MOTIVATION: Many diseases, such as cancer, are characterized by an alteration of cellular metabolism allowing cells to adapt to changes in the microenvironment. Stable isotope-resolved metabolomics (SIRM) and downstream data analyses are widely used techniques for unraveling cells' metabolic activity to understand the altered functioning of metabolic pathways in the diseased state. While a number of bioinformatic solutions exist for the differential analysis of SIRM data, there is currently no available resource providing a comprehensive toolbox. RESULTS: In this work, we present DIMet, a one-stop comprehensive tool for differential analysis of targeted tracer data. DIMet accepts metabolite total abundances, isotopologue contributions, and isotopic mean enrichment, and supports differential comparison (pairwise and multi-group), time-series analyses, and labeling profile comparison. Moreover, it integrates transcriptomics and targeted metabolomics data through network-based metabolograms. We illustrate the use of DIMet in real SIRM datasets obtained from Glioblastoma P3 cell-line samples. DIMet is open-source, and is readily available for routine downstream analysis of isotope-labeled targeted metabolomics data, as it can be used both in the command line interface or as a complete toolkit in the public Galaxy Europe and Workfow4Metabolomics web platforms. AVAILABILITY AND IMPLEMENTATION: DIMet is freely available at https://github.com/cbib/DIMet, and through https://usegalaxy.eu and https://workflow4metabolomics.usegalaxy.fr. All the datasets are available at Zenodo https://zenodo.org/records/10925786.
- MeSH
- glioblastom metabolismus MeSH
- izotopové značení * metody MeSH
- lidé MeSH
- metabolomika * metody MeSH
- nádorové buněčné linie MeSH
- software * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Ticks (Family Ixodidae) spend most of their life cycle as immature stages in the soil and litter, and as any other soil invertebrates, are likely to be controlled top-down by soil-dwelling predators. To date, the ability of soil invertebrate predators to control ixodid tick population remains little known, partly due to methodological difficulties. In the current study, we developed and successfully tested a novel method of labeling live Ixodes ricinus (L., 1758) (Ixodida: Ixodidae) nymphs with a 15N isotope label. Labeled ticks were used in a small-scale 8-day-long microcosm experiment to reveal soil predators attacking nymphs. Only a small fraction (4.1% of all samples) of soil generalist predators preyed upon nymphs. A strong 15N label was found in 5 predator species, namely 2 spiders (Pachygnatha listeri Sundevall, 1830, Tetragnathidae and Ozyptila sp., Theridiidae), 2 gamasid mites (Pergamasus beklemischevi Sellnick, 1929 and Pergamasus quisquiliarum [Canestrini, 1882], Parasitidae), and 1 staphylinid beetle (Geostiba circellaris [Gravenhorst, 1806], Staphylinidae). The isotopic labeling can be a useful tool in revealing a range of invertebrate predators that can control tick populations in soil.
- Klíčová slova
- Ixodes ricinus, laboratory experiment, natural enemies, soil food webs, tick ecology,
- MeSH
- brouci * MeSH
- Ixodidae * MeSH
- izotopové značení MeSH
- klíště * MeSH
- nymfa MeSH
- půda MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- půda MeSH
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of 13C, 18O, or 15N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.
- Klíčová slova
- DNA, Metagenomics, Metatranscriptomics, Protein, Proteomics, RNA, Stable-isotope probing,
- MeSH
- biologické markery MeSH
- DNA * chemie MeSH
- izotopové značení metody MeSH
- izotopy uhlíku chemie MeSH
- messenger RNA MeSH
- proteiny * chemie MeSH
- RNA ribozomální 16S genetika chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- biologické markery MeSH
- DNA * MeSH
- izotopy uhlíku MeSH
- messenger RNA MeSH
- proteiny * MeSH
- RNA ribozomální 16S MeSH
Stable isotope labeling by amino acids in cell culture (SILAC) and iodoacetyl tandem mass tag (iodoTMT) are well-implemented mass spectrometry-based approaches for quantification of proteins and for site-mapping of cysteine modification. We describe here a combination of SILAC and iodoTMT to assess ongoing changes in the global proteome and cysteine modification levels using liquid chromatography separation coupled with high-resolution mass spectrometry (LC-MS/MS).
- Klíčová slova
- Cysteine, Global proteome, IodoTMT, Liquid chromatography, Mass spectrometry, Redox, SILAC,
- MeSH
- chromatografie kapalinová metody MeSH
- cystein metabolismus MeSH
- izotopové značení metody MeSH
- oxidace-redukce MeSH
- proteom * metabolismus MeSH
- proteomika * metody MeSH
- tandemová hmotnostní spektrometrie metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- cystein MeSH
- proteom * MeSH
Affinity purification, combined with mass spectrometry (AP-MS) is considered a pivotal technique in protein-protein interaction studies enabling systematic detection at near physiological conditions. The addition of a quantitative proteomic method, like SILAC metabolic labeling, allows the elimination of non-specifically bound contaminants which greatly increases the confidence of the identified interaction partners. Compared to eukaryotic cells, the SILAC labeling of bacteria has specificities that must be considered. The protocol presented here describes the labeling of bacterial cultures with stable isotope-labeled amino acids, purification of an affinity-tagged protein, and sample preparation for MS measurement. Finally, we discuss the analysis and interpretation of MS data to identify and select the specific partners interacting with the protein of interest. As an example, this workflow is applied to the discovery of potential interaction partners of glyceraldehyde-3-phosphate dehydrogenase in the gram-negative bacterium Francisella tularensis.
