Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 22 min 4 sec ago

UPLC-ESI-IT-TOF-MS metabolomic study of the therapeutic effect of Xuefu Zhuyu decoction on rats with traumatic brain injury.

Mon, 12/08/2019 - 13:55
Related Articles UPLC-ESI-IT-TOF-MS metabolomic study of the therapeutic effect of Xuefu Zhuyu decoction on rats with traumatic brain injury. J Ethnopharmacol. 2019 Aug 08;:112149 Authors: Fu C, Wu Q, Zhang Z, Xia Z, Ji H, Lu H, Wang Y Abstract It has been widely reported that Xuefu Zhuyu decoction (XFZYD), a traditional Chinese medicine, is effective in the treatment of traumatic brain injury (TBI). However, the mechanism of the therapeutic process is still not fully understood. Metabolomic technique can be used to explore the mechanisms underlying the treatment of TBI with XFZYD. The purpose of this work was to investigate the metabolic characteristics of blood samples from rats with and without XFZYD treatment and the dynamic changes in metabolite profiles on days 1, 3, 7, 14 and 21 after injury (within the severe phase of TBI) based on untargeted UPLC-ESI-IT-TOF-MS analysis. Pattern recognition, clustering analysis and metabolic pathway analysis were used to analyse the metabolomic data of three groups (a sham-operated group, a TBI model, and an XFZYD-treated TBI model). The results showed that XFZYD reversed the abnormalities in the levels of small-molecule metabolites (such as L-acetylcarnitine, L-tryptophan, indoleacrylic acid, γ-aminobutyric acid, hypotaurine, LysoPC(18:1)(11Z), creatine, L-phenylalanine and L-leucine) in TBI rats through six metabolic pathways (including phenylalanine, tyrosine and tryptophan biosynthesis; phenylalanine metabolism; valine, leucine and isoleucine biosynthesis; taurine and hypotaurine metabolism; tryptophan metabolism; and alanine, aspartate and glutamate metabolism) involved in the therapy process. XFZYD regulated the metabolic disorders of endogenous markers by the possible mechanisms of neuroprotection, energy metabolism, inflammatory response and oxidative stress. This study revealed the holistic and dynamic metabolic changes caused by XFZYD in rats with TBI and provided important research methods and approaches for exploring the multiple metabolites and metabolic pathways involved in the therapeutic effect of XFZYD on TBI. PMID: 31401321 [PubMed - as supplied by publisher]

Synthetic microbial consortium with specific roles designated by genetic circuits for cooperative chemical production.

Mon, 12/08/2019 - 13:55
Related Articles Synthetic microbial consortium with specific roles designated by genetic circuits for cooperative chemical production. Metab Eng. 2019 Aug 08;: Authors: Honjo H, Iwasaki K, Soma Y, Tsuruno K, Hamada H, Hanai T Abstract Synthetic microbial consortia consisting of microorganisms with different synthetic genetic circuits or divided synthetic metabolic pathway components can exert functions that are beyond the capacities of single microorganisms. However, few consortia of microorganisms with different synthetic genetic circuits have been developed. We designed and constructed a synthetic microbial consortium composed of an enzyme-producing strain and a target chemical-producing strain using Escherichia coli for chemical production with efficient saccharification. The enzyme-producing strain harbored a synthetic genetic circuit to produce beta-glucosidase, which converts cellobiose to glucose, destroys itself via the lytic genes, and release the enzyme when the desired cell density is reached. The target chemical-producing strain was programmed by a synthetic genetic circuit to express enzymes in the synthetic metabolic pathway for isopropanol production when the enzyme-producing strain grows until release of the enzyme. Our results demonstrate the benefits of synthetic microbial consortia with distributed tasks for effective chemical production from biomass. PMID: 31401244 [PubMed - as supplied by publisher]

Integrated analysis of proteomics and metabolomics reveals the potential sex determination mechanism in Odontobutis potamophila.

