Metabolites

23 pages, 3091 KiB

Open AccessFeature PaperArticle

¹H-Nuclear Magnetic Resonance Analysis of Urine as Diagnostic Tool for Organic Acidemias and Aminoacidopathies

by Ninna Pulido, Johana M. Guevara-Morales, Alexander Rodriguez-López, Álvaro Pulido, Jhon Díaz, Ru Angelie Edrada-Ebel and Olga Y. Echeverri-Peña

Metabolites 2021, 11(12), 891; https://doi.org/10.3390/metabo11120891 - 20 Dec 2021

Cited by 6 | Viewed by 2996

Abstract

The utility of low-resolution ¹H-NMR analysis for the identification of biomarkers provided evidence for rapid biochemical diagnoses of organic acidemia and aminoacidopathy. ¹H-NMR, with a sensitivity expected for a field strength of 400 MHz at 64 scans was used to establish [...] Read more.

The utility of low-resolution ¹H-NMR analysis for the identification of biomarkers provided evidence for rapid biochemical diagnoses of organic acidemia and aminoacidopathy. ¹H-NMR, with a sensitivity expected for a field strength of 400 MHz at 64 scans was used to establish the metabolomic urine sample profiles of an infant population diagnosed with small molecule Inborn Errors of Metabolism (smIEM) compared to unaffected individuals. A qualitative differentiation of the ¹H-NMR spectral profiles of urine samples obtained from individuals affected by different organic acidemias and aminoacidopathies was achieved in combination with GC–MS. The smIEM disorders investigated in this study included phenylalanine metabolism; isovaleric, propionic, 3-methylglutaconicm and glutaric type I acidemia; and deficiencies in medium chain acyl-coenzyme and holocarboxylase synthase. The observed metabolites were comparable and similar to those reported in the literature, as well as to those detected with higher-resolution NMR. In this study, diagnostic marker metabolites were identified for the smIEM disorders. In some cases, changes in metabolite profiles differentiated post-treatments and follow-ups while allowing for the establishment of different clinical states of a biochemical disorder. In addition, for the first time, a ¹H-NMR-based biomarker profile was established for holocarboxylase synthase deficiency spectrum. Full article

(This article belongs to the Special Issue Urinary Metabolomic Profiling Analysis and Evaluation)

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17 pages, 1211 KiB

Open AccessArticle

Effect of the Length of Oat Hay on Growth Performance, Health Status, Behavior Parameters and Rumen Fermentation of Holstein Female Calves

by Jianxin Xiao, Tianyu Chen, Gibson Maswayi Alugongo, Muhammad Zahoor Khan, Tingting Li, Jing Ma, Shuai Liu, Wei Wang, Yajing Wang, Shengli Li and Zhijun Cao

Metabolites 2021, 11(12), 890; https://doi.org/10.3390/metabo11120890 - 20 Dec 2021

Cited by 6 | Viewed by 2264

Abstract

The aim of this study was to evaluate the effect of the length of oat hay on the performance, health, behavior, and rumen fermentation of dairy calves. For this purpose, two hundred and ten healthy two-day-old Holstein dairy calves were randomly allocated into [...] Read more.

The aim of this study was to evaluate the effect of the length of oat hay on the performance, health, behavior, and rumen fermentation of dairy calves. For this purpose, two hundred and ten healthy two-day-old Holstein dairy calves were randomly allocated into three groups: basic diet (calf starter) without hay (CON), or a basic diet with oat hay at either long (OL: 10–12 cm) or short (OS: 3–5 cm) length cut. The basic diet was fed from day 4, while the hay was offered from day 14. All calves were weaned at day 56 and remained in their individual hutches till the end of the trial (day 70). Calf starter intake and fecal scores were recorded daily. Bodyweight, body size, and rumen fluid samples were collected biweekly before weaning and weekly after weaning. Overall, providing oat hay (OS and OL) in the diet increased the body weight, starter intake, and average daily gain compared to the CON group. Similarly, feeding oat hay improved rumen fermentation. More specifically, hay enhanced the rumen pH and changed the rumen fermentation type. Hay fed calves spent more time on rumination but less time performing abnormal behaviors compared to control. As it can be concluded, feeding oat hay to calves enhances the growth performance, rumen fermentation, and normal calf behaviors, implying improved animal welfare irrespective of the hay length. Full article

(This article belongs to the Section Animal Metabolism)

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15 pages, 1243 KiB

Open AccessReview

Cardiac Metabolism and Contractile Function in Mice with Reduced Trans-Endothelial Fatty Acid Transport

by Tatsuya Iso and Masahiko Kurabayashi

Metabolites 2021, 11(12), 889; https://doi.org/10.3390/metabo11120889 - 19 Dec 2021

Cited by 3 | Viewed by 2638

Abstract

The heart is a metabolic omnivore that combusts a considerable amount of energy substrates, mainly long-chain fatty acids (FAs) and others such as glucose, lactate, ketone bodies, and amino acids. There is emerging evidence that muscle-type continuous capillaries comprise the rate-limiting barrier that [...] Read more.

The heart is a metabolic omnivore that combusts a considerable amount of energy substrates, mainly long-chain fatty acids (FAs) and others such as glucose, lactate, ketone bodies, and amino acids. There is emerging evidence that muscle-type continuous capillaries comprise the rate-limiting barrier that regulates FA uptake into cardiomyocytes. The transport of FAs across the capillary endothelium is composed of three major steps—the lipolysis of triglyceride on the luminal side of the endothelium, FA uptake by the plasma membrane, and intracellular FA transport by cytosolic proteins. In the heart, impaired trans-endothelial FA (TEFA) transport causes reduced FA uptake, with a compensatory increase in glucose use. In most cases, mice with reduced FA uptake exhibit preserved cardiac function under unstressed conditions. When the workload is increased, however, the total energy supply relative to its demand (estimated with pool size in the tricarboxylic acid (TCA) cycle) is significantly diminished, resulting in contractile dysfunction. The supplementation of alternative fuels, such as medium-chain FAs and ketone bodies, at least partially restores contractile dysfunction, indicating that energy insufficiency due to reduced FA supply is the predominant cause of cardiac dysfunction. Based on recent in vivo findings, this review provides the following information related to TEFA transport: (1) the mechanisms of FA uptake by the heart, including TEFA transport; (2) the molecular mechanisms underlying the induction of genes associated with TEFA transport; (3) in vivo cardiac metabolism and contractile function in mice with reduced TEFA transport under unstressed conditions; and (4) in vivo contractile dysfunction in mice with reduced TEFA transport under diseased conditions, including an increased afterload and streptozotocin-induced diabetes. Full article

(This article belongs to the Special Issue Insights into the Bioenergetics and Metabolism in Normal and Failing Heart)

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15 pages, 1963 KiB

Open AccessArticle

Optimized Workflow for On-Line Derivatization for Targeted Metabolomics Approach by Gas Chromatography-Mass Spectrometry

by Raphaela Fritsche-Guenther, Yoann Gloaguen, Anna Bauer, Tobias Opialla, Stefan Kempa, Christina A. Fleming, Henry Paul Redmond and Jennifer A. Kirwan

Metabolites 2021, 11(12), 888; https://doi.org/10.3390/metabo11120888 - 18 Dec 2021

Cited by 8 | Viewed by 2362

Abstract

Using manual derivatization in gas chromatography-mass spectrometry samples have varying equilibration times before analysis which increases technical variability and limits the number of potential samples analyzed. By contrast, automated derivatization methods can derivatize and inject each sample in an identical manner. We present [...] Read more.

