A CoA-Transferase and Acyl-CoA Dehydrogenase Convert 2-(Carboxymethyl)cyclohexane-1-Carboxyl-CoA During Anaerobic Naphthalene Degradation.

The CoA thioester of 2-(carboxymethyl)cyclohexane-1-carboxylic acid has been identified as a metabolite in anaerobic naphthalene degradation by the sulfate-reducing culture N47. This study identified and characterised two acyl-CoA dehydrogenases (ThnO/ThnT) and an intramolecular CoA-transferase (ThnP) encoded within the substrate-induced thn operon, which contains genes for anaerobic degradation of naphthalene. ThnP is a CoA transferase belonging to the family I (Cat 1 subgroup) that catalyses the intramolecular CoA transfer from the carboxyl group of 2-(carboxymethyl)cyclohexane-1-carboxyl-CoA to its carboxymethyl moiety, forming 2-carboxycyclohexylacetyl-CoA.

Pathogenic mitochondrial DNA mutations inhibit melanoma metastasis.

Mitochondrial DNA (mtDNA) mutations are frequent in cancer, yet their precise role in cancer progression remains debated. To functionally evaluate the impact of mtDNA variants on tumor growth and metastasis, we developed an enhanced cytoplasmic hybrid (cybrid) generation protocol and established isogenic human melanoma cybrid lines with wild-type mtDNA or pathogenic mtDNA mutations with partial or complete loss of mitochondrial oxidative function. Cybrids with homoplasmic levels of pathogenic mtDNA reliably established tumors despite dysfunctional oxidative phosphorylation.

Facile preparation of embedded polar group-containing pentafluorophenyl stationary phases for highly selective separations of diverse analytes.

Pentafluorophenyl (PFP) stationary phase is one of the most important phases after the C18 phase in terms of its applications. Three embedded polar groups (EPG)-containing stationary phases were newly synthesized to act the EPGs as additional interaction sites. The silica surface was initially modified with (3-aminopropyl)trimethoxysilane (APS).

Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation.

Liver metastasis (LM) confers poor survival and therapy resistance across cancer types, but the mechanisms of liver-metastatic organotropism remain unknown. Here, through in vivo CRISPR-Cas9 screens, we found that Pip4k2c loss conferred LM but had no impact on lung metastasis or primary tumor growth. Pip4k2c-deficient cells were hypersensitized to insulin-mediated PI3K/AKT signaling and exploited the insulin-rich liver milieu for organ-specific metastasis.

Fatty acids are crucial to fuel NK cells upon acute retrovirus infection.

Natural killer (NK) cells are cytotoxic innate immune cells, able to recognize and eliminate virus-infected as well as cancer cells. Metabolic reprogramming is crucial for their activity as they have enhanced energy and nutritional demands for their functions during an infection. Fatty acids (FAs) represent an important source of cellular energy and are essential for proliferation of immune cells.

Surface Modification of Silica with β-Alanine Derivatives for Unique Applications in Liquid Chromatography.

Column purchasing cost is an important issue for an analyst to analyze complex sample matrices. Here, we report the development of an amino acid (β-alanine)-derived stationary phase (Sil-Ala-C12) with strategic and effective interaction sites (amide and urea as embedded polar groups with C12 alkyl chain) able to separate various kinds of analytes. Owing to the balanced hydrophobicity and hydrophilicity of the phase, it showed exceptional separation abilities in both reversed-phase high-performance liquid chromatography (RP-HPLC) as a hydrophobic phase and hydrophilic interaction chromatography (HILIC) as a hydrophilic phase.

Unraveling the Double Bond Position of Fatty Acids by GC-MS Using Electron Capture APCI and In-Source Fragmentation Patterns.

The position of double bonds in unsaturated fatty acids is strongly connected to their biological effects, but their analytical characterization is still challenging. However, the ionization of unsaturated fatty acids by a GC-APCI leads to regiospecific in-source fragment ions, which can be used to identify the double bond position. The fragment ions are oxidized species that occur mostly at the double bond closest to the carboxylic acid group.

An overview of food lipids toward food lipidomics.

Increasing evidence regarding lipids' beneficial effects on human health has changed the common perception of consumers and dietary officials about the role(s) of food lipids in a healthy diet. However, lipids are a wide group of molecules with specific nutritional and bioactive properties. To understand their true nutritional and functional value, robust methods are needed for accurate identification and quantification.