Mon, 12/08/2019 - 13:55
Related Articles Integrated analysis of proteomics and metabolomics reveals the potential sex determination mechanism in Odontobutis potamophila. J Proteomics. 2019 Aug 08;:103482 Authors: Wang T, Zhu W, Zhang H, Wen X, Yin S, Jia Y Abstract Odontobutis potamophila is a valuable species for aquaculture in China, which shows asexually dimorphic growth pattern. In this study, the integrated proteomics and metabolomics were used to analyze the sex determination mechanism. A total of 2781 significantly different regulated proteins were identified by proteomics and 2693 significantly different expressed metabolites were identified by metabolomics. Among them, 2560 proteins and 1701 metabolites were significantly up-regulated in testes, whereas 221 proteins and 992 metabolites were significantly up-regulated in ovaries. Venn diagram analysis showed 513 proteins were differentially regulated at both protein and metabolite levels. Correlation analysis of differentially-regulated proteins and metabolites were identified by Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The results showed lipid metabolism plays an important role in sex determination. The metabolites decanoyl-CoA, leukotriene, 3-dehydrosphinganine, and arachidonate were the biomarkers in testes, whereas estrone and taurocholate were the biomarkers in ovaries. Interaction networks of the significant differentially co-regulated proteins and metabolites in the process of lipid metabolism showed arachidonic acid metabolism and steroid hormone biosynthesis were the most important pathways in sex determination. The findings of this study provide valuable information for selective breeding of O. potamophila. SIGNIFICANCE OF THE STUDY: The male O. potamophila grows substantially larger and at a quicker rate than the female. Thus, males have greater economic value than females. However, limited research was done to analyze the sex determination mechanism of O. potamophila, which seriously hindered the development of whole-male O. potamophila breeding. In this study, four key proteins (Ctnnb1, Piwil1, Hsd17b1, and Dnali1), six most important biomarkers (decanoyl-CoA, leukotriene, 3-dehydrosphinganine, arachidonate, estrone, and taurocholate) and two key pathways (arachidonic acid metabolism and steroid hormone biosynthesis) in sex determination of O. potamophila were found by integrated application of iTRAQ and LC-MS techniques. The results give valuable information for molecular breeding of O. potamophila in aquaculture. PMID: 31401171 [PubMed - as supplied by publisher]

Maternal Obesity/Diabetes, Plasma Branched-Chain Amino Acids, and Autism Spectrum Disorder Risk in Urban Low-Income Children: Evidence of Sex Difference.

Sun, 11/08/2019 - 13:43
Related Articles Maternal Obesity/Diabetes, Plasma Branched-Chain Amino Acids, and Autism Spectrum Disorder Risk in Urban Low-Income Children: Evidence of Sex Difference. Autism Res. 2019 Aug 09;: Authors: Panjwani AA, Ji Y, Fahey JW, Palmer A, Wang G, Hong X, Zuckerman B, Wang X Abstract Maternal metabolic conditions are known risk factors for child autism spectrum disorder (ASD). Branched-chain amino acids (BCAAs) are also associated with ASD. We examined the joint associations of maternal metabolic conditions and BCAAs on the risk of child ASD and whether the associations differed by child's sex. We analyzed 789 mother-infant pairs, a subset of the Boston Birth Cohort, from a predominantly urban, low-income, minority population. Maternal plasma BCAAs were measured by liquid chromatography-tandem mass spectrometry in samples collected 24-72 hr postpartum. A composite BCAA score was created using factor analysis, and prepregnancy obesity and diabetes (ob/DM) were combined into one variable. Logistic regression was used to explore the role of BCAAs as mediators or cofactors with ob/DM and child's sex on ASD risk. BCAA-ob/DM and BCAA-sex interactions were also examined. Maternal BCAAs alone were not associated with ASD and did not mediate the path between ob/DM and ASD. In the presence of maternal ob/DM, BCAA score was significantly associated with ASD (adjusted OR 2.33, 95% CI 1.18, 4.60). Interactions were present for valine with ob/DM and for valine and isoleucine with male sex on ASD risk. The odds ratio (OR) for risk of ASD was the greatest with all three risk factors combined-male sex, above median BCAA score, and ob/DM (OR 10.79, 95% CI 4.40, 26.42). Similar patterns were found for other developmental disorders, though not as strong as for ASD. Additional studies are warranted to clarify the role of maternal BCAAs, ob/DM, and child's sex in ASD. Autism Res 2019. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: This study investigated whether maternal obesity/diabetes and maternal circulating branched-chain amino acids (BCAAs) can jointly affect child ASD risk and whether the associations differ by child's sex. We found that the risk of ASD was greater among mothers with obesity/diabetes who also had elevated concentrations of BCAAs and that this risk was even greater for male children. These findings provide new evidence on fetal origins of ASD and sex difference and warrant additional investigation. PMID: 31400063 [PubMed - as supplied by publisher]

Fish-oil supplementation in pregnancy, child metabolomics and asthma risk.

Sun, 11/08/2019 - 13:43
Related Articles Fish-oil supplementation in pregnancy, child metabolomics and asthma risk. EBioMedicine. 2019 Aug 06;: Authors: Rago D, Rasmussen MA, Lee-Sarwar KA, Weiss ST, Lasky-Su J, Stokholm J, Bønnelykke K, Chawes BL, Bisgaard H Abstract BACKGROUND: We recently demonstrated that maternal dietary supplementation with fish oil-derived n-3 long-chain polyunsaturated fatty acids (n-3 LCPUFAs) during pregnancy reduces the risk of asthma in the offspring but the mechanisms involved are unknown. METHODS: Here we investigated potential metabolic mechanisms using untargeted liquid chromatography-mass spectrometry-based metabolomics on 577 plasma samples collected at age 6 months in the offspring of mothers participating in the n-3 LCPUFA randomized controlled trial. First, associations between the n-3 LCPUFA supplementation groups and child metabolite levels were investigated using univariate regression models and data-driven partial least square discriminant analyses (PLS-DA). Second, we analyzed the association between the n-3 LCPUFA metabolomic profile and asthma development using Cox-regression. Third, we conducted mediation analyses to investigate whether the protective effect of n-3 LCPUFA on asthma was mediated via the metabolome. FINDINGS: The univariate analyses and the PLS-DA showed that maternal fish oil supplementation affected the child's metabolome, especially with lower levels of the n-6 LCPUFA pathway-related metabolites and saturated and monounsaturated long-chain fatty acids-containing compounds, lower levels of metabolites of the tryptophan pathway, and higher levels of metabolites in the tyrosine and glutamic acid pathway. This fish oil-related metabolic profile at age 6 months was significantly associated with a reduced risk of asthma by age 5 and the metabolic profile explained 24% of the observed asthma-protective effect in the mediation analysis. INTERPRETATION: Several of the observed pathways may be involved in the asthma-protective effect of maternal n-3 LCPUFA supplementation and act as mediators between the intervention and disease development. FUNDING: COPSAC is funded by private and public research funds all listed on www.copsac.com. PMID: 31399385 [PubMed - as supplied by publisher]

Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.

Sun, 11/08/2019 - 13:43
Related Articles Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition. Cell Host Microbe. 2019 Aug 01;: Authors: Thingholm LB, Rühlemann MC, Koch M, Fuqua B, Laucke G, Boehm R, Bang C, Franzosa EA, Hübenthal M, Rahnavard A, Frost F, Lloyd-Price J, Schirmer M, Lusis AJ, Vulpe CD, Lerch MM, Homuth G, Kacprowski T, Schmidt CO, Nöthlings U, Karlsen TH, Lieb W, Laudes M, Franke A, Huttenhower C Abstract Obesity and type 2 diabetes (T2D) are metabolic disorders that are linked to microbiome alterations. However, their co-occurrence poses challenges in disentangling microbial features unique to each condition. We analyzed gut microbiomes of lean non-diabetic (n = 633), obese non-diabetic (n = 494), and obese individuals with T2D (n = 153) from German population and metabolic disease cohorts. Microbial taxonomic and functional profiles were analyzed along with medical histories, serum metabolomics, biometrics, and dietary data. Obesity was associated with alterations in microbiome composition, individual taxa, and functions with notable changes in Akkermansia, Faecalibacterium, Oscillibacter, and Alistipes, as well as in serum metabolites that correlated with gut microbial patterns. However, microbiome associations were modest for T2D, with nominal increases in Escherichia/Shigella. Medications, including antihypertensives and antidiabetics, along with dietary supplements including iron, were significantly associated with microbiome variation. These results differentiate microbial components of these interrelated metabolic diseases and identify dietary and medication exposures to consider in future studies. PMID: 31399369 [PubMed - as supplied by publisher]

Untargeted Metabolomics Reveals Molecular Effects of Ketogenic Diet on Healthy and Tumor Xenograft Mouse Models.

Sun, 11/08/2019 - 13:43
Related Articles Untargeted Metabolomics Reveals Molecular Effects of Ketogenic Diet on Healthy and Tumor Xenograft Mouse Models. Int J Mol Sci. 2019 Aug 08;20(16): Authors: Licha D, Vidali S, Aminzadeh-Gohari S, Alka O, Breitkreuz L, Kohlbacher O, Reischl RJ, Feichtinger RG, Kofler B, Huber CG Abstract The application of ketogenic diet (KD) (high fat/low carbohydrate/adequate protein) as an auxiliary cancer therapy is a field of growing attention. KD provides sufficient energy supply for healthy cells, while possibly impairing energy production in highly glycolytic tumor cells. Moreover, KD regulates insulin and tumor related growth factors (like insulin growth factor-1, IGF-1). In order to provide molecular evidence for the proposed additional inhibition of tumor growth when combining chemotherapy with KD, we applied untargeted quantitative metabolome analysis on a spontaneous breast cancer xenograft mouse model, using MDA-MB-468 cells. Healthy mice and mice bearing breast cancer xenografts and receiving cyclophosphamide chemotherapy were compared after treatment with control diet and KD. Metabolomic profiling was performed on plasma samples, applying high-performance liquid chromatography coupled to tandem mass spectrometry. Statistical analysis revealed metabolic fingerprints comprising numerous significantly regulated features in the group of mice bearing breast cancer. This fingerprint disappeared after treatment with KD, resulting in recovery to the metabolic status observed in healthy mice receiving control diet. Moreover, amino acid metabolism as well as fatty acid transport were found to be affected by both the tumor and the applied KD. Our results provide clear evidence of a significant molecular effect of adjuvant KD in the context of tumor growth inhibition and suggest additional mechanisms of tumor suppression beyond the proposed constrain in energy supply of tumor cells. PMID: 31398922 [PubMed - in process]

Genome-Wide Identification, Expression Pattern Analysis and Evolution of the Ces/Csl Gene Superfamily in Pineapple (Ananas comosus).

Sun, 11/08/2019 - 13:43
Related Articles Genome-Wide Identification, Expression Pattern Analysis and Evolution of the Ces/Csl Gene Superfamily in Pineapple (Ananas comosus). Plants (Basel). 2019 Aug 08;8(8): Authors: Cao S, Cheng H, Zhang J, Aslam M, Yan M, Hu A, Lin L, Ojolo SP, Zhao H, Priyadarshani SVGN, Yu Y, Cao G, Qin Y Abstract The cellulose synthase (Ces) and cellulose synthase-like (Csl) gene families belonging to the cellulose synthase gene superfamily, are responsible for the biosynthesis of cellulose and hemicellulose of the plant cell wall, and play critical roles in plant development, growth and evolution. However, the Ces/Csl gene family remains to be characterized in pineapple, a highly valued and delicious tropical fruit. Here, we carried out genome-wide study and identified a total of seven Ces genes and 25 Csl genes in pineapple. Genomic features and phylogeny analysis of Ces/Csl genes were carried out, including phylogenetic tree, chromosomal locations, gene structures, and conserved motifs identification. In addition, we identified 32 pineapple AcoCes/Csl genes with 31 Arabidopsis AtCes/Csl genes as orthologs by the syntenic and phylogenetic approaches. Furthermore, a RNA-seq investigation exhibited the expression profile of several AcoCes/Csl genes in various tissues and multiple developmental stages. Collectively, we provided comprehensive information of the evolution and function of pineapple Ces/Csl gene superfamily, which would be useful for screening out and characterization of the putative genes responsible for tissue development in pineapple. The present study laid the foundation for future functional characterization of Ces/Csl genes in pineapple. PMID: 31398920 [PubMed]

Identifying novel treeline biomarkers in lake sediments using an untargeted screening approach.

Sat, 10/08/2019 - 13:26
Related Articles Identifying novel treeline biomarkers in lake sediments using an untargeted screening approach. Sci Total Environ. 2019 Jul 30;694:133684 Authors: Saleem A, Bell MA, Kimpe LE, Korosi JB, Arnason JT, Blais JM Abstract Paleolimnology uses sedimentary biomarkers as proxies to reconstruct long-term changes in environmental conditions from lake sediment cores. This work describes an untargeted metabolomics-based approach and uniquely applies it to the field of paleolimnology to identify novel sediment biomarkers to track long-term patterns in treeline dynamics. We identified new potential biomarkers across the Canadian northern Arctic, non-alpine, treeline using high-resolution accurate mass spectrometry, and pattern recognition analysis. This method was applied to 120 sediment core extracts from 14 boreal, 25 forest-tundra, and 21 tundra lakes to assess long-term fluctuations in treeline position. High resolution accurate mass spectrometry resolved many compounds from complex mixtures with low mass accuracy errors. This generated a large dataset that required metabolomics styled statistical analyses to identify potential biomarkers. In total, 29 potential biomarkers discriminated between boreal and tundra lakes. Tetrapyrrole-type phorbides and squalene derivatives dominated in boreal regions, while biohopane-type lipids were in the tundra regions. Tetrapyrroles were in both surface and subsurface sediments of boreal lakes indicating these compounds can survive long-term burial in sediments. At the ecozone level, tetrapyrroles were more abundant in boreal Taiga Shield, and Taiga Plains. Boreal plant extracts belonging to Pinaceae and Ericaceae also contained tetrapyrroles. Squalene derivatives demonstrated long-term preservation, but wider distribution than tetrapyrroles. Hopanoids were present in tundra and forest-tundra lake regions, specifically the Low Arctic and Taiga Shield, and were absent in all boreal lake sediments. Herein, we describe a method that can systematically identify new paleolimnological biomarkers. Novel biomarkers would facilitate multi-proxy paleolimnological studies and potentially lead to more accurate paleoenvironmental reconstructions. PMID: 31398651 [PubMed - as supplied by publisher]

Maternal-to-zygotic transition as a potential target for niclosamide during early embryogenesis.

