PubMed

Nutrition, inflammation and cancer. Nat Immunol. 2017 Jul 19;18(8):843-850 Authors: Zitvogel L, Pietrocola F, Kroemer G Abstract Quantitative and qualitative aspects of nutrition have a profound effect on leukocytes and thereby affect proinflammatory carcinogenic effects or anticancer immune responses. As a result, nutrition affects the incidence, natural progression and therapeutic response of malignant diseases, both in humans and in preclinical animal models. Here we discuss the molecular mechanisms through which alimentary cues modulate metabolic, microbial and neuroendocrine circuitries and thus affect the probability of developing premalignant lesions that progress to clinically manifested disease and the response to therapeutic intervention. We examine each of the connections that compose the triangle of nutrition, immunological and inflammatory reactions and cancer while focusing on the mechanistic aspects of these relationships. PMID: 28722707 [PubMed - in process]

Follicular metabolic changes and effects on oocyte quality in polycystic ovary syndrome patients. Oncotarget. 2017 Jul 06;: Authors: Zhang Y, Liu L, Yin TL, Yang J, Xiong CL Abstract Polycystic ovary syndrome (PCOS) is a common complex and heterogeneous disorder, affecting up to 10% women at reproductive age. It causes three fourth of the ovulatory infertility and PCOS patients often give poor IVF quality. Although some metabolic profiles have been investigated in PCOS patient sera and urine, the follicular fluid, providing fruitful biochemical information about oocyte environment during development has been ignored. In this work, based on NMR metabolomics approach, metabolic profile of follicular fluid of PCOS patients has been explored and compared with healthy controls. Significant increases of glycoprotein, acetate, cholesterol, significant decreases of lactic acid, glutamine, pyruvate, and alanine, have been discovered in PCOS follicular fluids. Furthermore, the Pearson correlations analysis indicated significant relationship existed between ART results and NMR detected follicular metabolites. All these results indicated that PCOS may induce dyslipidemia, low-grade inflammation, and disorder of glycolysis, pyruvate and amino acid metabolism in follicular fluids. PMID: 28722670 [PubMed - as supplied by publisher]

First time view on human metabolome changes after a single intake of 3,4 methylenedioxymethamphetamine (MDMA) in healthy placebo-controlled subjects. J Proteome Res. 2017 Jul 19;: Authors: Boxler MI, Liechti ME, Schmid Y, Kraemer T, Steuer AE Abstract 3,4-methylenedioxymethamphetamine (MDMA; 'ecstasy') is widely consumed recreationally. Currently little is known about its effects on the human metabolome. Mapping biochemical changes after drug exposure can complement traditional approaches by revealing potential biomarkers of organ toxicity or discovering new metabolomic features in a time- and dose-dependent manner. We aimed to analyze for the first time plasma samples from a randomized, double-blind, placebo-controlled crossover study in healthy adults to explore changes in endogenous plasma metabolites following a single intake of MDMA. Plasma samples from 15 subjects taken at four different time points were analyzed with the commercially available AbsoluteIDQ® kit (Biocrates). Time series analysis revealed a total of nine metabolites which showed a significant concentration change after MDMA administration compared with placebo. Paired t-tests of the single time points showed statistically significant concentration changes mainly of glycerophospholipids and the metabolic ratio of methionine-sulfoxide over methionine. Changes of this metabolic ratio may be indicative for changes in systemic oxidative stress levels, the increased amount of glycerophospholipids could be interpreted as an upregulation of energy production. Baseline samples within the experimental study design were crucial for evaluation of metabolomics data as inter-day individuality within subjects was high otherwise resulting in overestimations of the findings. PMID: 28722422 [PubMed - as supplied by publisher]

