varies among biofluids. They constitute tantalizing biomarker candidates for several pathologies and have been demonstrated to be mediators of cellular communication. Little is known about their function in physiological and developmental settings, and most works are limited to in vitro studies. Here, we develop iTAG-RNA, a method for the unbiased tagging of RNA transcripts in mice in vivo. We use iTAG-RNA to isolate hepatocytes and kidney proximal epithelial cell-specific transcriptional responses to a dietary challenge without interfering with the tissue architecture and to identify multiple hepatocyte-secreted ccfRNAs in plasma. We also identify specific transfer of liver-derived ccfRNAs to adipose tissue and skeletal muscle, where they likely constitute a buffering system to maintain lipid homeostasis under acute high-fat-diet feeding. Our findings directly demonstrate in vivo transfer of RNAs between tissues and highlight its implications for endocrine signaling and homeostasis.
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http://dx.doi.org/10.1016/j.celrep.2020.02.020DOI Listing
March 2020

Using Genome-Scale Metabolic Networks for Analysis, Visualization, and Integration of Targeted Metabolomics Data.

Methods Mol Biol 2020 ;2104:361-386

Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany.

Interpretation of metabolomics data in the context of biological pathways is important to gain knowledge about underlying metabolic processes. In this chapter we present methods to analyze genome-scale models (GSMs) and metabolomics data together. This includes reading and mining of GSMs using the SBTab format to retrieve information on genes, reactions, and metabolites. Furthermore, the chapter showcases the generation of metabolic pathway maps using the Escher tool, which can be used for data visualization. Lastly, approaches to constrain flux balance analysis (FBA) by metabolomics data are presented.
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http://dx.doi.org/10.1007/978-1-0716-0239-3_18DOI Listing
January 2021

The metaRbolomics Toolbox in Bioconductor and beyond.

Metabolites 2019 Sep 23;9(10). Epub 2019 Sep 23.

Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.

Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub.
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http://dx.doi.org/10.3390/metabo9100200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6835268PMC
September 2019

Predicting Failure of Intravenous Access in Adults: The Value of Prior Difficulty.

J Emerg Med 2019 Jul 25;57(1):1-5. Epub 2019 Apr 25.

Department of Emergency Medicine, University of Maryland School of Medicine, Baltimore, Maryland.

Background: When intravenous access cannot be established using traditional methods of inspection/palpation, advanced methods are often required, leading to substantial delays in care. Knowing the likelihood of intravenous access failure can improve emergency department (ED) efficiency.

Objective: Our aim was to validate prior need for an advanced technique to establish intravenous access as a predictor of failure to achieve access via traditional methods and to estimate the risk difference associated with this finding.

Methods: We re-analyzed data collected for a clinical trial that randomized ED patients requiring intravenous access to one of two types of intravenous catheter; gauge size was selected by the inserter. The re-analysis pools data from both groups to examine predictors of failure to establish intravenous access by traditional methods, with failure defined as abandonment or use of an advanced technique (ultrasound guidance or external jugular vein catheterization). Confidence intervals for the difference between proportions were calculated using a normal binomial approximation.

Results: We obtained data from 600 patients, with a median age of 52 years (interquartile range 36-63 years). We noted failure of traditional methods in 28 (4.7%) patients, including 17 of 109 (16%) with prior need for advanced techniques. The risk difference for prior need for advanced techniques versus no prior difficulty was 14% (95% confidence interval 7-22).

Conclusions: Patients with a prior need for advanced techniques were 14% more likely to have failure of intravenous access by traditional methods than those without prior difficulty.
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http://dx.doi.org/10.1016/j.jemermed.2019.02.011DOI Listing
July 2019

The sphingolipidome of the model organism Caenorhabditis elegans.

Chem Phys Lipids 2019 08 24;222:15-22. Epub 2019 Apr 24.

Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85674 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technische Universität München, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany. Electronic address:

Sphingolipids are important lipids and integral members of membranes, where they form small microdomains called lipid rafts. These rafts are enriched in cholesterol and sphingolipids, which influences biophysical properties. Interestingly, the membranes of the biomedical model organism Caenorhabditis elegans contain only low amounts of cholesterol. Sphingolipids in C. elegans are based on an unusual C17iso branched sphingoid base. In order to analyze and the sphingolipidome of C. elegans in more detail, we performed fractionation of lipid extracts and depletion of glycero- and glycerophospholipids together with in-depth analysis using UPLC-UHR-ToF-MS. In total we were able to detect 82 different sphingolipids from different classes, including several isomeric species.
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http://dx.doi.org/10.1016/j.chemphyslip.2019.04.009DOI Listing
August 2019

Development and application of a HILIC UHPLC-MS method for polar fecal metabolome profiling.