- Klíčová slova
- Affinity purification, Bacteria, LC-MS/MS, Protein-protein interactions, SILAC,
- MeSH
- Bacteria metabolismus MeSH
- chromatografie afinitní MeSH
- hmotnostní spektrometrie metody MeSH
- izotopové značení metody MeSH
- proteiny * chemie MeSH
- proteomika * metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- proteiny * MeSH
There is a need to better understand lipid metabolism during mosquito ovarian development. Lipids are the major source of energy supporting ovarian follicles development in mosquitoes. In this paper, we describe the complementary use of stable isotope labeling (SIL) and high-resolution mass spectrometry-based tools for the investigation of de novo triglycerides (TG) and diglycerides (DG) during the ovarian previtellogenic (PVG) stage (4-6 days posteclosion) of female adult Aedes aegypti. Liquid chromatography coupled to high-resolution trapped ion mobility spectrometry-parallel accumulation sequential fragmentation-time-of-flight tandem mass spectrometry (LC-TIMS-PASEF-TOF MS/MS) allowed the separation and quantification of nonlabeled and 2H/13C-labeled TG and DG species. Three SIL strategies were evaluated (H2O/2H2O with 50:50 and 95:5 mixtures, 13C-sucrose, and 13C-glucose). Results showed wide applicability with no signs of lipid ovarian impairment by SIL induced toxicity. The analytical workflow based on LC-TIMS-TOF MS/MS provided high confidence and high reproducibility for lipid DG and TG identification and SIL incorporation based on their separation by retention time (RT), collision cross section (CCS), and accurate m/z. In addition, the SIL fatty acid chain incorporation was evaluated using PASEF MS/MS. The 2H/13C incorporation into the mosquito diet provided information on how TG lipids are consumed, stored, and recycled during the PVG stage of ovarian development.
- MeSH
- chromatografie kapalinová MeSH
- Culicidae * MeSH
- diglyceridy analýza chemie MeSH
- iontová mobilní spektrometrie MeSH
- izotopové značení MeSH
- reprodukovatelnost výsledků MeSH
- tandemová hmotnostní spektrometrie * metody MeSH
- zvířata MeSH
- Check Tag
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- diglyceridy MeSH
There is inconsistent information regarding the size effects of exogenously given hyaluronan on its in vivo fate. The data are often biased by the poor quality of hyaluronan and non-ideal labelling strategies used for resolving exogenous/endogenous hyaluronan, which only monitor the label and not hyaluronan itself. To overcome these drawbacks and establish the pharmacokinetics of intravenous hyaluronan in relation to its Mw, 13C-labelled HA of five Mws from 13.6-1562 kDa was prepared and administered to mice at doses 25-50 mg kg-1. The elimination efficiency increased with decreasing Mw. Low Mw hyaluronan was rapidly eliminated as small hyaluronan fragments in urine, while high Mw hyaluronan exhibited saturable kinetics and complete metabolization within 48 h. All tested Mws exhibited a similar uptake by liver cells and metabolization into activated sugars. 13C-labelling combined with LC-MS provides an excellent approach to elucidating in vivo fate and biological activities of hyaluronan.
- Klíčová slova
- Hyaluronan, Metabolism, Molecular weight, Pharmacokinetics, Stable isotope,
- MeSH
- cesty eliminace léčiva MeSH
- chrupavka metabolismus MeSH
- cyklická ADP-ribosa metabolismus MeSH
- intravenózní podání MeSH
- izotopové značení metody MeSH
- izotopy uhlíku chemie metabolismus farmakokinetika MeSH
- kosti a kostní tkáň metabolismus MeSH
- kyselina hyaluronová chemie metabolismus farmakokinetika MeSH
- molekulová hmotnost MeSH
- myši inbrední BALB C MeSH
- myši MeSH
- tkáňová distribuce MeSH
- uridindifosfát-N-acetylglukosamin metabolismus MeSH
- uridindifosfátglukosa metabolismus MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- Carbon-13 MeSH Prohlížeč
- cyklická ADP-ribosa MeSH
- izotopy uhlíku MeSH
- kyselina hyaluronová MeSH
- uridindifosfát-N-acetylglukosamin MeSH
- uridindifosfátglukosa MeSH
A proper internal standard choice is critical for accurate, precise, and reproducible mass spectrometry-based proteomics assays. Synthetic isotopically labeled (SIL) proteins are currently considered the gold standard. However, they are costly and challenging to obtain. An alternative approach uses SIL peptides or SIL "winged" peptides extended at C- or/and N-terminus with an amino acid sequence or a tag cleaved during enzymatic proteolysis. However, a consensus on the design of a winged peptide for absolute quantification is missing. In this study, we used human serum albumin as a model system to compare the quantitative performance of reference SIL protein with four different designs of SIL winged peptides: (i) commercially available SIL peptides with a proprietary trypsin cleavable tag at C-terminus, (ii) SIL peptides extended with five amino acid residues at C-terminus, (iii) SIL peptides extended with three and (iv) with five amino acid residues at both C- and N-termini. Our results demonstrate properties of various SIL extended peptides designs, e.g., water solubility and efficiency of trypsin enzymatic cleavage with primary influence on quantitative performance. SIL winged peptides extended with three amino acids at both C- and N-termini demonstrated optimal quantitative performance, equivalent to the SIL protein.