Using manual derivatization in gas chromatography-mass spectrometry samples have varying equilibration times before analysis which increases technical variability and limits the number of potential samples analyzed. By contrast, automated derivatization methods can derivatize and inject each sample in an identical manner. We present a fully automated (on-line) derivatization method used for targeted analysis of different matrices. We describe method optimization and compare results from using off-line and on-line derivatization protocols, including the robustness and reproducibility of the methods. Our final parameters for the derivatization process were 20 µL of methoxyamine (MeOx) in pyridine for 60 min at 30 °C followed by 80 µL N-Methyl-N-trimethylsilyltrifluoracetamide (MSTFA) for 30 min at 30 °C combined with 4 h of equilibration time. The repeatability test in plasma and liver revealed a median relative standard deviation (RSD) of 16% and 10%, respectively. Serum samples showed a consistent intra-batch median RSD of 20% with an inter-batch variability of 27% across three batches. The direct comparison of on-line versus off-line demonstrated that on-line was fit for purpose and improves repeatability with a measured median RSD of 11% compared to 17% using the same method off-line. In summary, we recommend that optimized on-line methods may improve results for metabolomics and should be used where available. Full article

(This article belongs to the Section Metabolomic Profiling Technology)

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9 pages, 2177 KiB

Open AccessArticle

Association of Neonatal Jaundice with Gut Dysbiosis Characterized by Decreased Bifidobacteriales

by Shohei Akagawa, Yuko Akagawa, Sohsaku Yamanouchi, Yoshiki Teramoto, Masahiro Yasuda, Sadayuki Fujishiro, Jiro Kino, Masato Hirabayashi, Kenji Mine, Takahisa Kimata, Masaki Hashiyada, Atsushi Akane, Shoji Tsuji and Kazunari Kaneko

Metabolites 2021, 11(12), 887; https://doi.org/10.3390/metabo11120887 - 18 Dec 2021

Cited by 5 | Viewed by 2425

Abstract

Neonatal jaundice, caused by excess serum bilirubin levels, is a common condition in neonates. Imbalance in the gut microbiota is believed to play a role in the development of neonatal jaundice. Thus, we aimed to reveal the gut microbiota characteristics in neonates with [...] Read more.

Neonatal jaundice, caused by excess serum bilirubin levels, is a common condition in neonates. Imbalance in the gut microbiota is believed to play a role in the development of neonatal jaundice. Thus, we aimed to reveal the gut microbiota characteristics in neonates with jaundice. 16S rRNA gene sequencing was performed on stool samples collected on day 4 from 26 neonates with jaundice (serum total bilirubin > 15.0 mg/dL) and 17 neonates without jaundice (total serum bilirubin < 10.0 mg/dL). All neonates were born full term, with normal weight, by vaginal delivery, and were breastfed. Neonates who were administered antibiotics, had serum direct bilirubin levels above 1 mg/dL, or had conditions possibly leading to hemolytic anemia were excluded. The median serum bilirubin was 16.0 mg/dL (interquartile range: 15.5–16.8) and 7.4 mg/dL (interquartile range: 6.8–8.3) for the jaundice and non-jaundice groups, respectively. There was no difference in the alpha diversity indices. Meanwhile, in the jaundice group, linear discriminant analysis effect size revealed that Bifidobacteriales were decreased at the order level, while Enterococcaceae were increased and Bifidobacteriaceae were decreased at the family level. Bifidobacteriaceae may act preventatively because of their suppressive effect on beta-glucuronidase, leading to accelerated deconjugation of conjugated bilirubin in the intestine. In summary, neonates with jaundice had dysbiosis characterized by a decreased abundance of Bifidobacteriales. Full article

(This article belongs to the Special Issue Gut Microbiota Metabolites in Health and Disease)

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11 pages, 2244 KiB

Open AccessArticle

The Effect of Glucose and Poloxamer 188 on Red-Blood-Cell Aggregation

by Alicja Szołna-Chodór and Bronisław Grzegorzewski

Metabolites 2021, 11(12), 886; https://doi.org/10.3390/metabo11120886 - 18 Dec 2021

Viewed by 1935

Abstract

Glucose metabolism disorders contribute to the development of various diseases. Numerous studies show that these disorders not only change the normal values of biochemical parameters but also affect the mechanical properties of blood. To show the influence of glucose and poloxamer 188 (P188) [...] Read more.

Glucose metabolism disorders contribute to the development of various diseases. Numerous studies show that these disorders not only change the normal values of biochemical parameters but also affect the mechanical properties of blood. To show the influence of glucose and poloxamer 188 (P188) on the mechanical properties of a red-blood-cell (RBC) suspension, we studied the aggregation of the cells. To show the mechanisms of the mechanical properties of blood, we studied the effects of glucose and poloxamer 188 (P188) on red-blood-cell aggregation. We used a model in which cells were suspended in a dextran 70 solution at a concentration of 2 g/dL with glucose and P188 at concentrations of 0–3 g/dL and 0–3 mg/mL, respectively. RBC aggregation was determined using an aggregometer, and measurements were performed every 4 min for 1 h. Such a procedure enabled the incubation of RBCs in solution. The aggregation index determined from the obtained syllectograms was used as a measure of aggregation. Both the presence of glucose and that of P188 increased the aggregation index with the incubation time until saturation was reached. The time needed for the saturation of the aggregation index increased with increasing glucose and P188 concentrations. As the concentrations of these components increased, the joint effect of glucose and P188 increased the weakening of RBC aggregation. The mechanisms of the observed changes in RBC aggregation in glucose and P188 solutions are discussed. Full article

(This article belongs to the Special Issue Hemorheology and Metabolism)

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13 pages, 1294 KiB

Open AccessArticle

Plasma Acylcarnitines during Pregnancy and Neonatal Anthropometry: A Longitudinal Study in a Multiracial Cohort

by Yiqing Song, Chen Lyu, Ming Li, Mohammad L. Rahman, Zhen Chen, Yeyi Zhu, Stefanie N. Hinkle, Liwei Chen, Susanna D. Mitro, Ling-Jun Li, Natalie L. Weir, Michael Y. Tsai and Cuilin Zhang

Metabolites 2021, 11(12), 885; https://doi.org/10.3390/metabo11120885 - 17 Dec 2021

Cited by 5 | Viewed by 2426

Abstract

As surrogate readouts reflecting mitochondrial dysfunction, elevated levels of plasma acylcarnitines have been associated with cardiometabolic disorders, such as obesity, gestational diabetes, and type 2 diabetes. This study aimed to examine prospective associations of acylcarnitine profiles across gestation with neonatal anthropometry, including birthweight, [...] Read more.

As surrogate readouts reflecting mitochondrial dysfunction, elevated levels of plasma acylcarnitines have been associated with cardiometabolic disorders, such as obesity, gestational diabetes, and type 2 diabetes. This study aimed to examine prospective associations of acylcarnitine profiles across gestation with neonatal anthropometry, including birthweight, birthweight z score, body length, sum of skinfolds, and sum of body circumferences. We quantified 28 acylcarnitines using electrospray ionization tandem mass spectrometry in plasma collected at gestational weeks 10–14, 15–26, 23–31, and 33–39 among 321 pregnant women from the National Institute of Child Health and Human Development (NICHD) Fetal Growth Studies-Singletons. A latent-class trajectory approach was applied to identify trajectories of acylcarnitines across gestation. We examined the associations of individual acylcarnitines and distinct trajectory groups with neonatal anthropometry using weighted generalized linear models adjusting for maternal age, race/ethnicity, education, parity, gestational age at blood collection, and pre-pregnancy body mass index (BMI). We identified three distinct trajectory groups in C2, C3, and C4 and two trajectory groups in C5, C10, C5–DC, C8:1, C10:1, and C12, respectively. Women with nonlinear decreasing C12 levels across gestation (5.7%) had offspring with significantly lower birthweight (−475 g; 95% CI, −942, −6.79), birthweight z score (−0.39, −0.71, −0.06), and birth length (−1.38 cm, −2.49, −0.27) than those with persistently stable C12 levels (94.3%) (all nominal p value < 0.05). Women with consistently higher levels of C10 (6.1%) had offspring with thicker sum of skinfolds (4.91 mm, 0.85, 8.98) than did women with lower levels (93.9%) during pregnancy, whereas women with lower C10:1 levels (12.6%) had offspring with thicker sum of skinfolds (3.23 mm, 0.19, 6.27) than did women with abruptly increasing levels (87.4%) (p < 0.05). In conclusion, this study suggests that distinctive trajectories of C10, C10:1, and C12 acylcarnitine levels throughout pregnancy were significantly associated with neonatal anthropometry. Full article

(This article belongs to the Section Advances in Metabolomics)

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18 pages, 5730 KiB

Open AccessArticle

Supervised Statistical Learning Prediction of Soybean Varieties and Cultivation Sites Using Rapid UPLC-MS Separation, Method Validation, and Targeted Metabolomic Analysis of 31 Phenolic Compounds in the Leaves

by Chan-Su Rha, Eun Kyu Jang, Yong Deog Hong and Won Seok Park

Metabolites 2021, 11(12), 884; https://doi.org/10.3390/metabo11120884 - 17 Dec 2021

Cited by 2 | Viewed by 2509

Abstract

Soybean (Glycine max; SB) leaf (SL) is an abundant non-conventional edible resource that possesses value-adding bioactive compounds. We predicted the attributes of SB based on the metabolomes of an SL using targeted metabolomics. The SB was planted in two cities, and [...] Read more.