J Chromatogr B Analyt Technol Biomed Life Sci 2019 Mar 4;1109:142-148. Epub 2019 Feb 4.

Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University of Munich, Freising, Germany. Electronic address:

The fecal metabolome is a complex mixture of endogenous, microbial metabolites, and food derived compounds. Hydrophilic interaction liquid chromatography (HILIC) enables the analysis of polar compounds, which is a valuable alternative to reversed-phase liquid chromatography in the field of metabolomics due to its ability to retain a greater portion of the polar metabolome. The objective of the study was to find the optimal chromatographic solution to perform non-targeted metabolomics of feces by means of HILIC ultra-high-pressure liquid chromatography mass spectrometry (UHPLC-Q-TOF-MS). The performance was systematically investigated analyzing a pooled fecal sample, and mixtures of 150 metabolites from different families, including for example amino acids, amines, indole derivatives, fatty acids and carbohydrates. Three different stationary phases (zwitterionic, amide and unbonded silica) were operated at three pH values (4.6, 6.8 and 9.0), and three salt gradient conditions (5-5, 5-10 and 5-25 mM ammonium acetate). Amide and zwitterionic stationary phases performed similarly at low pH, with highest number of detected standards, which increased by increasing the salt gradient. The amide column showed slightly better performance in terms of separation of isomers and peak widths and remarkably good performance at basic pH, with highest number of metabolite features in the non-targeted analysis. The zwitterionic column operated best in terms of number of detected standards, retention time distribution of standards and metabolite feature across whole chromatographic run. Thus, the zwitterionic column was proven to suit for non-targeted analysis of fecal samples, resulting in good coverage of especially amino acids and carbohydrates.
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http://dx.doi.org/10.1016/j.jchromb.2019.01.016DOI Listing
March 2019

Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism .

Front Mol Biosci 2018 14;5:96. Epub 2018 Nov 14.

Epigenetics Department, Babraham Institute, Cambridge, United Kingdom.

Metabolism is one of the attributes of life and supplies energy and building blocks to organisms. Therefore, understanding metabolism is crucial for the understanding of complex biological phenomena. Despite having been in the focus of research for centuries, our picture of metabolism is still incomplete. Metabolomics, the systematic analysis of all small molecules in a biological system, aims to close this gap. In order to facilitate such investigations a blueprint of the metabolic network is required. Recently, several metabolic network reconstructions for the model organism have been published, each having unique features. We have established the WormJam Community to merge and reconcile these (and other unpublished models) into a single consensus metabolic reconstruction. In a series of workshops and annotation seminars this model was refined with manual correction of incorrect assignments, metabolite structure and identifier curation as well as addition of new pathways. The WormJam consensus metabolic reconstruction represents a rich data source not only for network-based approaches like flux balance analysis, but also for metabolomics, as it includes a database of metabolites present in , which can be used for annotation. Here we present the process of model merging, correction and curation and give a detailed overview of the model. In the future it is intended to expand the model toward different tissues and put special emphasizes on lipid metabolism and secondary metabolism including ascaroside metabolism in accordance to their central role in physiology.
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http://dx.doi.org/10.3389/fmolb.2018.00096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6246695PMC
November 2018

Pharmacometabolic response to pirfenidone in pulmonary fibrosis detected by MALDI-FTICR-MSI.

Eur Respir J 2018 09 15;52(3). Epub 2018 Sep 15.

Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.