Urine metabonomics reveals early biomarkers in diabetic cognitive dysfunction. J Proteome Res. 2017 Jul 19;: Authors: Song L, Zhuang P, Lin M, Kang M, Liu H, Zhang Y, Yang Z, Chen Y, Zhang Y Abstract Recently, increasing attention has been paid to diabetic encephalopathy which is one of frequent diabetic complications and affects nearly 30% diabetics. Since cognitive dysfunction from diabetic encephalopathy might develop irreversible dementia, early diagnosis and detection of this disease is of great significance for its prevention and treatment. This study is to investigate the early specific metabolites biomarkers in the urine prior to the onset of diabetic cognitive dysfunction (DCD) by using metabolomics technology. Ultra high performance liquid-flight time-mass spectrometry (UPLC-Q/TOF-MS) platform was used to analyze the urine samples from the diabetic mice which were associated with mild cognitive impairment (MCI) and non-associated with MCI at the stage of diabetes (prior to the onset of DCD), and then screened and validated the early biomarkers using OPLS-DA model and support vector machine (SVM) method. Following multivariate statistical and integration analysis, we found 7 metabolites could be accepted as early biomarkers of DCD. And the SVM results showed that the prediction accuracy is as high as 91.66%. The identities of four biomarkers were determined by mass spectrometry. The identified biomarkers were largely involved in nicotinate and nicotinamide metabolism, glutathione metabolism, tryptophan metabolism and sphingolipid metabolism. The present study firstly revealed reliable biomarkers for early diagnosis of DCD. It would provide a new insight and strategy for the early diagnosis and treatment of DCD. PMID: 28722418 [PubMed - as supplied by publisher]

Related Articles Myopes have significantly higher serum melatonin concentrations than non-myopes. Ophthalmic Physiol Opt. 2017 Jul 18;: Authors: Kearney S, O'Donoghue L, Pourshahidi KL, Cobice D, Saunders KJ Abstract PURPOSE: Experimental animal models of myopia demonstrate that higher melatonin (Mel) and lower dopamine (DA) concentrations actively promote axial elongation. This study explored the association between myopia and serum concentrations of DA and Mel in humans. METHODS: Morning serum concentrations of DA and Mel were measured by solid phase extraction-liquid chromatography-tandem mass spectrometry from 54 participants (age 19.1 ± 0.81 years) in September/October 2014 (phase 1) and March/April 2016 (phase 2). Axial length (AL), corneal radii (CR) and spherical equivalent refraction (SER) were also recorded. Participants were defined as myopic if non-cycloplegic spherical equivalent refractive error ≤-0.50 DS at phase 1. RESULTS: Nine participants were lost to follow up. Mel concentrations were measurable for all myopes (phase 1 n = 25, phase 2 n = 22) and non-myopes (phase 1 n = 29, phase 2 n = 23). SER did not change significantly between phases (p = 0.51). DA concentrations were measurable for fewer myopes (phase 1 n = 13, phase 2 n = 12) and non-myopes (phase 1 n = 23, phase 2 n = 16). Myopes exhibited significantly higher Mel concentrations than non-myopes at phase 1 (Median difference: 10 pg mL(-1) , p < 0.001) and at phase 2 (Median difference: 7.3 pg mL(-1) , p < 0.001) and lower DA concentrations at phase 2 (Median difference: 4.7 pg mL(-1) , p = 0.006). Mel concentrations were positively associated with more negative SER (all r ≥ -0.53, all p < 0.001), longer AL (all r ≥ 0.37, all p ≤ 0.008) and higher AL/CR ratio (all r ≥ 0.51, all p < 0.001). CONCLUSION: This study reports for the first time in humans that myopes exhibit higher serum Mel concentrations than non-myopes. This may indicate a role for light exposure and circadian rhythm in the human myopic growth mechanism. Further research should focus on younger cohorts exhibiting more dynamic myopic progression and explore the profile of these neurochemicals alongside evaluation of sleep patterns in myopic and non-myopic groups. PMID: 28721695 [PubMed - as supplied by publisher]

Related Articles Increased oxidative phosphorylation in response to acute and chronic DNA damage. NPJ Aging Mech Dis. 2016;2:16022 Authors: Brace LE, Vose SC, Stanya K, Gathungu RM, Marur VR, Longchamp A, Treviño-Villarreal H, Mejia P, Vargas D, Inouye K, Bronson RT, Lee CH, Neilan E, Kristal BS, Mitchell JR Abstract Accumulation of DNA damage is intricately linked to aging, aging-related diseases and progeroid syndromes such as Cockayne syndrome (CS). Free radicals from endogenous oxidative energy metabolism can damage DNA, however the potential of acute or chronic DNA damage to modulate cellular and/or organismal energy metabolism remains largely unexplored. We modeled chronic endogenous genotoxic stress using a DNA repair-deficient Csa(-/-)|Xpa(-/-) mouse model of CS. Exogenous genotoxic stress was modeled in mice in vivo and primary cells in vitro treated with different genotoxins giving rise to diverse spectrums of lesions, including ultraviolet radiation, intrastrand crosslinking agents and ionizing radiation. Both chronic endogenous and acute exogenous genotoxic stress increased mitochondrial fatty acid oxidation (FAO) on the organismal level, manifested by increased oxygen consumption, reduced respiratory exchange ratio, progressive adipose loss and increased FAO in tissues ex vivo. In multiple primary cell types, the metabolic response to different genotoxins manifested as a cell-autonomous increase in oxidative phosphorylation (OXPHOS) subsequent to a transient decline in steady-state NAD+ and ATP levels, and required the DNA damage sensor PARP-1 and energy-sensing kinase AMPK. We conclude that increased FAO/OXPHOS is a general, beneficial, adaptive response to DNA damage on cellular and organismal levels, illustrating a fundamental link between genotoxic stress and energy metabolism driven by the energetic cost of DNA damage. Our study points to therapeutic opportunities to mitigate detrimental effects of DNA damage on primary cells in the context of radio/chemotherapy or progeroid syndromes. PMID: 28721274 [PubMed]

Related Articles Metabolomic analysis identifies altered metabolic pathways in Multiple Sclerosis. Int J Biochem Cell Biol. 2017 Jul 15;: Authors: Poddighe S, Murgia F, Lorefice L, Liggi S, Cocco E, Marrosu MG, Atzori L Abstract Multiple sclerosis (MS) is a chronic, demyelinating disease that affects the central nervous system and is characterized by a complex pathogenesis and difficult management. The identification of new biomarkers would be clinically useful for more accurate diagnoses and disease monitoring. Metabolomics, the identification of small endogenous molecules in, offers an instantaneous molecular snapshot of the MS phenotype. Here the metabolomic profiles (utilizing plasma from patients with MS) were characterized with a Gas cromatography-mass spectrometry-based platform followed by a multivariate statistical analysis and comparison with a healthy control (HC) population. The obtained partial least square discriminant analysis (PLS-DA) model identified and validated significant metabolic differences between individuals with MS and HC (R2X=0.223, R2Y=0.82, Q2=0.562; p<0.001). Among discriminant metabolites phosphate, fructose, myo-inositol, pyroglutamate, threonate, L-leucine, L-asparagine, L-ornithine, L-glutamine, and L-glutamate were correctly identified, and some resulted as unknown. A receiver operating characteristic (ROC) curve with AUC 0.84 (p=0.01; CI: 0.75-1) generated with the concentrations of the discriminant metabolites, supported the strength of the model. Pathway analysis indicated asparagine and citrulline biosynthesis as the main canonical pathways involved in MS. Changes in the citrulline biosynthesis pathway suggests the involvement of oxidative stress during neuronal damage. The results confirmed metabolomics as a useful approach to better understand the pathogenesis of MS and to provide new biomarkers for the disease to be used together with clinical data. PMID: 28720279 [PubMed - as supplied by publisher]

Related Articles Metabotyping and its application in targeted nutrition: an overview. Br J Nutr. 2017 Jul 19;:1-14 Authors: Riedl A, Gieger C, Hauner H, Daniel H, Linseisen J Abstract Metabolic diversity leads to differences in nutrient requirements and responses to diet and medication between individuals. Using the concept of metabotyping - that is, grouping metabolically similar individuals - tailored and more efficient recommendations may be achieved. The aim of this study was to review the current literature on metabotyping and to explore its potential for better targeted dietary intervention in subjects with and without metabolic diseases. A comprehensive literature search was performed in PubMed, Google and Google Scholar to find relevant articles on metabotyping in humans including healthy individuals, population-based samples and patients with chronic metabolic diseases. A total of thirty-four research articles on human studies were identified, which established more homogeneous subgroups of individuals using statistical methods for analysing metabolic data. Differences between studies were found with respect to the samples/populations studied, the clustering variables used, the statistical methods applied and the metabotypes defined. According to the number and type of the selected clustering variables, the definitions of metabotypes differed substantially; they ranged between general fasting metabotypes, more specific fasting parameter subgroups like plasma lipoprotein or fatty acid clusters and response groups to defined meal challenges or dietary interventions. This demonstrates that the term 'metabotype' has a subjective usage, calling for a formalised definition. In conclusion, this literature review shows that metabotyping can help identify subgroups of individuals responding differently to defined nutritional interventions. Targeted recommendations may be given at such metabotype group levels. Future studies should develop and validate definitions of generally valid metabotypes by exploiting the increasingly available metabolomics data sets. PMID: 28720150 [PubMed - as supplied by publisher]