Soybean (Glycine max; SB) leaf (SL) is an abundant non-conventional edible resource that possesses value-adding bioactive compounds. We predicted the attributes of SB based on the metabolomes of an SL using targeted metabolomics. The SB was planted in two cities, and SLs were regularly obtained from the SB plant. Nine flavonol glycosides were purified from SLs, and a validated simultaneous quantification method was used to establish rapid separation by ultrahigh-performance liquid chromatography-mass detection. Changes in 31 targeted compounds were monitored, and the compounds were discriminated by various supervised machine learning (ML) models. Isoflavones, quercetin derivatives, and flavonol derivatives were discriminators for cultivation days, varieties, and cultivation sites, respectively, using the combined criteria of supervised ML models. The neural model exhibited higher prediction power of the factors with high fitness and low misclassification rates while other models showed lower. We propose that a set of phytochemicals of SL is a useful predictor for discriminating characteristics of edible plants. Full article

(This article belongs to the Special Issue Plant Metabolomics II)

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17 pages, 2950 KiB

Open AccessArticle

Metabolic Fluctuations in the Human Stool Obtained from Blastocystis Carriers and Non-Carriers

by Emma L. Betts, Jamie M. Newton, Gary S. Thompson, Fakhriddin Sarzhanov, Vasana Jinatham, Moon-Ju Kim, Siam Popluechai, Funda Dogruman-Al, Eun-Jeong Won, Eleni Gentekaki and Anastasios D. Tsaousis

Metabolites 2021, 11(12), 883; https://doi.org/10.3390/metabo11120883 - 17 Dec 2021

Cited by 3 | Viewed by 2608

Abstract

Blastocystis is an obligate anaerobic microbial eukaryote that frequently inhabits the gastrointestinal tract. Despite this prevalence, very little is known about the extent of its genetic diversity, pathogenicity, and interaction with the rest of the microbiome and its host. Although the organism is [...] Read more.

Blastocystis is an obligate anaerobic microbial eukaryote that frequently inhabits the gastrointestinal tract. Despite this prevalence, very little is known about the extent of its genetic diversity, pathogenicity, and interaction with the rest of the microbiome and its host. Although the organism is morphologically static, it has no less than 28 genetically distinct subtypes (STs). Reports on the pathogenicity of Blastocystis are conflicting. The association between Blastocystis and intestinal bacterial communities is being increasingly explored. Nonetheless, similar investigations extending to the metabolome are non-existent.Using established NMR metabolomics protocols in 149 faecal samples from individuals from South Korea (n = 38), Thailand (n = 44) and Turkey (n = 69), we have provided a snapshot of the core metabolic compounds present in human stools with (B+) and without (B−) Blastocystis. Samples included hosts with gastrointestinal symptoms and asymptomatics. A total of nine, 62 and 98 significant metabolites were associated with Blastocystis carriage in the South Korean, Thai and Turkish sample sets respectively, with a number of metabolites increased in colonised groups. The metabolic profiles of B+ and B− samples from all countries were distinct and grouped separately in the partial least squares-discriminant analysis (PLS-DA). Typical inflammation-related metabolites negatively associated with Blastocystis positive samples. This data will assist in directing future studies underlying the involvement of Blastocystis in physiological processes of both the gut microbiome and the host. Future studies using metabolome and microbiome data along with host physiology and immune responses information will contribute significantly towards elucidating the role of Blastocystis in health and disease. Full article

(This article belongs to the Special Issue Microbiome and Metabolome)

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8 pages, 3779 KiB

Open AccessReview

Obesogens in Children—An Uncharted Territory

by Mirjam Močnik and Nataša Marčun Varda

Metabolites 2021, 11(12), 882; https://doi.org/10.3390/metabo11120882 - 17 Dec 2021

Cited by 6 | Viewed by 2663

Abstract

Obesogens are exogenous chemicals belonging to the group of endocrine-disrupting chemicals and are believed to interfere in obesity development. In children, several chemicals are under investigation, most commonly bisphenol A, phthalates, perfluorinated alkyl substances, and persistent organic pollutants, including organochlorinated pesticides, tributyltin, polychlorinated [...] Read more.

Obesogens are exogenous chemicals belonging to the group of endocrine-disrupting chemicals and are believed to interfere in obesity development. In children, several chemicals are under investigation, most commonly bisphenol A, phthalates, perfluorinated alkyl substances, and persistent organic pollutants, including organochlorinated pesticides, tributyltin, polychlorinated biphenyls and dioxins. Several associations have been studied between chemical exposure in utero and postnatally. Current opinion among researchers indicates that the obesogen theory is very likely; however, limited published studies show inconsistent support for the obesogenic effects of most substances in children and are limited by difficulty in providing the exact mechanisms of action, nor is their mutual effect in humans known, let alone in children. Existing data indicate that we have only scratched the surface and have much more to learn about obesogens. Hopefully, in the future, more information will provide an opportunity for policy makers to take action and protect public health. Full article

(This article belongs to the Special Issue Obesogens: Risks of Obesity and Metabolic Disease)

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11 pages, 1289 KiB

Open AccessArticle

Reduced Fatty Acid Use from CD36 Deficiency Deteriorates Streptozotocin-Induced Diabetic Cardiomyopathy in Mice

by Yogi Umbarawan, Ryo Kawakami, Mas Rizky A. A. Syamsunarno, Hideru Obinata, Aiko Yamaguchi, Hirofumi Hanaoka, Takako Hishiki, Noriyo Hayakawa, Norimichi Koitabashi, Hiroaki Sunaga, Hiroki Matsui, Masahiko Kurabayashi and Tatsuya Iso

Metabolites 2021, 11(12), 881; https://doi.org/10.3390/metabo11120881 - 17 Dec 2021

Cited by 2 | Viewed by 2766

Abstract

Cardiac dysfunction is induced by multifactorial mechanisms in diabetes. Deranged fatty acid (FA) utilization, known as lipotoxicity, has long been postulated as one of the upstream events in the development of diabetic cardiomyopathy. CD36, a transmembrane glycoprotein, plays a major role in FA [...] Read more.

Cardiac dysfunction is induced by multifactorial mechanisms in diabetes. Deranged fatty acid (FA) utilization, known as lipotoxicity, has long been postulated as one of the upstream events in the development of diabetic cardiomyopathy. CD36, a transmembrane glycoprotein, plays a major role in FA uptake in the heart. CD36 knockout (CD36KO) hearts exhibit reduced rates of FA transport with marked enhancement of glucose use. In this study, we explore whether reduced FA use by CD36 ablation suppresses the development of streptozotocin (STZ)-induced diabetic cardiomyopathy. We found that cardiac contractile dysfunction had deteriorated 16 weeks after STZ treatment in CD36KO mice. Although accelerated glucose uptake was not reduced in CD36KO-STZ hearts, the total energy supply, estimated by the pool size in the TCA cycle, was significantly reduced. The isotopomer analysis with ¹³C₆-glucose revealed that accelerated glycolysis, estimated by enrichment of ¹³C₂-citrate and ¹³C₂-malate, was markedly suppressed in CD36KO-STZ hearts. Levels of ceramides, which are cardiotoxic lipids, were not elevated in CD36KO-STZ hearts compared to wild-type-STZ ones. Furthermore, increased energy demand by transverse aortic constriction resulted in synergistic exacerbation of contractile dysfunction in CD36KO-STZ mice. These findings suggest that CD36KO-STZ hearts are energetically compromised by reduced FA use and suppressed glycolysis; therefore, the limitation of FA utilization is detrimental to cardiac energetics in this model of diabetic cardiomyopathy. Full article

(This article belongs to the Special Issue Insights into the Bioenergetics and Metabolism in Normal and Failing Heart)

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20 pages, 2971 KiB

Open AccessArticle

Comparative Metabolomics Reveals Two Metabolic Modules Affecting Seed Germination in Rice (Oryza sativa)

by Hao Guo, Yuanyuan Lyv, Weikang Zheng, Chenkun Yang, Yufei Li, Xuyang Wang, Ridong Chen, Chao Wang, Jie Luo and Lianghuan Qu

Metabolites 2021, 11(12), 880; https://doi.org/10.3390/metabo11120880 - 17 Dec 2021

Cited by 8 | Viewed by 2674

Abstract

The process of seed germination is crucial not only for the completion of the plant life cycle but also for agricultural production and food chemistry; however, the underlying metabolic regulation mechanism involved in this process is still far from being clearly revealed. In [...] Read more.