Sat, 10/08/2019 - 13:26
Related Articles Maternal-to-zygotic transition as a potential target for niclosamide during early embryogenesis. Toxicol Appl Pharmacol. 2019 Aug 06;:114699 Authors: Vliet SMF, Dasgupta S, Sparks NRL, Kirkwood JS, Vollaro A, Hur M, Zur Nieden NI, Volz DC Abstract Niclosamide is an antihelminthic drug used worldwide for the treatment of tapeworm infections. Recent drug repurposing screens have highlighted the broad bioactivity of niclosamide across diverse mechanisms of action. As a result, niclosamide is being evaluated for a range of alternative drug-repurposing applications, including the treatment of cancer, bacterial infections, and Zika virus. As new applications of niclosamide will require non-oral delivery routes that may lead to exposure in utero, it is important to understand the mechanism of niclosamide toxicity during early stages of embryonic development. Previously, we showed that niclosamide induces a concentration-dependent delay in epiboly progression in the absence of effects on oxidative phosphorylation - a well-established target for niclosamide. Therefore, the overall objective of this study was to further examine the mechanism of niclosamide-induced epiboly delay during zebrafish embryogenesis. Based on this study, we found that (1) niclosamide exposure during early zebrafish embryogenesis resulted in a decrease in yolk sac integrity with a concomitant decrease in the presence of yolk sac actin networks and increase in cell size; (2) within whole embryos, niclosamide exposure did not alter non-polar metabolites and lipids, but significantly altered amino acids specific to aminoacyl-tRNA biosynthesis; (3) niclosamide significantly altered transcripts related to translation, transcription, and mRNA processing pathways; and (4) niclosamide did not significantly alter levels of rRNA and tRNA. Overall, our findings suggest that niclosamide may be causing a systemic delay in embryonic development by disrupting the translation of maternally-supplied mRNAs, an effect that may be mediated through disruption of aminoacyl-tRNA biosynthesis. PMID: 31398420 [PubMed - as supplied by publisher]

Fast and Quantitative NMR Metabolite Analysis Afforded by a Paramagnetic Co-Solute.

Sat, 10/08/2019 - 13:26
Related Articles Fast and Quantitative NMR Metabolite Analysis Afforded by a Paramagnetic Co-Solute. Angew Chem Int Ed Engl. 2019 Aug 09;: Authors: Mulder FAA, Tenori L, Luchinat C Abstract NMR spectroscopy is an indispensable technique for the determination of the chemical identity and structure of small molecules. The technique is especially recognized for its robustness and intrinsically quantitative nature and has manifested itself as a key analytical platform for diverse fields of application, ranging from chemical synthesis to metabolomics. Unfortunately, the slow recovery of nuclear spin polarization by spin-lattice (T1) relaxation causes most experiment time to be lost on idle waiting. In addition, truly quantitative NMR (qNMR) requires waiting times of 5 times the longest T1 in the sample, making qNMR slow and inefficient. We demonstrate here that co-solute paramagnetic relaxation can mitigate these two problems simultaneously; Addition of a small amount of paramagnetic gadolinium chelate, available in the form of commercial contrast agent solutions, actuates cheap, quantitative and efficient high-throughput mixture analysis. PMID: 31398278 [PubMed - as supplied by publisher]

Synergistic combination of DT-13 and Topotecan inhibits aerobic glycolysis in human gastric carcinoma BGC-823 cells via NM IIA/EGFR/HK II axis.

Sat, 10/08/2019 - 13:26
Related Articles Synergistic combination of DT-13 and Topotecan inhibits aerobic glycolysis in human gastric carcinoma BGC-823 cells via NM IIA/EGFR/HK II axis. J Cell Mol Med. 2019 Aug 09;: Authors: Yu XW, Wei D, Gao YS, Du HZ, Yu BY, Li RM, Qian CM, Luo XJ, Yuan ST, Wang JS, Sun L Abstract DT-13 combined with topotecan (TPT) showed stronger antitumour effects in mice subcutaneous xenograft model compared with their individual effects in our previous research. Here, we further observed the synergistically effect in mice orthotopic xenograft model. Metabolomics analysis showed DT-13 combined with TPT alleviated metabolic disorders induced by tumour and synergistically inhibited the activity of the aerobic glycolysis-related enzymes in vivo and in vitro. Mechanistic studies revealed that the combination treatment promoted epidermal growth factor receptor (EGFR) degradation through non-muscle myosin IIA (NM IIA)-induced endocytosis of EGFR, further inhibited the activity of hexokinase II (HK II), and eventually promoted the aerobic glycolysis inhibition activity more efficiently compared with TPT or DT-13 monotherapy. The combination therapy also inhibited the specific binding of HK II to mitochondria. When using the NM II inhibitor (-)002Dblebbistatin or MYH-9 shRNA, the synergistic inhibition effect of DT-13 and TPT on aerobic glycolysis was eliminated in BGC-823 cells. Immunohistochemical analysis revealed selective up-regulation of NM IIA while specific down-regulation of p-CREB, EGFR, and HK II by the combination therapy. Collectively, these findings suggested that this regimen has significant clinical implications, warranted further investigation. PMID: 31397978 [PubMed - as supplied by publisher]

The alternative splicing of SKU5-Similar3 in Arabidopsis.