Related Articles Profiling of the perturbed metabolomic state of mouse spleen during acute and chronic toxoplasmosis. Parasit Vectors. 2017 Jul 18;10(1):339 Authors: Chen XQ, Zhou CX, Elsheikha HM, He S, Hu GX, Zhu XQ Abstract BACKGROUND: Toxoplasma gondii, a common opportunistic protozoan, is a leading cause of illness and mortality among immunosuppressed individuals and during congenital infections. Current therapeutic strategies for toxoplasmosis are not fully effective at curtailing disease progression in these cases. Given the parasite ability to influence host immunity and metabolism, understanding of the metabolic alterations in the host's immune organs during T. gondii infection may enhance the understanding of the molecular mechanisms that define the pathophysiology of T. gondii infection. METHODS: We investigated the global metabolic changes in the spleen of BALB/c mice at early and late stage of infection with T. gondii using LC-MS/MS-based metabolomics. Multivariate data analysis methods, principal components analysis (PCA) and partial least squares discriminant analysis (PLS-DA), were used to identify metabolites that are influenced by T. gondii infection. RESULTS: Multivariate analyses clearly separated the metabolites of spleen of infected and control mice. A total of 132 differential metabolites were identified, 23 metabolites from acutely infected versus control mice and 109 metabolites from chronically infected versus control mice. Lipids, hormones, lactones, acids, peptides, antibiotics, alkaloids and natural toxins were the most influenced chemical groups. There were 12 shared differential metabolites between acutely infected versus control mice and chronically infected versus control mice, of which 4,4-Dimethyl-5alpha-cholesta-8,14,24-trien-3beta-ol was significantly upregulated and ubiquinone-8 was significantly downregulated. Major perturbed metabolic pathways included primary bile acid biosynthesis, steroid hormone biosynthesis, biotin metabolism, and steroid biosynthesis, with arachidonic acid metabolism being the most significantly impacted pathway. These metabolic changes suggest a multifactorial nature of the immunometabolic responses of mouse spleen to T. gondii infection. CONCLUSIONS: This study demonstrated that T. gondii infection can cause significant metabolomic alterations in the spleen of infected mice. These findings provide new insights into the molecular mechanisms that underpin the pathogenesis of T. gondii infection. PMID: 28720125 [PubMed - in process]

Related Articles Lipid Emulsion Added to a Liquid High-Carbohydrate Diet and Voluntary Running Exercise Reduce Lipogenesis and Ameliorate Early-Stage Hepatic Steatosis in Mice. J Nutr. 2017 May;147(5):746-753 Authors: Huang KH, Hao L, Smith PB, Rogers CJ, Patterson AD, Ross AC Abstract Background: The use of parenteral nutrition formulas is often associated with the development of hepatic steatosis. We have shown previously that the addition of a lipid emulsion (LE) rich in n-6 (ω-6) fatty acids (FAs) ameliorated triglyceride (TG) accumulation in the livers of nonobese mice fed a high-carbohydrate diet (HCD) for 5 wk. However, it remains unclear how rapidly this condition develops and whether it can be prevented by LE with or without a running wheel for voluntary exercise (Exe).Objective: We investigated in an 8-d study whether mice develop steatosis and whether the administration of LE with or without Exe reduces the concentration of total FAs and prevents an increase in the expression of genes in the liver associated with lipogenesis.Methods: Male C57BL/6 mice aged 5 wk were randomized into 5 groups: standard feed pellet (SFP); a liquid HCD (77% of total energy from carbohydrates and 0.5% from fat); HCD + Exe; HCD + 13.5% LE (67% carbohydrates and 13.5% fat); or HCD + 13.5% LE + Exe. Hepatic TG concentration, lipogenic genes, and total FAs were measured on day 8.Results: Oil Red O staining and TG quantification showed hepatic TG accumulation on day 8; the addition of 13.5% LE either with or without Exe suppressed the TG accumulation compared with HCD (P < 0.005). With the use of quantitative reverse transcriptase-polymerase chain reaction analysis, the expression concentrations of lipogenic genes [ATP-citrate lyase, acetyl coenzyme A carboxylase 1, FA synthase (Fasn), and stearoyl coenzyme A desaturase 1 (Scd1)] in the HCD + 13.5% LE group were 26-60% of HCD (P < 0.01) and 11-38% of HCD in the HCD + 13.5% LE + Exe group (P < 0.001), with interactions for Fasn and Scd1 (P < 0.05). With the use of gas chromatography-mass spectrometry analysis, the HCD + 13.5% LE group had lower monounsaturated fatty acids (38.7% of HCD) but higher polyunsaturated fatty acids (164% of HCD) (P < 0.001).Conclusions: In short-term studies designed to resemble the early dynamic stage of the development of hepatic steatosis, the addition of 13.5% LE to a liquid HCD reduced hepatic lipogenesis. Exe exerted an independent protective effect and interacted with LE to further reduce the expression of Scd1. PMID: 28298542 [PubMed - indexed for MEDLINE]