Design of β-Alanine-Derived Novel C18 Stationary Phase Containing Embedded Urea and Amide Groups for the Separation of Versatile Analytes.

Novel stationary phases have been emerging recently. A β-alanine-derived embedded urea and amide group-containing C18 phase (Sil-Ala-C18) was prepared for the first time. The media were packed into a 150 × 2.

Post-fast refeeding enhances intestinal stem cell-mediated regeneration and tumourigenesis through mTORC1-dependent polyamine synthesis.

For more than a century, fasting regimens have improved health, lifespan, and tissue regeneration in diverse organisms, including humans. However, how fasting and post-fast refeeding impact adult stem cells and tumour formation has yet to be explored in depth. Here, we demonstrate that post-fast refeeding increases intestinal stem cell (ISC) proliferation and tumour formation: Post-fast refeeding augments the regenerative capacity of 5 intestinal stem cells (ISCs), and loss of the tumour suppressor in ISCs under post-fast refeeding leads to a higher tumour incidence in the small intestine and colon than in the fasted or (AL) fed states.

Review on atmospheric pressure ionization sources for gas chromatography-mass spectrometry. Part II: Current applications.

The application of atmospheric pressure ionization (API) sources in gas chromatography-mass spectrometry (GC-MS) determinations is becoming more popular since they have shown great capabilities to sort out the main drawbacks of vacuum ionization techniques like electron ionization (EI) and chemical ionization (CI). The development of new API techniques and set-ups have grown in the last decades, opening the field of GC-MS to new applications and facing some of the major issues in current analytical methodologies such as the requirement of a compromise between sensitivity and selectivity. Thus, this review is mainly focused on the use of GC-API-MS in different application fields such as food analysis (food safety and food metabolomics), environmental analysis, clinical analysis, drug and pharmaceutical analysis, and petroleomics, among others.

Review on atmospheric pressure ionization sources for gas chromatography-mass spectrometry. Part I: Current ion source developments and improvements in ionization strategies.

The use of atmospheric pressure ionization (API) sources has become very popular for gas chromatography-mass spectrometry (GC-MS) determinations. GC-API-MS shows important advantages over traditional vacuum ionization sources such as a lower fragmentation preserving the molecular or quasi-molecular ion, the combination of GC separations with advanced mass spectrometers typically developed for liquid chromatography (LC) systems, a significantly higher sensitivity, or the reduction of costs due to the capability to use the same MS for both LC- and GC- couplings. For these reasons, the development of new API sources and GC-API-MS platforms has exponentially increased during the last years.

Potential of atmospheric pressure ionization sources for the analysis of free fatty acids in clinical and biological samples by gas chromatography-mass spectrometry.

Because of the central role of fatty acids in biological systems, their accurate quantification is still important. However, the impact of the complex matrix of biologically and clinically relevant samples such as plasma, serum, or cells makes the analysis still challenging, especially, when free non-esterified fatty acids have to be quantified. Here we developed and characterized a novel GC-MS method using pentafluorobenzyl bromide as a derivatization agent and compared different ionization techniques such as atmospheric pressure chemical ionization (APCI), atmospheric pressure chemical photoionization (APPI), and negative ion chemical ionization (NICI).

Characterization of the Extracellular Volatile Metabolome of Applying an Biofilm Model under Cystic Fibrosis-Like Conditions.

Background: Cystic fibrosis (CF) is an autosomal recessive hereditary disease that leads to the production of thickened mucus in the lungs, favouring polymicrobial infections, such as chronic lung infections with the bacterial opportunistic pathogen .

Method: A biofilm model in combination with an adapted sampling and GC-MS analysis method were applied to studies on different variables influencing the composition of the extracellular volatile metabolome of .

Results: A significant influence on the metabolome could be demonstrated for the culture medium as well as the atmosphere during cultivation (aerobic or anaerobic).

Ultrafast cold-brewing of coffee by picosecond-pulsed laser extraction.

Coffee is typically brewed by extracting roasted and milled beans with hot water, but alternative methods such as cold brewing became increasingly popular over the past years. Cold-brewed coffee is attributed to health benefits, fewer acids, and bitter substances. But the preparation of cold brew typically needs several hours or even days.