The process of seed germination is crucial not only for the completion of the plant life cycle but also for agricultural production and food chemistry; however, the underlying metabolic regulation mechanism involved in this process is still far from being clearly revealed. In this study, one indica variety (Zhenshan 97, with rapid germination) and one japonica variety (Nipponbare, with slow germination) in rice were used for in-depth analysis of the metabolome at different germination stages (0, 3, 6, 9, 12, 24, 36, and 48 h after imbibition, HAI) and exploration of key metabolites/metabolic pathways. In total, 380 annotated metabolites were analyzed by using a high-performance liquid chromatography (HPLC)-based targeted method combined with a nontargeted metabolic profiling method. By using bioinformatics and statistical methods, the dynamic changes in metabolites during germination in the two varieties were compared. Through correlation analysis, coefficient of variation analysis and differential accumulation analysis, 74 candidate metabolites that may be closely related to seed germination were finally screened. Among these candidates, 29 members belong to the ornithine–asparagine–polyamine module and the shikimic acid–tyrosine–tryptamine–phenylalanine–flavonoid module. As the core member of the second module, shikimic acid’s function in the promotion of seed germination was confirmed by exogenous treatment. These results told that nitrogen flow and antioxidation/defense responses are potentially crucial for germinating seeds and seedlings. It deepens our understanding of the metabolic regulation mechanism of seed germination and points out the direction for our future research. Full article

(This article belongs to the Section Plant Metabolism)

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25 pages, 8659 KiB

Open AccessArticle

Metabolomics Insights into Chemical Convergence in Xanthomonas perforans and Metabolic Changes Following Treatment with the Small Molecule Carvacrol

by Mustafa Ojonuba Jibrin, Qingchun Liu, Joy Guingab-Cagmat, Jeffrey B. Jones, Timothy J. Garrett and Shouan Zhang

Metabolites 2021, 11(12), 879; https://doi.org/10.3390/metabo11120879 - 16 Dec 2021

Cited by 4 | Viewed by 3342

Abstract

Microbes are natural chemical factories and their metabolome comprise diverse arrays of chemicals. The genus Xanthomonas comprises some of the most important plant pathogens causing devastating yield losses globally and previous studies suggested that species in the genus are untapped chemical minefields. In [...] Read more.

Microbes are natural chemical factories and their metabolome comprise diverse arrays of chemicals. The genus Xanthomonas comprises some of the most important plant pathogens causing devastating yield losses globally and previous studies suggested that species in the genus are untapped chemical minefields. In this study, we applied an untargeted metabolomics approach to study the metabolome of a globally spread important xanthomonad, X. perforans. The pathogen is difficult to manage, but recent studies suggest that the small molecule carvacrol was efficient in disease control. Bacterial strains were treated with carvacrol, and samples were taken at time intervals (1 and 6 h). An untreated control was also included. There were five replicates for each sample and samples were prepared for metabolomics profiling using the standard procedure. Metabolomics profiling was carried out using a thermo Q-Exactive orbitrap mass spectrometer with Dionex ultra high-performance liquid chromatography (UHPLC) and an autosampler. Annotation of significant metabolites using the Metabolomics Standards Initiative level 2 identified an array of novel metabolites that were previously not reported in Xanthomonas perforans. These metabolites include methoxybrassinin and cyclobrassinone, which are known metabolites of brassicas; sarmentosin, a metabolite of the Passiflora-heliconiine butterfly system; and monatin, a naturally occurring sweetener found in Sclerochiton ilicifolius. To our knowledge, this is the first report of these metabolites in a microbial system. Other significant metabolites previously identified in non-Xanthomonas systems but reported in this study include maculosin; piperidine; β-carboline alkaloids, such as harman and derivatives; and several important medically relevant metabolites, such as valsartan, metharbital, pirbuterol, and ozagrel. This finding is consistent with convergent evolution found in reported biological systems. Analyses of the effect of carvacrol in time-series and associated pathways suggest that carvacrol has a global effect on the metabolome of X. perforans, showing marked changes in metabolites that are critical in energy biosynthesis and degradation pathways, amino acid pathways, nucleic acid pathways, as well as the newly identified metabolites whose pathways are unknown. This study provides the first insight into the X. perforans metabolome and additionally lays a metabolomics-guided foundation for characterization of novel metabolites and pathways in xanthomonad systems. Full article

(This article belongs to the Section Plant Metabolism)

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19 pages, 1730 KiB

Open AccessArticle

The Effects of Fermentation of Low or High Tannin Fava Bean-Based Diets on Glucose Response, Cardiovascular Function, and Fecal Bile Acid Excretion during a 28-Day Feeding Period in Dogs: Comparison with Commercial Diets with Normal vs. High Protein

by Luciana G. Reis, Tressa Morris, Chloe Quilliam, Lucas A. Rodrigues, Matthew E. Loewen and Lynn P. Weber

Metabolites 2021, 11(12), 878; https://doi.org/10.3390/metabo11120878 - 16 Dec 2021

Cited by 3 | Viewed by 2598

Abstract

We have shown that feeding dogs fava bean (FB)-based diets for 7 days is safe and FB flour fermentation with Candida utilis has the potential to decrease FB anti-nutritional factors. In the present study, the effects of 28-day feeding of 4 different FB-based [...] Read more.

We have shown that feeding dogs fava bean (FB)-based diets for 7 days is safe and FB flour fermentation with Candida utilis has the potential to decrease FB anti-nutritional factors. In the present study, the effects of 28-day feeding of 4 different FB-based test dog foods containing moderate protein (~27% dry matter (DM)) were compared with two commercial diets with normal protein (NP, grain-containing, ~31% DM protein) or high protein (HP, grain-free, ~41% DM protein). Health parameters were investigated in beagles fed the NP or HP diets or using a randomized, crossover, 2 × 2 Latin square design of the FB diets: unfermented high-tannin (UF-HT), fermented high-tannin (FM-HT), unfermented low-tannin (UF-LT), and fermented low-tannin (FM-LT). The results showed that fermentation increased glucose tolerance, increased red blood cell numbers and increased systolic blood pressure, but decreased flow-mediated vasodilation. Taken together, the overall effect of fermentation appears to be beneficial and improved FB nutritional value. Most interesting, even though the HP diet was grain-free, the diet did contain added taurine, and no adverse effects on cardiac function were observed, while glucose tolerance was impaired compared to NP-fed dogs. In summary, this study did not find evidence of adverse cardiac effects of pulses in ‘grain-free’ diets, at least not in the relatively resistant beagle breed over a 28-day period. More importantly, fermentation with C. utilis shows promise to enhance health benefits of pulses such as FB in dog food. Full article

(This article belongs to the Special Issue Effects of Diet on Protein and Energy Metabolism in Companion Animals)

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10 pages, 6210 KiB

Open AccessArticle

Exploring the Link between Leaky-Gut-Related Markers and Metabolic Health in a Large Dutch Adult Population

by Hiroyuki Hoshiko, Edith J. M. Feskens, Els Oosterink, Renata M. C. Ariens, Jurriaan J. Mes and Nicole J. W. de Wit

Metabolites 2021, 11(12), 877; https://doi.org/10.3390/metabo11120877 - 16 Dec 2021

Viewed by 2212

Abstract

A leaky gut can trigger chronic inflammation and poses a primary risk for metabolic diseases. This study established a relationship between intestinal integrity (leaky gut) and metabolic health in a general population. Leaky-gut markers (LGMs) were studied in a large population of Dutch [...] Read more.