Sat, 10/08/2019 - 13:26
Related Articles The alternative splicing of SKU5-Similar3 in Arabidopsis. Plant Signal Behav. 2019 Aug 09;:1-4 Authors: Zhou K Abstract Alternative splicing largely enhanced the diversity of transcriptome and proteome in eukaryas. Along with technological development, more and more genes are reported to be alternatively spliced during mRNA maturation. Here, I report the alternative splicing of SKU5-Similar 3 (SKS3) and its special splicing site in Arabidopsis. SKS3 was predicted to be alternatively transcribed into two variants, SKS3.1 and SKS3.2, which encoded a GPI-anchored protein and a soluble secretory protein, respectively. But, according to experimental data, instead of SKS3.2, a novel variant, SKS3.3, which encodes a protein with a transmembrane region at its C-terminus, was demonstrated. Interestingly, it exhibites a different organ-specific expression pattern with SKS3.1, and an unusual intron splicing site not following 'GT-AG' rule or any reported rule. PMID: 31397618 [PubMed - as supplied by publisher]

Guidelines for the Use of Deuterium Oxide (D2O) in 1H NMR Metabolomics.

Sat, 10/08/2019 - 13:26
Related Articles Guidelines for the Use of Deuterium Oxide (D2O) in 1H NMR Metabolomics. Anal Chem. 2019 Aug 09;: Authors: Haslauer KE, Hemmler D, Schmitt-Kopplin P, Heinzmann SS Abstract In metabolomics, NMR spectroscopy allows to identify and quantify compounds in biological samples. The sample preparation generally requires only few steps; however, an indispensable factor is the addition of a locking substance into the biofluid sample, such as deuterium oxide (D2O). While creatinine loss in pure D2O is well described, the effects of different D2O concentrations on the signal profile of biological samples are unknown. In this work, we investigated the effect of D2O levels in the NMR buffer system in urine samples, in dependence on dwell time and temperature exposition. We reveal a decrease of the urinary creatinine peak area up to 35% after 24 h dwell time at room temperature (RT) using 25% (v/v) D2O, but only 4% loss using 2.5% D2O, respectively. 1H, (IG) 13C and DEPT-HSQC NMR and MS experiments confirmed a proton-deuterium (H/D) exchange at the CH2. This leads to underestimation of creatinine levels and has an extensive effect when creatinine is used for normalization. This work offers a sample stability examination depending on the D2O concentration, dwell time and temperature and enables a method to correct for the successive loss. We propose an equation to correct the creatinine loss for samples prepared with various D2O concentrations and storage temperatures for dwell times up to 24 h. The correction function was validated against an external dataset with n = 26 samples. To ensure sufficient creatinine stability in future studies, we suggest that a maximum of 10% D2O should be used at 4 °C or 2.5% D2O at RT, respectively. PMID: 31397558 [PubMed - as supplied by publisher]

Oxidative phosphorylation as a potential therapeutic target for cancer therapy.

Sat, 10/08/2019 - 13:26
Related Articles Oxidative phosphorylation as a potential therapeutic target for cancer therapy. Int J Cancer. 2019 Aug 09;: Authors: Sica V, Bravo-San Pedro JM, Stoll G, Kroemer G Abstract In contrast to prior belief, cancer cells require oxidative phosphorylation (OXPHOS) to strive, and exacerbated OXPHOS dependency frequently characterizes cancer stem cells, as well as primary or acquired resistance against chemotherapy or tyrosine kinase inhibitors. A growing arsenal of therapeutic agents is being designed to suppress the transfer of mitochondria from stromal to malignant cells, to interfere with mitochondrial biogenesis, to directly inhibit respiratory chain complexes, or to disrupt mitochondrial function in other ways. For the experimental treatment of cancers, OXPHOS inhibitors can be advantageously combined with tyrosine kinase inhibitors, as well as with other strategies to inhibit glycolysis, thereby causing a lethal energy crisis. Unfortunately, most of the preclinical data arguing in favor of OXPHOS inhibition have been obtained in xenograft models, in which human cancer cells are implanted in immunodeficient mice. Future studies on OXPHOS inhibitors should elaborate optimal treatment schedules and combination regimens that stimulate - or at least are compatible with - anticancer immune responses for long-term tumor control. This article is protected by copyright. All rights reserved. PMID: 31396957 [PubMed - as supplied by publisher]

Wine aging: a bottleneck story.