Differentiation of industrial hemp strains by their cannabinoid and phenolic compounds using LC × LC-HRMS.

Cannabis is an ancient plant that has been used for therapeutic and recreational purposes. Nowadays, industrial hemp, a variety with low concentration of the psychoactive cannabinoid Δ-tetrahydrocannabinol (THC) and high concentration of non-psychoactive cannabinoids, is getting more and more interest in the food, pharmaceutical, and cosmetic industry. However, cannabis not only contains cannabinoids as bioactive components but also other metabolites like terpenes and phenolic compounds, and the content of these interesting secondary metabolites greatly differs with the genetic variety of the plant.

Oxylipin metabolism is controlled by mitochondrial β-oxidation during bacterial inflammation.

Oxylipins are potent biological mediators requiring strict control, but how they are removed en masse during infection and inflammation is unknown. Here we show that lipopolysaccharide (LPS) dynamically enhances oxylipin removal via mitochondrial β-oxidation. Specifically, genetic or pharmacological targeting of carnitine palmitoyl transferase 1 (CPT1), a mitochondrial importer of fatty acids, reveal that many oxylipins are removed by this protein during inflammation in vitro and in vivo.

Comparative study for analysis of carbohydrates in biological samples.

This work presents a comparative study for the analysis of carbohydrates for four common chromatographic methods, each coupled to mass spectrometry. Supercritical fluid chromatography (SFC), hydrophilic interaction liquid chromatography (HILIC), reversed-phase liquid chromatography (RP-LC) and gas chromatography (GC) with detection by triple quadrupole mass spectrometer (QqQ-MS) are compared. It is shown that gas chromatography and reversed-phase liquid chromatography, each after derivatisation, are superior to the other two methods in terms of separation performance.

Effect of Sampling Rate and Data Pretreatment for Targeted and Nontargeted Analysis by Means of Liquid Chromatography Coupled to Drift Time Ion Mobility Quadruple Time-of-Flight Mass Spectrometry.

Ion mobility as an additional separation dimension can help to resolve and annotate metabolite and lipid biomarkers and provides important information about the components in a sample. Identifying relevant information in the resulting data is challenging because of the complexity of the data and data evaluation strategies for both targeted or nontargeted workflows. Frequently, feature analysis is used as a first step to search for differences between samples in discovery workflows.

Chemical characterization of eight herbal liqueurs by means of liquid chromatography coupled with ion mobility quadrupole time-of-flight mass spectrometry.

Herbal liqueurs are a large group of diverse alcoholic beverages with an ancient tradition produced by maceration of various herbs and spices and are commonly drunken before or after a meal to aid in the digestion because of their potential functional properties. In the presented work, eight different commercial herbal liqueurs were investigated with regard to their composition of phenolic compounds by liquid chromatography ion mobility quadrupole time-of-flight mass spectrometry (LC-IM-QTOF-MS). This multidimensional analytical platform uses all-ion fragmentation for a deep coverage of the foodome.

Non-targeted and targeted analysis of oxylipins in combination with charge-switch derivatization by ion mobility high-resolution mass spectrometry.

Eicosanoids and other oxylipins play an important role in mediating inflammation as well as other biological processes. For the investigation of their biological role(s), comprehensive analytical methods are necessary, which are able to provide reliable identification and quantification of these compounds in biological matrices. Using charge-switch derivatization with AMPP (N-(4-aminomethylphenyl)pyridinium chloride) in combination with liquid chromatography ion mobility quadrupole time-of-flight mass spectrometry (LC-IM-QTOF-MS), we developed a non-target approach to analyze oxylipins in plasma, serum, and cells.

Metabolic Dysregulation of the Lysophospholipid/Autotaxin Axis in the Chromosome 9p21 Gene SNP rs10757274.

Background: Common chromosome 9p21 single nucleotide polymorphisms (SNPs) increase coronary heart disease risk, independent of traditional lipid risk factors. However, lipids comprise large numbers of structurally related molecules not measured in traditional risk measurements, and many have inflammatory bioactivities. Here, we applied lipidomic and genomic approaches to 3 model systems to characterize lipid metabolic changes in common Chr9p21 SNPs, which confer ≈30% elevated coronary heart disease risk associated with altered expression of ANRIL, a long ncRNA.

LipidCreator workbench to probe the lipidomic landscape.

Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes.