Animal Metabolite Database: Metabolite Concentrations in Animal Tissues and Convenient Comparison of Quantitative Metabolomic Data.

The Animal Metabolite Database (AMDB, https://amdb.online) is a freely accessible database with built-in statistical analysis tools, allowing one to browse and compare quantitative metabolomics data and raw NMR and MS data, as well as sample metadata, with a focus on the metabolite concentrations rather than on the raw data itself. AMDB also functions as a platform for the metabolomics community, providing convenient deposition and exchange of quantitative metabolomic data. To date, the majority of the data in AMDB relate to the metabolite content of the eye lens and blood of vertebrates, primarily wild species from Siberia, Russia and laboratory rodents. However, data on other tissues (muscle, heart, liver, brain, and more) are also present, and the list of species and tissues is constantly growing. Typically, every sample in AMDB contains concentrations of 60-90 of the most abundant metabolites, provided in nanomoles per gram of wet tissue weight (nmol/g). We believe that AMDB will become a widely used tool in the community, as typical metabolite baseline concentrations in tissues of animal models will aid in a wide variety of fundamental and applied scientific fields, including, but not limited to, animal modeling of human diseases, assessment of medical formulations, and evolutionary and environmental studies.

Fluorescently labeled human apurinic/apyrimidinic endonuclease APE1 reveals effects of DNA polymerase ß on the APE1-DNA interaction.

The base excision repair (BER) pathway involves sequential action of DNA glycosylases and apurinic/apyrimidinic (AP) endonucleases to incise damaged DNA and prepare DNA termini for incorporation of a correct nucleotide by DNA polymerases. It has been suggested that the enzymatic steps in BER include recognition of a product-enzyme complex by the next enzyme in the pathway, resulting in the "passing-the-baton" model of transfer of DNA intermediates between enzymes. To verify this model, in this work, we aimed to create a suitable experimental system. We prepared APE1 site-specifically labeled with a fluorescent reporter that is sensitive to stages of APE1-DNA binding, of formation of the catalytic complex, and of subsequent dissociation of the enzyme-product complex. Interactions of the labeled APE1 with various model DNA substrates (containing an abasic site) of varied lengths revealed that the enzyme remains mostly in complex with the DNA product. By means of the fluorescently labeled APE1 in combination with a stopped-flow fluorescence assay, it was found that Polß stimulates both i) APE1 binding to an abasic-site-containing DNA duplex with the formation of a catalytically competent complex and ii) the dissociation of APE1 from its product. These findings confirm DNA-mediated coordination of APE1 and Polß activities and suggest that Polß is the key trigger of the DNA transfer between the enzymes participating in initial steps of BER.

Stability of Metabolomic Content during Sample Preparation: Blood and Brain Tissues.

Thermal and enzymatic reactions can significantly change the tissue metabolomic content during the sample preparation. In this work, we evaluated the stability of metabolites in human whole blood, serum, and rat brain, as well as in metabolomic extracts from these tissues. We measured the concentrations of 63 metabolites in brain and 52 metabolites in blood. We have shown that metabolites in the extracts from biological tissues are stable within 24 h at 4 °C. Serum and whole blood metabolomes are also rather stable, changes in metabolomic content of the whole blood homogenate become apparent only after 1-2 h of incubation at 4 °C, and become strong after 24 h. The most significant changes correspond to energy metabolites: the concentrations of ATP and ADP decrease fivefold, and the concentrations of NAD, NADH, and NADPH decrease below the detectable level. A statistically significant increase was observed for AMP, IMP, hypoxanthine, and nicotinamide. The brain tissue is much more metabolically active than human blood, and significant metabolomic changes occur already within the first several minutes during the brain harvest and sample homogenization. At a longer timescale (hours), noticeable changes were observed for all classes of compounds, including amino acids, organic acids, alcohols, amines, sugars, nitrogenous bases, nucleotides, and nucleosides.

The Application of Quantitative Metabolomics for the Taxonomic Differentiation of Birds.