A leaky gut can trigger chronic inflammation and poses a primary risk for metabolic diseases. This study established a relationship between intestinal integrity (leaky gut) and metabolic health in a general population. Leaky-gut markers (LGMs) were studied in a large population of Dutch adults with a broad spectrum of metabolic health. This study enrolled 500 individuals selected within the NQplus cohort study (n = 2048) by stratified randomization, based on waist circumference, fasting glucose, and high-density lipoprotein (HDL) cholesterol to obtain a representative and balanced population in terms of metabolic health parameters, sex (male/female), and age (<54/≥54 years). LGMs—zonulin, lipopolysaccharide-binding protein (LBP), and soluble CD14 (sCD14)—were measured in EDTA plasma or serum. Zonulin was most strongly associated with metabolic health. Zonulin and LBP were most strongly associated with the inflammatory marker C-reactive protein (CRP). The quartile analysis for zonulin and LBP showed that most metabolic health parameters and CRP levels increased from Q1 to Q4, with significant differences between quartiles, except for markers related to glucose homeostasis (glucose and glycated hemoglobin A1c (HbA1c)). Associations between LGMs and metabolic health parameters in this large Dutch adult population indicate that LGMs are valuable markers for identifying people at risk of a leaky gut and subsequent chronic inflammation linked to metabolic disorders. Full article

(This article belongs to the Section Endocrinology and Clinical Metabolic Research)

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13 pages, 1240 KiB

Open AccessArticle

Activity of Semi-Synthetic Mulinanes against MDR, Pre-XDR, and XDR Strains of Mycobacterium tuberculosis

by María Alejandrina Martínez-González, Luis Manuel Peña-Rodríguez, Andrés Humberto Uc-Cachón, Jorge Bórquez, Mario J. Simirgiotis, Hugo Brígido Barrios-García, Rogelio Hernández-Pando, Luis Alberto Loyola, Carlos Areche, Angel de Jesús Dzul-Beh, Jorge Alberto Barrios-Payán, Dulce Mata-Espinosa, Fabiola Escalante-Erosa, Karlina García-Sosa and Gloria María Molina-Salinas

Metabolites 2021, 11(12), 876; https://doi.org/10.3390/metabo11120876 - 16 Dec 2021

Cited by 1 | Viewed by 2272

Abstract

Tuberculosis causes more than 1.2 million deaths each year. Worldwide, it is the first cause of death by a single infectious agent. The emergence of drug-resistant strains has limited pharmacological treatment of the disease and today, new drugs are urgently needed. Semi-synthetic mulinanes [...] Read more.

Tuberculosis causes more than 1.2 million deaths each year. Worldwide, it is the first cause of death by a single infectious agent. The emergence of drug-resistant strains has limited pharmacological treatment of the disease and today, new drugs are urgently needed. Semi-synthetic mulinanes have previously shown important activity against multidrug-resistant (MDR) Mycobacterium tuberculosis. In this investigation, a new set of semi-synthetic mulinanes were synthetized, characterized, and evaluated for their in vitro activity against three drug-resistant clinical isolates of M. tuberculosis: MDR, pre-extensively Drug-Resistant (pre-XDR), and extensively Drug-Resistant (XDR), and against the drug-susceptible laboratory reference strain H37Rv. Derivative 1a showed the best anti-TB activity (minimum inhibitory concentration [MIC] = 5.4 µM) against the susceptible strain and was twice as potent (MIC = 2.7 µM) on the MDR, pre-XDR, and XDR strains and also possessed a bactericidal effect. Derivative 1a was also tested for its anti-TB activity in mice infected with the MDR strain. In this case, 1a produced a significant reduction of pulmonary bacilli loads, six times lower than the control, when tested at 0.2536 mg/Kg. In addition, 1a demonstrated an adjuvant effect by shortening second-line chemotherapy. Finally, the selectivity index of >15.64 shown by 1a when tested on Vero cells makes this derivative an important candidate for future studies in the development of novel antitubercular agents. Full article

(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics Volume 2)

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16 pages, 2227 KiB

Open AccessReview

Metabolic Volume Measurements in Multiple Myeloma

by Maria Emilia Seren Takahashi, Irene Lorand-Metze, Carmino Antonio de Souza, Claudio Tinoco Mesquita, Fernando Amorim Fernandes, José Barreto Campello Carvalheira and Celso Dario Ramos

Metabolites 2021, 11(12), 875; https://doi.org/10.3390/metabo11120875 - 16 Dec 2021

Cited by 3 | Viewed by 2762

Abstract

Multiple myeloma (MM) accounts for 10–15% of all hematologic malignancies, as well as 20% of deaths related to hematologic malignant tumors, predominantly affecting bone and bone marrow. Positron emission tomography/computed tomography with 18F-fluorodeoxyglucose (FDG-PET/CT) is an important method to assess the tumor burden [...] Read more.

Multiple myeloma (MM) accounts for 10–15% of all hematologic malignancies, as well as 20% of deaths related to hematologic malignant tumors, predominantly affecting bone and bone marrow. Positron emission tomography/computed tomography with 18F-fluorodeoxyglucose (FDG-PET/CT) is an important method to assess the tumor burden of these patients. It is often challenging to classify the extent of disease involvement in the PET scans for many of these patients because both focal and diffuse bone lesions may coexist, with varying degrees of FDG uptake. Different metrics involving volumetric parameters and texture features have been proposed to objectively assess these images. Here, we review some metabolic parameters that can be extracted from FDG-PET/CT images of MM patients, including technical aspects and predicting MM outcome impact. Metabolic tumor volume (MTV) and total lesion glycolysis (TLG) are volumetric parameters known to be independent predictors of MM outcome. However, they have not been adopted in clinical practice due to the lack of measuring standards. CT-based segmentation allows automated, and therefore reproducible, calculation of bone metabolic metrics in patients with MM, such as maximum, mean and standard deviation of the standardized uptake values (SUV) for the entire skeleton. Intensity of bone involvement (IBI) is a new parameter that also takes advantage of this approach with promising results. Other indirect parameters obtained from FDG-PET/CT images, such as visceral adipose tissue glucose uptake and subcutaneous adipose tissue radiodensity, may also be useful to evaluate the prognosis of MM patients. Furthermore, the use and quantification of new radiotracers can address different metabolic aspects of MM and may have important prognostic implications. Full article

(This article belongs to the Special Issue Metabolic Volume Measurements)

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17 pages, 3622 KiB

Open AccessArticle

Serum Metabolic Profiles Based on Nuclear Magnetic Resonance Spectroscopy among Patients with Deep Vein Thrombosis and Healthy Controls

by Melissa Quintero Escobar, Ljubica Tasic, Tassia Brena Barroso Carneiro da Costa, Danijela Stanisic, Silmara Montalvão, Stephany Huber and Joyce Maria Annichino-Bizzacchi

Metabolites 2021, 11(12), 874; https://doi.org/10.3390/metabo11120874 - 16 Dec 2021

Cited by 6 | Viewed by 2583

Abstract

Deep venous thrombosis (DVT) is associated with significant morbidity and mortality. Studies on changes in the level of metabolites could have the potential to reveal biomarkers that can assist in the early detection, diagnosis, monitoring of DVT progression, response to treatment, or recurrence [...] Read more.