Related Articles Integrated Physiological, Proteomic, and Metabolomic Analysis of Ultra Violet (UV) Stress Responses and Adaptation Mechanisms in Pinus radiata. Mol Cell Proteomics. 2017 Mar;16(3):485-501 Authors: Pascual J, Cañal MJ, Escandón M, Meijón M, Weckwerth W, Valledor L Abstract Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce. Pinus spp. are commercially relevant trees and not much is known about their adaptation to UV. In this work, UV treatment and recovery of Pinus radiata plants with dosages mimicking future scenarios, based on current models of UV radiation, were performed in a time-dependent manner. The combined metabolome and proteome analysis were complemented with measurements of + physiological parameters and gene expression. Sparse PLS analysis revealed complex molecular interaction networks of molecular and physiological data. Early responses prevented phototoxicity by reducing photosystem activity and the electron transfer chain together with the accumulation of photoprotectors and photorespiration. Apart from the reduction in photosynthesis as consequence of the direct UV damage on the photosystems, the primary metabolism was rearranged to deal with the oxidative stress while minimizing ROS production. New protein kinases and proteases related to signaling, coordination, and regulation of UV stress responses were revealed. All these processes demonstrate a complex molecular interaction network extending the current knowledge on UV-stress adaptation in pine. PMID: 28096192 [PubMed - indexed for MEDLINE]

Related Articles Metabolism-Based Click-Mediated Platform for Specific Imaging and Quantification of Cell Surface Sialic Acids. Anal Chem. 2017 01 03;89(1):538-543 Authors: Liang Y, Jiang X, Yuan R, Zhou Y, Ji C, Yang L, Chen H, Wang Q Abstract Although we believe that the cell surface sialic acids (Sias) are playing an important role in cell-cell interactions and related tumor metastasis processes, acquisition of their quantitative information has yet been a challenge to date. Here, we reported the construction of a new analytical platform for Sias-specific imaging and quantification. We used N-azidoacetyl-mannosamine tetraacylated as a metabolic sugar substrate to bioassemble azido-Sias on the surface of cells via the metabolic pathway of Sias de novo synthesis. These azido-Sias allow us to perform a duplex Sias-specific analysis with various fluorescent and elemental reporters such as DIBO-Alexa Fluor 647, DBCO-DOTA-Eu, and DBCO-PEG4-BODIPY, which can be easily labeled and/or tagged through an effective copper-free bioorthogonal click reaction. Compared to the previous reported strategies, we quantified the cell surface Sias with the LODs (3σ) down to 8.9 fmol and 0.24 pmol using (153)Eu- and (10)B-species unspecific isotope dilution ICPMS, in addition to their red- and green-CLSM profiling. Such a platform enables us to evaluate Sias regulation under the administration of paclitaxel, finding that 1 μM paclitaxel induced a significant Sias decrease of 67% on the surface of hepatic tumor cell SMMC-7721, while had no obvious adverse effect to that of para-carcinomatous liver cell LO2. Besides Sias, we believe that this metabolism-based click-mediated platform will provide opportunities to study other monosaccharides and their corresponding biological roles when more corresponding chemically modified sugar substrates and specific bioorthogonal reactions are developed. PMID: 27935295 [PubMed - indexed for MEDLINE]