Sat, 10/08/2019 - 13:26
Related Articles Wine aging: a bottleneck story. NPJ Sci Food. 2019;3:14 Authors: Karbowiak T, Crouvisier-Urion K, Lagorce A, Ballester J, Geoffroy A, Roullier-Gall C, Chanut J, Gougeon RD, Schmitt-Kopplin P, Bellat JP Abstract The sporadic oxidation of white wines remains an open question, making wine shelf life a subjective debate. Through a multidisciplinary synoptic approach performed as a remarkable case study on aged bottles of white wine, this work unraveled a yet unexplored route for uncontrolled oxidation. By combining sensory evaluation, chemical and metabolomics analyses of the wine, and investigating oxygen transfer through the bottleneck/stopper, this work elucidates the importance of the glass/cork interface. It shows unambiguously that the transfer of oxygen at the interface between the cork stopper and the glass bottleneck must be considered a potentially significant contributor to oxidation state during the bottle aging, leading to a notable modification of a wine's chemical signature. PMID: 31396559 [PubMed]

Modulation of plasma and urine metabolome in colorectal cancer survivors consuming rice bran.

Sat, 10/08/2019 - 13:26
Related Articles Modulation of plasma and urine metabolome in colorectal cancer survivors consuming rice bran. Integr Food Nutr Metab. 2019 May;6(3): Authors: Zarei I, Oppel RC, Borresen EC, Brown RJ, Ryan EP Abstract Rice bran has bioactive phytochemicals with cancer protective actions that involve metabolism by the host and the gut microbiome. Globally, colorectal cancer (CRC) is the third leading cause of cancer-related death and the increased incidence is largely attributed to poor dietary patterns, including low daily fiber intake. A dietary intervention trial was performed to investigate the impact of rice bran consumption on the plasma and urine metabolome of CRC survivors. Nineteen CRC survivors participated in a randomized-controlled trial that included consumption of heat-stabilized rice bran (30 g/day) or a control diet without rice bran for 4 weeks. A fasting plasma and first void of the morning urine sample were analyzed by non-targeted metabolomics using ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). After 4 weeks of either rice bran or control diets, 12 plasma and 16 urine metabolites were significantly different between the groups (p≤0.05). Rice bran intake increased relative abundance of plasma mannose (1.373-fold) and beta-citrylglutamate (BCG) (1.593-fold), as well as increased urine N-formylphenylalanine (2.191-fold) and dehydroisoandrosterone sulfate (DHEA-S) (4.488-fold). Diet affected metabolites, such as benzoate, mannose, eicosapentaenoate (20:5n3) (EPA), and N-formylphenylalanine have been previously reported for cancer protection and were identified from the rice bran food metabolome. Nutritional metabolome changes following increased consumption of whole grains such as rice bran warrants continued investigation for colon cancer control and prevention attributes as dietary biomarkers for positive effects are needed to reduce high risk for colorectal cancer recurrence. PMID: 31396400 [PubMed]

Metabolites of the Nitric Oxide (NO) Pathway Are Altered and Indicative of Reduced NO and Arginine Bioavailability in Patients with Cardiometabolic Diseases Complicated with Chronic Wounds of Lower Extremities: Targeted Metabolomics Approach (LC-MS/MS).

Sat, 10/08/2019 - 13:26
Related Articles Metabolites of the Nitric Oxide (NO) Pathway Are Altered and Indicative of Reduced NO and Arginine Bioavailability in Patients with Cardiometabolic Diseases Complicated with Chronic Wounds of Lower Extremities: Targeted Metabolomics Approach (LC-MS/MS). Oxid Med Cell Longev. 2019;2019:5965721 Authors: Krzystek-Korpacka M, Wiśniewski J, Fleszar MG, Bednarz-Misa I, Bronowicka-Szydełko A, Gacka M, Masłowski L, Kędzior K, Witkiewicz W, Gamian A Abstract Objective: The status of metabolites of the nitric oxide (NO) pathway in patients with chronic wounds in the course of cardiometabolic diseases is largely unknown. Yet arginine supplementation and citrulline supplementation as novel therapeutic modalities aimed at increasing NO are tested. Material and Methods: Targeted metabolomics approach (LC-MS/MS) was applied to determine the concentrations of L-arginine, L-citrulline, asymmetric and symmetric dimethylarginines (ADMA and SDMA), and arginine/ADMA and arginine/SDMA ratios as surrogate markers of NO and arginine availability in ulnar and femoral veins, representing systemic and local levels of metabolites, in patients with chronic wounds in the course of cardiometabolic diseases (n = 59) as compared to patients without chronic wounds but with similar cardiometabolic burden (n = 55) and healthy individuals (n = 88). Results: Patients with chronic wounds had significantly lower systemic L-citrulline and higher ADMA and SDMA concentrations and lower L-arginine/ADMA and L-arginine/SDMA as compared to healthy controls. The presence of chronic wounds in patients with cardiometabolic diseases was associated with decreased L-arginine but with increased L-citrulline, ADMA, and SDMA concentrations and decreased L-arginine/ADMA and L-arginine/SDMA. Serum obtained from the ulnar and femoral veins of patients with chronic wounds differed by L-arginine concentrations and L-arginine/SDMA ratio, both lower in the femoral vein. Wound etiology affected L-citrulline and SDMA concentrations, lower and higher, respectively, in patients with venous stasis, and the L-arginine/SDMA ratio-lower in venous stasis. The wound type affected L-arginine/ADMA and citrulline-lower in patients with ulcerations or gangrene. IL-6 was an independent predictor of L-arginine/ADMA, VEGF-A of ADMA, G-CSF of L-arginine/SDMA, and GM-CSF of L-citrulline and SDMA. Conclusion: Chronic wounds in the course of cardiometabolic diseases are associated with reduced NO and arginine availability due to ADMA and SDMA accumulation rather than arginine deficiency, not supporting its supplementation. Wound character seems to affect NO bioavailability and wound etiology-arginine bioavailability. Arginine concentration and its availability are more markedly reduced at the local level than the systemic level. PMID: 31396302 [PubMed - in process]