Deep venous thrombosis (DVT) is associated with significant morbidity and mortality. Studies on changes in the level of metabolites could have the potential to reveal biomarkers that can assist in the early detection, diagnosis, monitoring of DVT progression, response to treatment, or recurrence of DVT. In this scenario, the metabolomic analysis can provide a better understanding of the biochemical dysregulations of thrombosis. Using an untargeted metabolomic approach through magnetic resonance spectroscopy and multi- and univariate statistical analysis, we compared 40 patients with previous venous thrombosis and 40 healthy individuals, and we showed important serum differences between patients and controls, especially in the spectral regions that correspond to glucose, lipids, unsaturated lipids, and glycoprotein A. Considering the groups depending on risk factors and the local of the previous episode (lower limbs or cerebral system), we also noticed differences in metabolites linked to lipids and lactate. Comparative analyses pointed to altered ratios of glucose/lactate and branched-chain amino acids (BCAAs)/alanine, which might be associated with the fingerprints of thrombosis. Although samples for metabolomic analysis were collected months after the acute episode, these results highlighted that, alterations can still remain and may contribute to a better understanding of the complications of the disease. Full article

(This article belongs to the Special Issue Thrombosis and Metabolism)

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16 pages, 3118 KiB

Open AccessArticle

Promotion of In Vitro Hair Cell-like Cell Differentiation from Human Embryonic Stem Cells through the Regulation of Notch Signaling

by Fengjiao Chen, Ying Yang, Jianling Chen, Zihua Tang, Qian Peng, Jinfu Wang and Jie Ding

Metabolites 2021, 11(12), 873; https://doi.org/10.3390/metabo11120873 - 15 Dec 2021

Cited by 1 | Viewed by 2418

Abstract

The Notch signaling pathway plays an important role in otic neurogenesis by regulating the differentiation of inner ear hair cells and supporting cells. Notch-regulated differentiation is required for the regeneration of hair cells in the inner ear. The temporal expression pattern of Notch [...] Read more.

The Notch signaling pathway plays an important role in otic neurogenesis by regulating the differentiation of inner ear hair cells and supporting cells. Notch-regulated differentiation is required for the regeneration of hair cells in the inner ear. The temporal expression pattern of Notch ligands and receptors during in vitro hair cell-like cell differentiation from human embryonic stem cells (hESCs) was detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Subsequently, pAJ-U6-shRNA-CMV-Puro/GFP recombinant lentiviral vectors encoding short hairpin RNAs were used to silence JAG-1, JAG-2, and DLL-1, according to the temporal expression pattern of Notch ligands. Then, the effect of each ligand on the in vitro differentiation of hair cells was examined by RT-PCR, immunofluorescence, and scanning electron microscopy (SEM). The results showed that the individual deletion of JAG-2 or DLL-1 had no significant effect on the differentiation of hair cell-like cells. However, the simultaneous inhibition of both DLL-1 and JAG-2 increased the number of hair cell-like cells and decreased the number of supporting cells. JAG-2 and DLL-1 may have a synergistic role in in vitro hair cell differentiation. Full article

(This article belongs to the Collection Advances in Metabolomics)

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11 pages, 728 KiB

Open AccessArticle

Exhaled Metabolite Patterns to Identify Recent Asthma Exacerbations

by Job J. M. H. van Bragt, Stefania Principe, Simone Hashimoto, D. Naomi Versteeg, Paul Brinkman, Susanne J. H. Vijverberg, Els J. M. Weersink, Nicola Scichilone and Anke H. Maitland-van der Zee

Metabolites 2021, 11(12), 872; https://doi.org/10.3390/metabo11120872 - 15 Dec 2021

Cited by 2 | Viewed by 1928

Abstract

Asthma is a chronic respiratory disease that can lead to exacerbations, defined as acute episodes of worsening respiratory symptoms and lung function. Predicting the occurrence of these exacerbations is an important goal in asthma management. The measurement of exhaled breath by electronic nose [...] Read more.

Asthma is a chronic respiratory disease that can lead to exacerbations, defined as acute episodes of worsening respiratory symptoms and lung function. Predicting the occurrence of these exacerbations is an important goal in asthma management. The measurement of exhaled breath by electronic nose (eNose) may allow for the monitoring of clinically unstable asthma and exacerbations. However, data on its ability to perform this is lacking. We aimed to evaluate whether eNose could identify patients that recently had asthma exacerbations. We performed a cross-sectional study, measuring exhaled breath using the SpiroNose in adults with a physician-reported diagnosis of asthma. Patients were randomly divided into a training (n = 252) and validation (n = 109) set. For the analysis of eNose signals, principal component (PC) and linear discriminant analysis (LDA) were performed. LDA, based on PC1-4, reliably discriminated between patients who had a recent exacerbation from those who had not (training receiver operating characteristic (ROC)–area under the curve (AUC) = 0.76,95% CI 0.69–0.82), (validation AUC = 0.76, 95% CI 0.64–0.87). Our study showed that, exhaled breath analysis using eNose could accurately identify asthma patients who recently had an exacerbation, and could indicate that asthma exacerbations have a specific exhaled breath pattern detectable by eNose. Full article

(This article belongs to the Special Issue Using Metabolomics to Subphenotype Disease and Therapeutic Response)

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20 pages, 2271 KiB

Open AccessArticle

Distribution and Associated Factors of Hepatic Iron—A Population-Based Imaging Study

by Lisa Maier, Ricarda von Krüchten, Roberto Lorbeer, Jule Filler, Johanna Nattenmüller, Barbara Thorand, Wolfgang Koenig, Wolfgang Rathmann, Fabian Bamberg, Christopher L. Schlett, Annette Peters and Susanne Rospleszcz

Metabolites 2021, 11(12), 871; https://doi.org/10.3390/metabo11120871 - 15 Dec 2021

Cited by 2 | Viewed by 2588

Abstract

Hepatic iron overload can cause severe organ damage; therefore, an early diagnosis and the identification of potential risk factors is crucial. We aimed to investigate the sex-specific distribution of hepatic iron content (HIC) in a population-based cohort and identify relevant associated factors from [...] Read more.

Hepatic iron overload can cause severe organ damage; therefore, an early diagnosis and the identification of potential risk factors is crucial. We aimed to investigate the sex-specific distribution of hepatic iron content (HIC) in a population-based cohort and identify relevant associated factors from a panel of markers. We analyzed N = 353 participants from a cross-sectional sample (KORA FF4) who underwent whole-body magnetic resonance imaging. HIC was assessed by single-voxel spectroscopy with a high-speed T2-corrected multi-echo technique. A large panel of markers, including anthropometric, genetic, and laboratory values, as well as behavioral risk factors were assessed. Relevant factors associated with HIC were identified by variable selection based on LASSO regression with bootstrap resampling. HIC in the study sample (mean age at examination: 56.0 years, 58.4% men) was significantly lower in women (mean ± SD: 39.2 ± 4.1 s⁻¹) than in men (41.8 ± 4.7 s⁻¹, p < 0.001). Relevant factors associated with HIC were HbA1c as well as prediabetes for men and visceral adipose tissue as well as age for women. Hepatic fat, alcohol consumption, and genetic risk score for iron levels were associated with HIC in both sexes. In conclusion, there are sex-specific associations of HIC with markers of body composition, glucose metabolism, and alcohol consumption. Full article

(This article belongs to the Special Issue The Application of Imaging Technology in Studying Liver Metabolism)

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13 pages, 1158 KiB

Open AccessArticle

Alterations of Selected Hemorheological and Metabolic Parameters Induced by Physical Activity in Untrained Men and Sportsmen

by Sandor Szanto, Tobias Mody, Zsuzsanna Gyurcsik, Laszlo Balint Babjak, Viktoria Somogyi, Barbara Barath, Adam Varga, Adam Attila Matrai and Norbert Nemeth

Metabolites 2021, 11(12), 870; https://doi.org/10.3390/metabo11120870 - 14 Dec 2021

Cited by 9 | Viewed by 2056

Abstract

Optimal tissue oxygen supply is essential for proper athletic performance and endurance. It also depends on perfusion, so on hemorheological properties and microcirculation. Regular exercise is beneficial to the rheological status, depending on its type, intensity, and duration. We aimed to investigate macro [...] Read more.