Idiopathic pulmonary fibrosis (IPF) is a fatal condition that reduces life expectancy and shows a limited response to available therapies. Pirfenidone has been approved for treatment of IPF, but little is known about the distinct metabolic changes that occur in the lung upon pirfenidone administration.Here, we performed a proof-of-concept study using high-resolution quantitative matrix-assisted laser desorption/ionisation Fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FTICR-MSI) to simultaneously detect, visualise and quantify endogenous and exogenous metabolites in lungs of mice subjected to experimental fibrosis and human patients with IPF, and to assess the effect of pirfenidone treatment on metabolite levels.Metabolic pathway analysis and endogenous metabolite quantification revealed that pirfenidone treatment restores redox imbalance and glycolysis in IPF tissues, and downregulates ascorbate and aldarate metabolism, thereby likely contributing to modulation of collagen processing. As such, we detected specific alterations in metabolite pathways in fibrosis and, importantly, metabolic recalibration following pirfenidone treatment.Together, these results highlight the suitability of high-resolution MALDI-FTICR-MSI for deciphering the therapeutic effects of pirfenidone and provide a preliminary analysis of the metabolic changes that occur during pirfenidone treatment These data may therefore contribute to improvement of currently available therapies for IPF.
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http://dx.doi.org/10.1183/13993003.02314-2017DOI Listing
September 2018

Metabotype variation in a field population of tansy plants influences aphid host selection.

Plant Cell Environ 2018 12 17;41(12):2791-2805. Epub 2018 Aug 17.

Helmholtz Zentrum München, Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation (EUS), Neuherberg, Germany.

It is well known that plant volatiles influence herbivores in their selection of a host plant; however, less is known about how the nonvolatile metabolome affects herbivore host selection. Metabolic diversity between intraspecific plants can be characterized using non-targeted mass spectrometry that gives us a snapshot overview of all metabolic processes occurring within a plant at a particular time. Here, we show that non-targeted metabolomics can be used to reveal links between intraspecific chemical diversity and ecological processes in tansy (Tanacetum vulgare). First, we show that tansy plants can be categorized into five subgroups based up on their metabolic profiles, and that these "metabotypes" influenced natural aphid colonization in the field. Second, this grouping was not due to induced metabolomic changes within the plant due to aphid feeding but rather resulted from constitutive differences in chemical diversity between plants. These findings highlight the importance of intraspecific chemical diversity within one plant population and provide the first report of a non-targeted metabolomic field study in chemical ecology.
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http://dx.doi.org/10.1111/pce.13407DOI Listing
December 2018

Prospective, randomized controlled comparison of a flash-tip catheter and a traditional intravenous catheter in an urban emergency department.

J Vasc Access 2018 Jul 5;19(4):387-391. Epub 2018 Mar 5.

1 Department of Emergency Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.

Introduction: Safe and efficient intravenous access is paramount to the practice of emergency medicine. We compared the first-stick success rates and blood spillage of two peripheral intravenous catheters in a busy urban emergency department.

Methods: In this randomized controlled trial, we assigned emergency department patients requiring peripheral intravenous access to use of either a flash-tip catheter (SurFlash Plus, Terumo Medical Corporation, Somerset, New Jersey) or a widely used control catheter (Insyte Autoguard; Becton, Dickinson and Company, Franklin Lakes, New Jersey). We compared frequency of first-stick success and blood contamination between catheters using chi-squared analysis.

Results: We enrolled 600 patients, randomizing 309 to the flash-tip catheter and 291 to the control catheter. The first-stick success rate of each device was 79%. Blood contamination, defined as spillage of blood on the patient's skin, bedding, or the inserter, occurred in 8 of 309 cases (2.6%) with the flash-tip catheter versus 92 of 291 cases (31.6%) for the control catheter.

Conclusion: The two catheters tested in this study had comparable rates of first-stick success, but the flash-tip catheter was associated with significantly less blood contamination during insertion attempts.
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http://dx.doi.org/10.1177/1129729817747530DOI Listing
July 2018

Effectiveness of a Rural Emergency Department (ED)-Based Pain Contract on ED Visits Among ED Frequent Users.

J Emerg Med 2018 09 29;55(3):327-332.e1. Epub 2018 May 29.

Department of Emergency Medicine, University of Maryland, Baltimore, Maryland.

Background: Caring for patients with chronic pain in emergency departments (EDs) can be particularly challenging, for both patients and physicians.

Objective: This study sought to determine, in a rural setting, the effect of an ED-based pain contract on the rate of ED visits among patients with frequent visits for pain not related to cancer.

Methods: This is a multi-ED, retrospective, before-and-after chart review assessing the effect of a rural ED-based pain contract on the frequency of ED visits. The study setting consisted of four rural EDs representing over 85,000 annual visits. Medical records of patients eligible for a standardized pain contract during a 10-year period (December 2005-December 2015) were reviewed. Only visits involving complaints of pain were included. The number of visits during the year prior to contract initiation was compared with the number of visits during the year after enrollment, using a paired t-test.