Related Articles Glycolytic Metabolism Plays a Functional Role in Regulating Human Pluripotent Stem Cell State. Cell Stem Cell. 2016 Oct 06;19(4):476-490 Authors: Gu W, Gaeta X, Sahakyan A, Chan AB, Hong CS, Kim R, Braas D, Plath K, Lowry WE, Christofk HR Abstract The rate of glycolytic metabolism changes during differentiation of human embryonic stem cells (hESCs) and reprogramming of somatic cells to pluripotency. However, the functional contribution of glycolytic metabolism to the pluripotent state is unclear. Here we show that naive hESCs exhibit increased glycolytic flux, MYC transcriptional activity, and nuclear N-MYC localization relative to primed hESCs. This status is consistent with the inner cell mass of human blastocysts, where MYC transcriptional activity is higher than in primed hESCs and nuclear N-MYC levels are elevated. Reduction of glycolysis decreases self-renewal of naive hESCs and feeder-free primed hESCs, but not primed hESCs grown in feeder-supported conditions. Reduction of glycolysis in feeder-free primed hESCs also enhances neural specification. These findings reveal associations between glycolytic metabolism and human naive pluripotency and differences in the metabolism of feeder-/feeder-free cultured hESCs. They may also suggest methods for regulating self-renewal and initial cell fate specification of hESCs. PMID: 27618217 [PubMed - indexed for MEDLINE]

Related Articles Mitochondrial Dynamics Impacts Stem Cell Identity and Fate Decisions by Regulating a Nuclear Transcriptional Program. Cell Stem Cell. 2016 Aug 04;19(2):232-47 Authors: Khacho M, Clark A, Svoboda DS, Azzi J, MacLaurin JG, Meghaizel C, Sesaki H, Lagace DC, Germain M, Harper ME, Park DS, Slack RS Abstract Regulated mechanisms of stem cell maintenance are key to preventing stem cell depletion and aging. While mitochondrial morphology plays a fundamental role in tissue development and homeostasis, its role in stem cells remains unknown. Here, we uncover that mitochondrial dynamics regulates stem cell identity, self-renewal, and fate decisions by orchestrating a transcriptional program. Manipulation of mitochondrial structure, through OPA1 or MFN1/2 deletion, impaired neural stem cell (NSC) self-renewal, with consequent age-dependent depletion, neurogenesis defects, and cognitive impairments. Gene expression profiling revealed ectopic expression of the Notch self-renewal inhibitor Botch and premature induction of transcription factors that promote differentiation. Changes in mitochondrial dynamics regulate stem cell fate decisions by driving a physiological reactive oxygen species (ROS)-mediated process, which triggers a dual program to suppress self-renewal and promote differentiation via NRF2-mediated retrograde signaling. These findings reveal mitochondrial dynamics as an upstream regulator of essential mechanisms governing stem cell self-renewal and fate decisions through transcriptional programming. PMID: 27237737 [PubMed - indexed for MEDLINE]