Optimal tissue oxygen supply is essential for proper athletic performance and endurance. It also depends on perfusion, so on hemorheological properties and microcirculation. Regular exercise is beneficial to the rheological status, depending on its type, intensity, and duration. We aimed to investigate macro and microrheological changes due to short, high-intensity exercise in professional athletes (soccer and ice hockey players) and untrained individuals. The exercise was performed on a treadmill ergometer during a spiroergometry examination. Blood samples were taken before and after exercise to analyze lactate concentration, hematological parameters, blood and plasma viscosity, and red blood cell (RBC) deformability and aggregation. Leukocyte, RBC and platelet counts, and blood viscosity increased with exercise, by the largest magnitude in the untrained group. RBC deformability slightly impaired after exercise, but showed better values in ice hockey versus soccer players. RBC aggregation increased with exercise, dominantly in ice hockey players. Lactate increased mostly in soccer players, and the respiratory exchange rate was the lowest in ice hockey players. Overall, short, high-intensity exercise altered macro and microrheological parameters, mostly in the untrained group. Significant differences were found between the two sports. The data can be useful in training status monitoring, selection, and in revealing the causes of physical loading symptoms. Full article

(This article belongs to the Special Issue Hemorheology and Metabolism)

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18 pages, 643 KiB

Open AccessReview

Metabolic Syndrome and PCOS: Pathogenesis and the Role of Metabolites

by Weixuan Chen and Yanli Pang

Metabolites 2021, 11(12), 869; https://doi.org/10.3390/metabo11120869 - 14 Dec 2021

Cited by 52 | Viewed by 7935

Abstract

Polycystic ovary syndrome (PCOS) is one of the most common endocrine diseases among women of reproductive age and is associated with many metabolic manifestations, such as obesity, insulin resistance (IR) and hyperandrogenism. The underlying pathogenesis of these metabolic symptoms has not yet been [...] Read more.

Polycystic ovary syndrome (PCOS) is one of the most common endocrine diseases among women of reproductive age and is associated with many metabolic manifestations, such as obesity, insulin resistance (IR) and hyperandrogenism. The underlying pathogenesis of these metabolic symptoms has not yet been fully elucidated. With the application of metabolomics techniques, a variety of metabolite changes have been observed in the serum and follicular fluid (FF) of PCOS patients and animal models. Changes in metabolites result from the daily diet and occur during uncommon physiological routines. However, some of these metabolite changes may provide evidence to explain possible mechanisms and new approaches for prevention and therapy. This article reviews the pathogenesis of PCOS metabolic symptoms and the relationship between metabolites and the pathophysiology of PCOS. Furthermore, the potential clinical application of some specific metabolites will be discussed. Full article

(This article belongs to the Special Issue Metabolism and Reproduction)

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14 pages, 1156 KiB

Open AccessArticle

Circulating Metabolites Indicate Differences in High and Low Residual Feed Intake Holstein Dairy Cows

by Malia J. Martin, Ryan S. Pralle, Isabelle R. Bernstein, Michael J. VandeHaar, Kent A. Weigel, Zheng Zhou and Heather M. White

Metabolites 2021, 11(12), 868; https://doi.org/10.3390/metabo11120868 - 14 Dec 2021

Cited by 7 | Viewed by 2317

Abstract

Selection for more feed efficient dairy cows is key to improving sustainability and profitability of dairy production; however, underlying mechanisms contributing to individual animal feed efficiency are not fully understood. The objective of this study was to identify circulating metabolites, and pathways associated [...] Read more.

Selection for more feed efficient dairy cows is key to improving sustainability and profitability of dairy production; however, underlying mechanisms contributing to individual animal feed efficiency are not fully understood. The objective of this study was to identify circulating metabolites, and pathways associated with those metabolites, that differ between efficient and inefficient Holstein dairy cows using targeted metabolite quantification and untargeted metabolomics. The top and bottom fifteen percent of cows (n = 28/group) with the lowest and highest residual feed intake in mid-lactation feed efficiency trials were grouped retrospectively as high-efficient (HE) and low-efficient (LE). Blood samples were collected for quantification of energy metabolites, markers of hepatic function, and acylcarnitines, in addition to a broader investigation using untargeted metabolomics. Short-chain acylcarnitines, C3-acylcarnitine, and C4-acylcarntine were lower in HE cows (n = 18/group). Untargeted metabolomics and multivariate analysis identified thirty-nine differential metabolites between HE and LE (n = 8/group), of which twenty-five were lower and fourteen were higher in HE. Pathway enrichment analysis indicated differences in tryptophan metabolism. Combined results from targeted metabolite quantification and untargeted metabolomics indicate differences in fatty acid and amino acid metabolism between HE and LE cows. These differences may indicate post-absorptive nutrient use efficiency as a contributor to individual animal variation in feed efficiency. Full article

(This article belongs to the Special Issue Multi-Omics Methods in Dairy Research)

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14 pages, 1891 KiB

Open AccessArticle

Nitrogen Availability Affects the Metabolic Profile in Cyanobacteria

by Kosuke Inabe, Ayaka Miichi, Mami Matsuda, Takanobu Yoshida, Yuichi Kato, Ryota Hidese, Akihiko Kondo and Tomohisa Hasunuma

Metabolites 2021, 11(12), 867; https://doi.org/10.3390/metabo11120867 - 14 Dec 2021

Cited by 4 | Viewed by 2575

Abstract

Nitrogen is essential for the biosynthesis of various molecules in cells, such as amino acids and nucleotides, as well as several types of lipids and sugars. Cyanobacteria can assimilate several forms of nitrogen, including nitrate, ammonium, and urea, and the physiological and genetic [...] Read more.

Nitrogen is essential for the biosynthesis of various molecules in cells, such as amino acids and nucleotides, as well as several types of lipids and sugars. Cyanobacteria can assimilate several forms of nitrogen, including nitrate, ammonium, and urea, and the physiological and genetic responses to these nitrogen sources have been studied previously. However, the metabolic changes in cyanobacteria caused by different nitrogen sources have not yet been characterized. This study aimed to elucidate the influence of nitrate and ammonium on the metabolic profiles of the cyanobacterium Synechocystis sp. strain PCC 6803. When supplemented with NaNO₃ or NH₄Cl as the nitrogen source, Synechocystis sp. PCC 6803 grew faster in NH₄Cl medium than in NaNO₃ medium. Metabolome analysis indicated that some metabolites in the CBB cycle, glycolysis, and TCA cycle, and amino acids were more abundant when grown in NH₄Cl medium than NaNO₃ medium. ¹⁵N turnover rate analysis revealed that the nitrogen assimilation rate in NH₄Cl medium was higher than in NaNO₃ medium. These results indicate that the mechanism of nitrogen assimilation in the GS-GOGAT cycle differs between NaNO₃ and NH₄Cl. We conclude that the amounts and biosynthetic rate of cyanobacterial metabolites varies depending on the type of nitrogen. Full article

(This article belongs to the Special Issue Stable Isotope Guided Metabolomics II)

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17 pages, 2577 KiB

Open AccessArticle

Enhanced β-carotene and Biomass Production by Induced Mixotrophy in Dunaliella salina across a Combined Strategy of Glycerol, Salinity, and Light

by Willian Capa-Robles, Ernesto García-Mendoza and José de Jesús Paniagua-Michel

Metabolites 2021, 11(12), 866; https://doi.org/10.3390/metabo11120866 - 13 Dec 2021

Cited by 8 | Viewed by 3428

Abstract

Current mixotrophic culture systems for Dunaliella salina have technical limitations to achieve high growth and productivity. The purpose of this study was to optimize the mixotrophic conditions imposed by glycerol, light, and salinity that lead to the highest biomass and β-carotene yields in [...] Read more.