Results: We enrolled 314 patients, 185 (59%) of whom were female. The study group's median age was 48 years. The mean number of ED visits was 12.4 visits (95% confidence interval [CI] 11.5-13.3) 1 year prior to the pain contract and 6.5 (95% CI 5.6-7.3) 1 year afterward (p < 0.0001). The mean number of ED visits decreased by 6.0 (95% CI 5.0-7.2).

Conclusion: A pain contract protocol was associated with a significant reduction in the number of ED visits to multiple rural EDs.
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http://dx.doi.org/10.1016/j.jemermed.2018.04.056DOI Listing
September 2018

No Radiographic Safe Margin Found in the "Easy IJ" Internal Jugular Vein Procedure.

J Emerg Med 2018 07;55(1):29-33

Department of Emergency Medicine, University of Maryland School of Medicine, Baltimore, Maryland.

Background: The Easy IJ procedure involves placement of a 4.8-cm intravenous catheter into the internal jugular (IJ) vein using ultrasound guidance. It is not known whether this needle length has the potential to cause a pneumothorax.

Objective: The objective of this study was to determine if a radiographic "safe margin" exists. We hypothesized that an average margin of ≥2 cm would exist between the catheter tip and the pleura.

Methods: Operators used a central approach to the IJ vein. We reviewed radiographic images taken immediately after the Easy IJ procedure. Using digital software, we measured the distance from the catheter tip to the closest point of the pleura and from the catheter tip to the level of the lung apex. We defined distances exceeding the margin of safety-either passing the pleura or ending inferior to the apex-as negative for the purpose of calculating an average. We used the t distribution to calculate 95% confidence intervals (CIs) for average values.

Results: Radiographs showing the catheter tip were available from 62 patients. The mean needle-to-pleura distance was -0.1 cm (95% CI -0.7 to 0.5 cm). The mean vertical distance to the apex was -0.2 cm (95% CI -0.8 to 0.3 cm), with a standard deviation of 2.25 cm.

Conclusion: Radiographic analysis failed to show a margin of safety for the Easy IJ procedure. Postprocedure imaging may still be necessary to exclude pneumothorax.
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http://dx.doi.org/10.1016/j.jemermed.2018.04.011DOI Listing
July 2018

Bio- and Chemoinformatics Approaches for Metabolomics Data Analysis.

Authors:
Michael Witting

Methods Mol Biol 2018 ;1738:41-61

Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.

Metabolomics data analysis includes several repetitive tasks, including data sorting, calculation of exact masses or other physicochemical properties, or searching for identifiers in different databases. Several of these tasks can be automated using command line tools or short scripts in different scripting languages like Perl, Python, or R. This chapter presents simple solutions and short scripts written in R that can be used for the interaction with specific web services or for the calculation of physicochemical properties or molecular formulae.
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http://dx.doi.org/10.1007/978-1-4939-7643-0_4DOI Listing
January 2019

Tandem HILIC-RP liquid chromatography for increased polarity coverage in food analysis.

Electrophoresis 2018 07 24;39(13):1645-1653. Epub 2018 Apr 24.

Chair of Analytical Food Chemistry, Technische Universität München, Freising, Germany.

Comprehensive non-targeted analysis of food products normally requires two complementary chromatographic runs to achieve maximum compound coverage. In this study, we present a sensitive tandem-LC method, which combines RP and HILIC separation in a single run. The setup consists of a C18 trap column and two subsequently coupled analytical columns (HILIC and C18) which are operated in parallel. First, hydrophobic compounds are retained on the RP trap column while rather hydrophilic compounds are directly transferred onto a HILIC phase. Next, the pre-fractionated sample composition is analyzed by HILIC or RP chromatography, respectively. The presented setup allows individual and independent gradient elution as well as interfacing with mass spectrometry. The performance of the method has been proven by means of food relevant standards and analysis of complex food samples (e.g. red wine, meat extract). The simple and robust setup provides high flexibility in the selection of column combinations and does not require sophisticated instrumental setups or software. The method significantly increases the covered polarity range compared to classical one-dimensional chromatography. Our results indicate that tandem LC is a valuable and universal tool in the non-targeted screening of various types of complex food samples.
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http://dx.doi.org/10.1002/elps.201800038DOI Listing
July 2018