In the current pilot study, we propose the use of quantitative metabolomics to reconstruct the phylogeny of vertebrates, namely birds. We determined the concentrations of the 67 most abundant metabolites in the eye lenses of the following 14 species from 6 orders of the class Aves (Birds): the Black kite (Milvus migrans), Eurasian magpie (Pica pica), Northern raven (Corvus corax), Eurasian coot (Fulica atra), Godlewski's bunting (Emberiza godlewskii), Great crested grebe (Podiceps cristatus), Great tit (Parus major), Hawfinch (Coccothraustes coccothraustes), Hooded crow (Corvus cornix), House sparrow (Passer domesticus), Rock dove (Columba livia), Rook (Corvus frugilegus), Short-eared owl (Asio flammeus) and Ural owl (Strix uralensis). Further analysis shows that the statistical approaches generally used in metabolomics can be applied for differentiation between species, and the most fruitful results were obtained with hierarchical clustering analysis (HCA). We observed the grouping of conspecific samples independently of the sampling place and date. The HCA tree structure supports the key role of genomics in the formation of the lens metabolome, but it also indicates the influence of the species lifestyle. A combination of genomics-based and metabolomics-based phylogeny could potentially resolve arising issues and yield a more reliable tree of life.

Most abundant metabolites in tissues of freshwater fish pike-perch (Sander lucioperca).

Quantitative metabolomic analysis was performed for eleven tissues of freshwater fish pike-perch (Sander lucioperca), including gill, heart, liver, kidney, spleen, muscle, brain, milt, lens, aqueous (AH) and vitreous (VH) humors with the use of NMR spectroscopy. The absolute values of concentrations were determined for more than 65 most abundant metabolites in every tissue. It was found that from the metabolomic viewpoint, kidney and gill are the most similar tissues, while the metabolomic compositions of ocular tissues-lens, AH, and VH significantly differ from that of other tissues. The combinations of intracellular osmolytes and antioxidants are specific for every tissue. In particular, the concentration of antioxidant ovothiol A in the lens is much higher than in any other tissue, while the brain enjoys the elevated level of ascorbate. The most abundant osmolyte in the fish spleen, muscle, and heart is taurine, and in the brain, gill, and lens-myo-inositol. Other important osmolytes specific for particular tissues are N-acetyl-histidine, N-acetyl-aspartate, betaine, threonine-phosphoethanolamine, and serine-phosphoethanolamine. The quantitative data obtained in the present work can be used as the baseline metabolite concentrations in the fish tissues to evaluate the influence of seasonal, ecological and other factors on the fish metabolism.

Comparative Metabolomic Profiling of Rat Embryonic and Induced Pluripotent Stem Cells.

Metabolomic profiles of somatic cells, embryonic stem cells (ESCs), and induced pluripotent stem cells (iPSCs) reflect their metabolic phenotypes. The comparative study of metabolomes of these cells is important for understanding the differences in metabolism between somatic and pluripotent cells, and also the possible differences between ESCs and iPSCs. Here, we performed for the first time the metabolomic analysis of rat ESCs, iPSCs, and embryonic fibroblasts (EFs) at both quantitative and semi-quantitative levels using NMR spectroscopy and liquid chromatography with mass spectrometric detection, respectively. The total of 106 metabolites has been identified, and the concentrations of 51 compounds have been measured. It is found that the reprogramming of rat EFs into iPSCs affects virtually all metabolic pathways and causes drastic changes in the cell metabolomic profile. The difference between ESCs and iPSCs is much less pronounced: the concentrations of the majority of metabolites in ESCs and iPSCs are similar, and significant differences were observed for only several compounds, including adenosine, cysteic acid, glycerophosphoglycerol, inositol phosphate, glucose, myo-inositol, phosphoserine, xanthosine, guanosine. The observed differences between the metabolomic compositions of ESCs and iPSCs do not influence the pluripotent ability of iPSCs. Graphical Abstract.

Metabolic response of the Siberian wood frog Rana amurensis to extreme hypoxia.

The Siberian wood frog Rana amurensis is a recently discovered example of extreme hypoxia tolerance that is able to survive several months without oxygen. We studied metabolomic profiles of heart and liver of R. amurensis exposed to 17 days of extreme hypoxia. Without oxygen, the studied tissues experience considerable stress with a drastic decrease of ATP, phosphocreatine, and NAD+ concentrations, and concomitant increase of AMP, creatine, and NADH. Heart and liver switch to different pathways of glycolysis with differential accumulation of lactate, alanine, succinate, as well as 2,3-butanediol (previously not reported for vertebrates as an end product of glycolysis) and depletion of aspartate. We also observed statistically significant changes in concentrations of certain osmolytes and choline-related compounds. Low succinate/fumarate ratio and high glutathione levels indicate adaptations to reoxygenation stress. Our data suggest that maintenance of the ATP/ADP pool is not required for survival of R. amurensis, in contrast to anoxia-tolerant turtles.

Post-mortem changes in metabolomic profiles of human serum, aqueous humor and vitreous humor.

INTRODUCTION: Application of metabolomic methods to forensic studies may expand the limits of the post-mortem interval (PMI) estimation, and improve the accuracy of the estimation. To this end, it is important to determine which tissue is the most suitable for analysis, and which compounds are the most promising candidates for PMI estimation. OBJECTIVES: This work is aimed at the comparison of human serum, aqueous humor (AH), and vitreous humor (VH) as perspective tissues for metabolomic-based PMI estimation, at the determination of most promising PMI biomarkers, and at the development of method of PMI estimation based on the measurement of concentrations of PMI biomarkers. METHODS: Quantitative metabolomic profiling of samples of the human serum, AH, and VH taken at different PMIs has been performed with the use of NMR spectroscopy. RESULTS: It is found that the metabolomic changes in anatomically isolated ocular fluids are slower and smoother than that in blood. A good positive time correlation (Pearson coefficient r > 0.5) was observed for several metabolites, including hypoxanthine, choline, creatine, betaine, glutamate, and glycine. A model for PMI estimation based on concentrations of several metabolites in AH and VH is proposed. CONCLUSIONS: The obtained results demonstrate that the metabolomic analysis of AH and VH is more suitable for the PMI estimation than that of serum. The compounds with good positive time correlation can be considered as potential PMI biomarkers.

Seasonal Variations and Interspecific Differences in Metabolomes of Freshwater Fish Tissues: Quantitative Metabolomic Profiles of Lenses and Gills.

This work represents the first comprehensive report on quantitative metabolomic composition of tissues of pike-perch (Sander lucioperca) and Siberian roach (Rutilus rutilus lacustris). The total of 68 most abundant metabolites are identified and quantified in the fish lenses and gills by the combination of LC-MS and NMR. It is shown that the concentrations of some compounds in the lens are much higher than that in the gills; that indicates the importance of these metabolites for the adaptation to the specific living conditions and maintaining the homeostasis of the fish lens. The lens metabolome undergoes significant seasonal changes due to the variations of dissolved oxygen level and fish feeding activity. The most season-affected metabolites are osmolytes and antioxidants, and the most affected metabolic pathway is the histidine pathway. In late autumn, the major lens osmolytes are N-acetyl-histidine and threonine phosphoethanolamine (Thr-PETA), while in winter the highest concentrations were observed for serine phosphoethanolamine (Ser-PETA) and myo-inositol. The presence of Thr-PETA and Ser-PETA in fish tissues and their role in cell osmotic protection are reported for the first time. The obtained concentrations can be used as baseline levels for studying the influence of environmental factors on fish health.

Ovothiol A is the Main Antioxidant in Fish Lens.

Tissue protection from oxidative stress by antioxidants is of vital importance for cellular metabolism. The lens mostly consists of fiber cells lacking nuclei and organelles, having minimal metabolic activity; therefore, the defense of the lens tissue from the oxidative stress strongly relies on metabolites. Protein-free extracts from lenses and gills of freshwater fish, Sander lucioperca and Rutilus rutilus lacustris, were subjected to analysis using high-field 1H NMR spectroscopy and HPLC with optical and high-resolution mass spectrometric detection. It was found that the eye lenses of freshwater fish contain high concentrations of ovothiol A (OSH), i.e., one of the most powerful antioxidants exciting in nature. OSH was identified and quantified in millimolar concentrations. The concentration of OSH in the lens and gills depends on the fish genus and on the season. A possible mechanism of the reactive oxygen species deactivation in fish lenses is discussed. This work is the first to report on the presence of OSH in vertebrates. The presence of ovothiol in the fish tissue implies that it may be a significantly more common antioxidant in freshwater and marine animals than was previously thought.

Quantitative metabolomic analysis of changes in the lens and aqueous humor under development of age-related nuclear cataract.

INTRODUCTION: Metabolites are essential for the proper functioning of the eye lens, they either enter the lens from the aqueous humor (AH), or are synthesized in the lens epithelium. Antioxidants, osmolytes and UV filters are especially important for the lens protection, and their lack may cause the development of ophthalmic diseases. OBJECTIVES: Comparison of the metabolomic compositions of lenses and AH taken from cataract patients with that taken from human cadavers without cataract can shed light onto molecular mechanisms underlying onset of age-related nuclear cataract. METHODS: Combined use of 1H nuclear magnetic resonance and high performance liquid chromatography with optical and high-resolution mass spectrometric detection for the identification and quantification of metabolites in the lens and AH extracts. RESULTS: The concentrations of 86 metabolites were determined for four groups of samples, including lenses and AH from cataract patients and from human cadavers. In cataractous lens the most abundant metabolites are (in descending order): myo-inositol, lactate, acetate, glutamate, glutathione; in AH-lactate, glucose, glutamine, alanine, valine. The concentrations of the majority of metabolites in normal post-mortem samples of both lens and AH are higher than that in samples from the cataract patients. CONCLUSIONS: Comparison of metabolite concentrations in lens and corresponding AH reveal that the most important for the lens protection metabolites are synthesized in the lens epithelial cells. The reduced levels of antioxidants, UV filters, and osmolytes were found in the cataractous lenses what cannot be explained by post-mortem changes in normal lens; that indicates that the age-related nuclear cataract development may originate from the dysfunction of the lens epithelial cells.

Optical properties of the human lens constituents.

The absorption and fluorescence properties of the metabolomic (MET), water-soluble and urea-soluble protein fractions from the middle-age, aged, and cataractous human lenses have been measured. At 280nm and 300nm the major lens absorbers are crystallins, which absorb more than 90% of light in the UV-B region (280-315nm). In middle-aged lenses, the absorption at 360nm is mostly provided by UV filters contained in the MET fraction. With aging, and especially with the cataract development, the absorption of MET fraction in UV-A region (315-400nm) decreases due to the drop of the UV filter concentration, while the absorption of protein fractions increases due to the accumulation of post-translational modifications. Consequently, the contribution of the MET fraction into the total lens absorption at 360nm decays from 63% in middle-aged lenses to 25% in aged lenses to 3% in cataractous lenses. The fluorescence yield of the MET fraction from cataractous lenses also significantly increases. Therefore, the protection of the lens tissue against UV radiation in aged and cataractous lenses weakens: the absorption of UV-A light is mostly provided by modified crystallins and non-UV-filter metabolites, which are photochemically more active than the UV filters. The obtained data indicate that the aged and cataractous human lenses are more vulnerable to UV-A light than the middle-aged lenses.

Spatial distribution of metabolites in the human lens.

Spatial distribution of 34 metabolites along the optical and equatorial axes of the human lens has been determined. For the majority of metabolites, the homogeneous distribution has been observed. That suggests that the rate of the metabolite transformation in the lens is low due to the general metabolic passivity of the lens fiber cells. However, the redox processes are active in the lens; as a result, some metabolites, including antioxidants, demonstrate the "nucleus-depleted" type of distribution, whereas secondary UV filters show the "nucleus-enriched" type. The metabolite concentrations at the lens poles and equator are similar for all metabolites under study. The concentric pattern of the "nucleus-depleted" and "nucleus-enriched" distributions testifies that the metabolite distribution inside the lens is mostly governed by a passive diffusion, relatively free along the fiber cells and retarded in the radial direction across the cells. No significant difference in the metabolite distribution between the normal and cataractous human lenses was found.

Metabolomic composition of normal aged and cataractous human lenses.

Quantitative metabolomic profiles of normal and cataractous human lenses were obtained with the combined use of high-frequency nuclear magnetic resonance (NMR) and high-performance liquid chromatography with high-resolution mass-spectrometric detection (LC-MS) methods. The concentration of more than fifty metabolites in the lens cortex and nucleus has been determined. For the majority of metabolites, their concentrations in the lens cortex and nucleus are similar, which confirms low metabolic activity in the lens core. The difference between the metabolite levels in the cortex and nucleus of the normal lens is observed for antioxidants and UV filters, which demonstrates the activity of redox processes in the lens. A huge difference is found between the metabolomic compositions of normal and age-matched cataractous lenses: the concentrations of almost all metabolites in the normal lens are higher than in the cataractous one. The most pronounced difference is observed for compounds playing a key role in the lens cell protection and metabolic activity, including antioxidants, UV filters, and osmolytes. The results obtained imply that the development of the age-related cataracts might originate from the metabolic dysfunction of the lens epithelial cells.