Current mixotrophic culture systems for Dunaliella salina have technical limitations to achieve high growth and productivity. The purpose of this study was to optimize the mixotrophic conditions imposed by glycerol, light, and salinity that lead to the highest biomass and β-carotene yields in D. salina. The combination of 12.5 mM glycerol, 3.0 M salinity, and 50 μmol photons m⁻² s⁻¹ light intensity enabled significant assimilation of glycerol by D. salina and consequently enhanced growth (2.1 × 10⁶ cell mL⁻¹) and β-carotene accumulation (4.43 pg cell⁻¹). The saline and light shock induced the assimilation of glycerol by this microalga. At last stage of growth, the increase in light intensity (300 μmol photons m⁻² s⁻¹) caused the β-carotene to reach values higher than 30 pg cell⁻¹ and tripled the β-carotene values obtained from photoautotrophic cultures using the same light intensity. Increasing the salt concentration from 1.5 to 3.0 M NaCl (non-isosmotic salinity) produced higher growth and microalgal β-carotene than the isosmotic salinity 3.0 M NaCl. The mixotrophic strategy developed in this work is evidenced in the metabolic capability of D. salina to use both photosynthesis and organic carbon, viz., glycerol that leads to higher biomass and β-carotene productivity than that of an either phototrophic or heterotrophic process alone. The findings provide insights into the key role of exogenous glycerol with a strategic combination of salinity and light, which evidenced unknown roles of this polyol other than that in osmoregulation, mainly on the growth, pigment accumulation, and carotenogenesis of D. salina. Full article

(This article belongs to the Special Issue Marine Natural Products: Chemical Ecology and Metabolomics)

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17 pages, 4494 KiB

Open AccessFeature PaperReview

Perspective on the Structural Basis for Human Aldo-Keto Reductase 1B10 Inhibition

by Francesc Xavier Ruiz, Xavier Parés and Jaume Farrés

Metabolites 2021, 11(12), 865; https://doi.org/10.3390/metabo11120865 - 13 Dec 2021

Cited by 2 | Viewed by 2334

Abstract

Human aldo-keto reductase 1B10 (AKR1B10) is overexpressed in many cancer types and is involved in chemoresistance. This makes AKR1B10 to be an interesting drug target and thus many enzyme inhibitors have been investigated. High-resolution crystallographic structures of AKR1B10 with various reversible inhibitors were [...] Read more.

Human aldo-keto reductase 1B10 (AKR1B10) is overexpressed in many cancer types and is involved in chemoresistance. This makes AKR1B10 to be an interesting drug target and thus many enzyme inhibitors have been investigated. High-resolution crystallographic structures of AKR1B10 with various reversible inhibitors were deeply analyzed and compared to those of analogous complexes with aldose reductase (AR). In both enzymes, the active site included an anion-binding pocket and, in some cases, inhibitor binding caused the opening of a transient specificity pocket. Different structural conformers were revealed upon inhibitor binding, emphasizing the importance of the highly variable loops, which participate in the transient opening of additional binding subpockets. Two key differences between AKR1B10 and AR were observed regarding the role of external loops in inhibitor binding. The first corresponded to the alternative conformation of Trp112 (Trp111 in AR). The second difference dealt with loop A mobility, which defined a larger and more loosely packed subpocket in AKR1B10. From this analysis, the general features that a selective AKR1B10 inhibitor should comply with are the following: an anchoring moiety to the anion-binding pocket, keeping Trp112 in its native conformation (AKR1B10-like), and not opening the specificity pocket in AR. Full article

(This article belongs to the Special Issue Metabolic Regulation of Aldo-Keto Reductases)

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14 pages, 2637 KiB

Open AccessArticle

Methodology for Single Bee and Bee Brain ¹H-NMR Metabolomics

by Jayne C. McDevitt, Riju A. Gupta, Sydney G. Dickinson, Phillip L. Martin, Jean Rieuthavorn, Amy Freund, Marie C. Pizzorno, Elizabeth A. Capaldi and David Rovnyak

Metabolites 2021, 11(12), 864; https://doi.org/10.3390/metabo11120864 - 13 Dec 2021

Cited by 1 | Viewed by 3271

Abstract

The feasibility of metabolomic ¹H NMR spectroscopy is demonstrated for its potential to help unravel the complex factors that are impacting honeybee health and behavior. Targeted and non-targeted ¹H NMR metabolic profiles of liquid and tissue samples of organisms could provide [...] Read more.

The feasibility of metabolomic ¹H NMR spectroscopy is demonstrated for its potential to help unravel the complex factors that are impacting honeybee health and behavior. Targeted and non-targeted ¹H NMR metabolic profiles of liquid and tissue samples of organisms could provide information on the pathology of infections and on environmentally induced stresses. This work reports on establishing extraction methods for NMR metabolic characterization of Apis mellifera, the European honeybee, describes the currently assignable aqueous metabolome, and gives examples of diverse samples (brain, head, body, whole bee) and biologically meaningful metabolic variation (drone, forager, day old, deformed wing virus). Both high-field (600 MHz) and low-field (80 MHz) methods are applicable, and ¹H NMR can observe a useful subset of the metabolome of single bees using accessible NMR instrumentation (600 MHz, inverse room temperature probe) in order to avoid pooling several bees. Metabolite levels and changes can be measured by NMR in the bee brain, where dysregulation of metabolic processes has been implicated in colony collapse. For a targeted study, the ability to recover 10-hydroxy-2-decenoic acid in mandibular glands is shown, as well as markers of interest in the bee brain such as GABA (4-aminobutyrate), proline, and arginine. The findings here support the growing use of ¹H NMR more broadly in bees, native pollinators, and insects. Full article

(This article belongs to the Special Issue Metabolomics 2021 Online)

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13 pages, 2995 KiB

Open AccessArticle

Deep Learning for Rapid Identification of Microbes Using Metabolomics Profiles

by Danhui Wang, Peyton Greenwood and Matthias S. Klein

Metabolites 2021, 11(12), 863; https://doi.org/10.3390/metabo11120863 - 13 Dec 2021

Cited by 6 | Viewed by 2965

Abstract

Rapid detection of viable microbes remains a challenge in fields such as microbial food safety. We here present the application of deep learning algorithms to the rapid detection of pathogenic and non-pathogenic microbes using metabolomics data. Microbes were incubated for 4 h in [...] Read more.

Rapid detection of viable microbes remains a challenge in fields such as microbial food safety. We here present the application of deep learning algorithms to the rapid detection of pathogenic and non-pathogenic microbes using metabolomics data. Microbes were incubated for 4 h in a protein-free defined medium, followed by 1D ¹H nuclear magnetic resonance (NMR) spectroscopy measurements. NMR spectra were analyzed by spectral binning in an untargeted metabolomics approach. We trained multilayer (“deep”) artificial neural networks (ANN) on the data and used the resulting models to predict spectra of unknown microbes. ANN predicted unknown microbes in this laboratory setting with an average accuracy of 99.2% when using a simple feature selection method. We also describe learning behavior of the employed ANN and the optimization strategies that worked well with these networks for our datasets. Performance was compared to other current data analysis methods, and ANN consistently scored higher than random forest models and support vector machines, highlighting the potential of deep learning in metabolomics data analysis. Full article

(This article belongs to the Section Bioinformatics and Data Analysis)

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18 pages, 1374 KiB

Open AccessEditor’s ChoiceArticle

Untargeted Metabolomics Reveals a Complex Impact on Different Metabolic Pathways in Scallop Mimachlamys varia (Linnaeus, 1758) after Short-Term Exposure to Copper at Environmental Dose

by Vincent Hamani, Pascaline Ory, Pierre-Edouard Bodet, Laurence Murillo and Marianne Graber

Metabolites 2021, 11(12), 862; https://doi.org/10.3390/metabo11120862 - 11 Dec 2021

Cited by 7 | Viewed by 2651

Abstract

Ports are a good example of how coastal environments, gathering a set of diverse ecosystems, are subjected to pollution factors coming from human activities both on land and at sea. Among them, trace element as copper represents a major factor. Abundant in port [...] Read more.

Ports are a good example of how coastal environments, gathering a set of diverse ecosystems, are subjected to pollution factors coming from human activities both on land and at sea. Among them, trace element as copper represents a major factor. Abundant in port ecosystem, copper is transported by runoff water and results from diverse port features (corrosion of structures, fuel, anti-fouling products, etc.). The variegated scallop Mimachlamys varia is common in the Atlantic port areas and is likely to be directly influenced by copper pollution, due to its sessile and filtering lifestyle. Thus, the aim of the present study is to investigate the disruption of the variegated scallop metabolism, under a short exposure (48 h) to a copper concentration frequently encountered in the waters of the largest marina in Europe (82 μg/L). For this, we chose a non-targeted metabolomic approach using ultra-high performance liquid chromatography coupled to high resolution mass spectrometry (UHPLC-HRMS), offering a high level of sensitivity and allowing the study without a priori of the entire metabolome. We described 28 metabolites clearly modulated by copper. They reflected the action of copper on several biological functions such as osmoregulation, oxidative stress, reproduction and energy metabolism. Full article

(This article belongs to the Special Issue Application of Metabolomic in Ecotoxicology)

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