Related Articles Integrated Metabolo-Transcriptomics Reveals Fusarium Head Blight Candidate Resistance Genes in Wheat QTL-Fhb2. PLoS One. 2016;11(5):e0155851 Authors: Dhokane D, Karre S, Kushalappa AC, McCartney C Abstract BACKGROUND: Fusarium head blight (FHB) caused by Fusarium graminearum not only causes severe losses in yield, but also reduces quality of wheat grain by accumulating mycotoxins. Breeding for host plant resistance is considered as the best strategy to manage FHB. Resistance in wheat to FHB is quantitative in nature, involving cumulative effects of many genes governing resistance. The poor understanding of genetics and lack of precise phenotyping has hindered the development of FHB resistant cultivars. Though more than 100 QTLs imparting FHB resistance have been reported, none discovered the specific genes localized within the QTL region, nor the underlying mechanisms of resistance. FINDINGS: In our study recombinant inbred lines (RILs) carrying resistant (R-RIL) and susceptible (S-RIL) alleles of QTL-Fhb2 were subjected to metabolome and transcriptome profiling to discover the candidate genes. Metabolome profiling detected a higher abundance of metabolites belonging to phenylpropanoid, lignin, glycerophospholipid, flavonoid, fatty acid, and terpenoid biosynthetic pathways in R-RIL than in S-RIL. Transcriptome analysis revealed up-regulation of several receptor kinases, transcription factors, signaling, mycotoxin detoxification and resistance related genes. The dissection of QTL-Fhb2 using flanking marker sequences, integrating metabolomic and transcriptomic datasets, identified 4-Coumarate: CoA ligase (4CL), callose synthase (CS), basic Helix Loop Helix (bHLH041) transcription factor, glutathione S-transferase (GST), ABC transporter-4 (ABC4) and cinnamyl alcohol dehydrogenase (CAD) as putative resistance genes localized within the QTL-Fhb2 region. CONCLUSION: Some of the identified genes within the QTL region are associated with structural resistance through cell wall reinforcement, reducing the spread of pathogen through rachis within a spike and few other genes that detoxify DON, the virulence factor, thus eventually reducing disease severity. In conclusion, we report that the wheat resistance QTL-Fhb2 is associated with high rachis resistance through additive resistance effects of genes, based on cell wall enforcement and detoxification of DON. Following further functional characterization and validation, these resistance genes can be used to replace the genes in susceptible commercial cultivars, if nonfunctional, based on genome editing to improve FHB resistance. PMID: 27232496 [PubMed - indexed for MEDLINE]

Related Articles Secondary Necrosis: Accidental No More. Trends Cancer. 2017 Jan;3(1):1-2 Authors: Galluzzi L, Kroemer G Abstract Recent data demonstrate that secondary necrosis is not an accidental epiphenomenon of apoptosis, but a finely regulated process with prominent pathophysiological and therapeutic implications. The molecular machinery that controls secondary necrosis stands out as a promising target for the development of novel drugs that may increase the immunogenicity of cancer cells succumbing to treatment. PMID: 28718422 [PubMed - in process]

Related Articles Certified Reference Material for Use in (1)H, (31)P, and (19)F Quantitative NMR, Ensuring Traceability to the International System of Units. J AOAC Int. 2017 Jul 18;: Authors: Rigger R, Rück A, Hellriegel C, Sauermoser R, Morf F, Breitruck K, Obkircher M Abstract In recent years, quantitative NMR (qNMR) spectroscopy has become one of the most important tools for content determination of organic substances and quantitative evaluation of impurities. Using Certified Reference Materials (CRMs) as internal or external standards, the extensively used qNMR method can be applied for purity determination, including unbroken traceability to the International System of Units (SI). The implementation of qNMR toward new application fields, e.g., metabolomics, environmental analysis, and physiological pathway studies, brings along more complex molecules and systems, thus making use of (1)H qNMR challenging. A smart workaround is possible by the use of other NMR active nuclei, namely (31)P and (19)F. This article presents the development of three classes of qNMR CRMs based on different NMR active nuclei ((1)H, (31)P, and (19)F), and the corresponding approaches to establish traceability to the SI through primary CRMs from the National Institute of Standards and Technology and the National Metrology Institute of Japan. These <italic>Trace</italic>CERT(&#x00AE;) qNMR CRMs are produced under ISO/IEC 17025 and ISO Guide 34 using high-performance qNMR. PMID: 28718399 [PubMed - as supplied by publisher]