Beneficial effects of melatonin in a rat model of sporadic Alzheimer's disease.

Melatonin synthesis is disordered in patients with Alzheimer's disease (AD). To determine the role of melatonin in the pathogenesis of AD, suitable animal models are needed. The OXYS rats are an experimental model of accelerated senescence that has also been proposed as a spontaneous rat model of AD-like pathology. In the present study, we demonstrate that disturbances in melatonin secretion occur in OXYS rats at 4 months of age. These disturbances occur simultaneously with manifestation of behavioral abnormalities against the background of neurodegeneration and alterations in hormonal status but before the signs of amyloid-ß accumulation. We examined whether oral administration of melatonin could normalize the melatonin secretion and have beneficial effects on OXYS rats before progression to AD-like pathology. The results showed that melatonin treatment restored melatonin secretion in the pineal gland of OXYS rats as well as the serum levels of growth hormone and IGF-1, the level of BDNF in the hippocampus and the healthy state of hippocampal neurons. Additionally, melatonin treatment of OXYS rats prevented an increase in anxiety and the decline of locomotor activity, of exploratory activity, and of reference memory. Thus, melatonin may be involved in AD progression, whereas oral administration of melatonin could be a prophylactic strategy to prevent or slow down the progression of some features of AD pathology.

Metabolomics of the rat lens: a combined LC-MS and NMR study.

This work is the first comprehensive report on the quantitative metabolomic composition of the rat lens. Quantitative metabolomic profiles of lenses were acquired with the combined use of high-frequency nuclear magnetic resonance (NMR) and high-performance liquid chromatography with high-resolution mass-spectrometric detection (LC-MS) methods. More than forty low molecular weight compounds found in the lens have been reliably identified and quantified. The most abundant metabolites in the 3-month-old Wistar rat lens are taurine, hypotaurine, lactate, phosphocholine and reduced glutathione. The analysis of age-related changes in the lens metabolomic composition shows a gradual decrease of the content of most metabolites. This decrease is the most pronounced between 1 and 3 months, which probably corresponds to the completion of the lens maturation in one-month-old rats and to the high rate of the young lens growth. The enhanced levels of tryptophan, tyrosine, carnitine, glycerophosphate, GSH and GSSG were found in lenses of senescence-accelerated OXYS rats; for some metabolites, this effect may probably be attributed to the compensatory response to oxidative stress.

Cataract-specific posttranslational modifications and changes in the composition of urea-soluble protein fraction from the rat lens.

PURPOSE: To determine age-related changes in the composition of the urea-soluble (US) protein fraction from lenses of senescence-accelerated OXYS (cataract model) and Wistar (control) rats and to establish posttranslational modifications (PTMs) occurring under enhanced oxidative stress in OXYS lenses. METHODS: The identity and the relative abundance of crystallins in the US fractions were determined using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MS). The identities and the positions of PTMs were established using MS/MS measurements. RESULTS: Two-dimensional gel electrophoresis maps of US protein fractions were obtained for lenses of 3-, 12-, and 62-week-old Wistar and OXYS rats, and the relative abundance of different isoforms of α-, ß-, and γ-crystallins was determined. ß-Crystallins were the major contributor of the US fraction in 3-week-old lenses (above 50%), γ-crystallins in 12-week-old lenses (50-60%), and in 62-week-old lenses, the contributions from all three crystallin families leveled out. The major interstrain difference was the elevated level of α-crystallins in the US fraction from 12-week-old OXYS lenses. Spots with increased relative abundance in OXYS maps were attributed to the cataract-specific spots of interest. The crystallins from these spots were subjected to MS/MS analysis, and the positions of acetylation, oxidation, deamidation, and phosphorylation were established. CONCLUSIONS: The increased relative abundance of α-crystallins in the US fraction from 12-week-old OXYS lenses points to the fast insolubilization of α-crystallins under oxidative stress. Most of the PTMs attributed to the cataract-specific modifications also correspond to α-crystallins. These PTMs include oxidation of methionine residues, deamidation of asparagine and glutamine residues, and phosphorylation of serine and threonine residues.