- MeSH
- biotest metody normy MeSH
- izotopové značení MeSH
- kinetika MeSH
- konformace proteinů MeSH
- lidé MeSH
- peptidy chemická syntéza chemie MeSH
- proteiny analýza chemie MeSH
- proteolýza MeSH
- proteomika metody MeSH
- referenční standardy MeSH
- rozpouštědla MeSH
- rozpustnost MeSH
- sekvence aminokyselin MeSH
- trypsin metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- peptidy MeSH
- proteiny MeSH
- rozpouštědla MeSH
- trypsin MeSH
Present-day domestic cattle are reproductively active throughout the year, which is a major asset for dairy production. Large wild ungulates, in contrast, are seasonal breeders, as were the last historic representatives of the aurochs, the wild ancestors of cattle. Aseasonal reproduction in cattle is a consequence of domestication and herding, but exactly when this capacity developed in domestic cattle is still unknown and the extent to which early farming communities controlled the seasonality of reproduction is debated. Seasonal or aseasonal calving would have shaped the socio-economic practices of ancient farming societies differently, structuring the agropastoral calendar and determining milk availability where dairying is attested. In this study, we reconstruct the calving pattern through the analysis of stable oxygen isotope ratios of cattle tooth enamel from 18 sites across Europe, dating from the 6th mill. cal BC (Early Neolithic) in the Balkans to the 4th mill. cal BC (Middle Neolithic) in Western Europe. Seasonal calving prevailed in Europe between the 6th and 4th millennia cal BC. These results suggest that cattle agropastoral systems in Neolithic Europe were strongly constrained by environmental factors, in particular forage resources. The ensuing fluctuations in milk availability would account for cheese-making, transforming a seasonal milk supply into a storable product.
- MeSH
- chov zvířat dějiny MeSH
- dějiny středověku MeSH
- domestikace MeSH
- izotopové značení MeSH
- kyslík analýza chemie MeSH
- mlékárenství MeSH
- mléko metabolismus MeSH
- roční období MeSH
- skot MeSH
- zuby chemie MeSH
- zvířata MeSH
- Check Tag
- dějiny středověku MeSH
- skot MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- historické články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Balkánský poloostrov MeSH
- Názvy látek
- kyslík MeSH
RATIONALE: Tracing isotopically labeled water into proteins allows for the detection of species-specific metabolic activity in complex communities. However, a stress response may alter the newly synthesized proteins. METHODS: We traced 18-oxygen from heavy water into proteins of Escherichia coli K12 grown from permissive to retardant temperatures. All samples were analyzed using UPLC/Orbitrap Q-Exactive-MS/MS operating in positive electrospray ionization mode. RESULTS: We found that warmer temperatures resulted in significantly (P-value < 0.05) higher incorporation of 18-oxygen as seen by both substrate utilization as relative isotope abundance (RIA) and growth as labeling ratio (LR). However, the absolute number of peptides with incorporation of 18-oxygen showed no significant correlation to temperature, potentially caused by the synthesis of different proteins at low temperatures, namely, proteins related to cold stress response. CONCLUSIONS: Our results unveil the species-specific cold stress response of E. coli K12 that could be misinterpreted as general growth; this is why the quantity as RIA and LR but also the quality as absolute number of peptides with incorporation (relative abundance, RA) and their function must be considered to fully understand the activity of microbial communities.
- MeSH
- Escherichia coli K12 * chemie metabolismus fyziologie MeSH
- izotopové značení metody MeSH
- izotopy kyslíku * analýza metabolismus MeSH
- nízká teplota MeSH
- proteiny z Escherichia coli * analýza chemie metabolismus MeSH
- reakce na chladový šok fyziologie MeSH
- tandemová hmotnostní spektrometrie metody MeSH
- vysokoúčinná kapalinová chromatografie metody MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- izotopy kyslíku * MeSH
- Oxygen-18 MeSH Prohlížeč
- proteiny z Escherichia coli * MeSH