Related Articles Optimization of lipid extraction and analytical protocols for UHPLC-ESI-HRMS-based lipidomic analysis of adherent mammalian cancer cells. Anal Bioanal Chem. 2017 Jul 17;: Authors: Zhang H, Gao Y, Sun J, Fan S, Yao X, Ran X, Zheng C, Huang M, Bi H Abstract Lipidomics, which reveals comprehensive characterization of molecular lipids, is a rapidly growing technology used in biomedical research. Lipid extraction is a critical step in lipidomic analysis. However, the effectiveness of different lipid extract solvent systems from cellular samples still remains unclear. In the current study, the protocol of reverse-phase liquid chromatography mass spectrometry (LC/MS)-based lipidomics was optimized for extraction and detection of lipids from human pancreatic cancer cell line PANC-1. Four different extraction methods were compared, including methanol/methyl-tert-butyl ether (MTBE)/H2O, methanol/chloroform, methanol/MTBE/chloroform, and hexane/isopropanol. Data were acquired using high-resolution mass spectrometry in positive and negative ion modes respectively. The number of total detected and identified lipids was assessed with the aid of automated lipid identification software LipidSearch. Results demonstrated that methanol/MTBE/H2O provided a better extraction efficiency for different lipid classes, which was chosen as the optimized extraction solvent system. This validated method enables highly sensitive and reproducible analysis for a variety of cellular lipids, which was further applied to an untargeted lipidomic study on human pancreatic cancer PANC-1 cell lines. Moreover, this optimized extraction solvent system can be further applied to other cancer cell lines with similar chemical and physical properties. Graphical abstract Optimized UHPLC-ESI-HRMS-based lipidomic analysis of cancer cells. PMID: 28717896 [PubMed - as supplied by publisher]

Related Articles A novel community driven software for functional enrichment analysis of extracellular vesicles data. J Extracell Vesicles. 2017;6(1):1321455 Authors: Pathan M, Keerthikumar S, Chisanga D, Alessandro R, Ang CS, Askenase P, Batagov AO, Benito-Martin A, Camussi G, Clayton A, Collino F, Di Vizio D, Falcon-Perez JM, Fonseca P, Fonseka P, Fontana S, Gho YS, Hendrix A, Hoen EN, Iraci N, Kastaniegaard K, Kislinger T, Kowal J, Kurochkin IV, Leonardi T, Liang Y, Llorente A, Lunavat TR, Maji S, Monteleone F, Øverbye A, Panaretakis T, Patel T, Peinado H, Pluchino S, Principe S, Ronquist G, Royo F, Sahoo S, Spinelli C, Stensballe A, Théry C, van Herwijnen MJC, Wauben M, Welton JL, Zhao K, Mathivanan S Abstract Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture "what the community needs in a tool". Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes. Remarkably, with the enthusiastic participation of the community, we were able to implement 90% of the requested features. FunRich enables plugin for extracellular vesicles wherein users can download and analyse data from Vesiclepedia database. By involving researchers early through community needs software development, we believe that comprehensive analysis tools can be developed in various scientific disciplines. PMID: 28717418 [PubMed]

Related Articles Metabolomics of an in vitro liver model containing primary hepatocytes assembling around an endothelial cell network: comparative study on the metabolic stability and the effect of acetaminophen treatment. J Toxicol Sci. 2017;42(4):445-454 Authors: Toyoda Y, Kashikura K, Soga T, Tagawa YI Abstract Recently, a novel culture system consisting of primary hepatocytes structured over a network of endothelial cells on the Engelbreth-Holm-Swarm (EHS) gel has been reported. This in vitro liver model on the EHS gel (IVLEHS) has been shown to maintain the expression of hepatic genes and their functional activity. Moreover, the IVLEHS was more sensitive to xenobiotics than hepatocyte monocultures, suggesting the potential utility of this culture system for compound hepatotoxicity screening. However, the effect of this three-dimensional structure formation on the cellular metabolic profile of hepatocytes in the IVLEHS is not well understood. To address this concern, we performed metabolome analysis using capillary electrophoresis-time of flight mass spectrometry. Between the IVLEHS and mono-cultured hepatocytes on the EHS gel, there was no significant difference in the levels of metabolites of the urea cycle and the tricarboxylic acid cycle, essential amino acids, and adenylate energy charge (AEC) which is an important indicator of cellular energy status. On the other hand, acetaminophen-dependent decrease of the AEC in the IVLEHS was greater than that in the monoculture, suggesting the higher sensitivity of IVLEHS to acetaminophen-induced hepatotoxicity which is caused by metabolic activation of this drug. Further analysis showed that the levels of taurocholate, one of the major conjugated bile acids, were higher in the IVLEHS than in the monoculture. Considering that the construction of the IVLEHS did not seem to disturb the major cellular metabolism, our findings would strengthen the concept that IVLEHS would have beneficial effects on the maintenance of hepatic functions. PMID: 28717103 [PubMed - in process]