LC-MS/MS analysis of the central energy and carbon metabolites in biological samples following derivatization by dimethylaminophenacyl bromide.

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Related Articles LC-MS/MS analysis of the central energy and carbon metabolites in biological samples following derivatization by dimethylaminophenacyl bromide. J Chromatogr A. 2019 Jul 31;:460413 Authors: Willacey CCW, Naaktgeboren M, Lucumi Moreno E, Wegrzyn AB, van der Es D, Karu N, Fleming RMT, Harms AC, Hankemeier T Abstract Recent advances in metabolomics have enabled larger proportions of the human metabolome to be analyzed quantitatively. However, this usually requires the use of several chromatographic methods coupled to mass spectrometry to cover the wide range of polarity, acidity/basicity and concentration of metabolites. Chemical derivatization allows in principle a wide coverage in a single method, as it affects both the separation and the detection of metabolites: it increases retention, stabilizes the analytes and improves the sensitivity of the analytes. The majority of quantitative derivatization techniques for LC-MS in metabolomics react with amines, phenols and thiols; however, there are unfortunately very few methods that can target carboxylic acids at the same time, which contribute to a large proportion of the human metabolome. Here, we describe a derivatization technique which simultaneously labels carboxylic acids, thiols and amines using the reagent dimethylaminophenacyl bromide (DmPABr). We further improve the quantitation by employing isotope-coded derivatization (ICD), which uses internal standards derivatized with an isotopically-labelled reagent (DmPABr-D6). We demonstrate the ability to measure and quantify 64 central carbon and energy-related metabolites including amino acids, N-acetylated amino acids, metabolites from the TCA cycle and pyruvate metabolism, acylcarnitines and medium-/long-chain fatty acids. To demonstrate the applicability of the analytical approach, we analyzed urine and SUIT-2 cells utilizing a 15-minute single UPLC-MS/MS method in positive ionization mode. SUIT-2 cells exposed to rotenone showed definitive changes in 28 out of the 64 metabolites, including metabolites from all 7 classes mentioned. By realizing the full potential of DmPABr to derivatize and quantify amines and thiols in addition to carboxylic acids, we extended the coverage of the metabolome, producing a strong platform that can be further applied to a variety of biological studies. PMID: 31395359 [PubMed - as supplied by publisher]

1H NMR and LC-MS-based metabolomic approach for evaluation of the seasonality and viticultural practices in wines from São Francisco River Valley, a Brazilian semi-arid region.

Sat, 10/08/2019 - 13:26
Related Articles 1H NMR and LC-MS-based metabolomic approach for evaluation of the seasonality and viticultural practices in wines from São Francisco River Valley, a Brazilian semi-arid region. Food Chem. 2019 Aug 15;289:558-567 Authors: Alves Filho EG, Silva LMA, Ribeiro PRV, de Brito ES, Zocolo GJ, Souza-Leão PC, Marques ATB, Quintela AL, Larsen FH, Canuto KM Abstract São Francisco River Valley (SFRV) is a wine-producing semi-arid region in Brazil. Therefore, we used a 1H NMR and UPLC-MS-based metabolomic approach coupled to chemometrics to evaluate the variability in Chenin Blanc and Syrah wines for two harvest seasons, two vine training system and six rootstocks. Overall, the secondary metabolites were influenced by the three factors studied, whereas the primary metabolites were only by the seasonality. Chenin Blanc wines made in December presented higher content of an unidentified carbohydrate. In Syrah wines, glycerol, tartaric acid, succinic acid and 2,3-butanediol were greater in December, while proline and lactic acid were more abundant in July. For training system, caffeic acid derivatives were increased in wines produced from espalier. Lyre system increased phenolic compounds, organic acids and apocarotenoids. The effect of the rootstocks was less pronounced, affecting basically caffeic acid derivatives. Thus, we expect that our results may assist the winemakers to improve the SFRV wine quality. PMID: 30955648 [PubMed - indexed for MEDLINE]

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