PubMed

Optimized Method for Untargeted Metabolomics Analysis of MDA-MB-231 Breast Cancer Cells. Metabolites. 2016;6(4) Authors: Peterson AL, Walker AK, Sloan EK, Creek DJ Abstract Cancer cells often have dysregulated metabolism, which is largely characterized by the Warburg effect-an increase in glycolytic activity at the expense of oxidative phosphorylation-and increased glutamine utilization. Modern metabolomics tools offer an efficient means to investigate metabolism in cancer cells. Currently, a number of protocols have been described for harvesting adherent cells for metabolomics analysis, but the techniques vary greatly and they lack specificity to particular cancer cell lines with diverse metabolic and structural features. Here we present an optimized method for untargeted metabolomics characterization of MDA-MB-231 triple negative breast cancer cells, which are commonly used to study metastatic breast cancer. We found that an approach that extracted all metabolites in a single step within the culture dish optimally detected both polar and non-polar metabolite classes with higher relative abundance than methods that involved removal of cells from the dish. We show that this method is highly suited to diverse applications, including the characterization of central metabolic flux by stable isotope labelling and differential analysis of cells subjected to specific pharmacological interventions. PMID: 27669323 [PubMed - as supplied by publisher]

Potential of LC Coupled to Fluorescence Detection in Food Metabolomics: Determination of Phenolic Compounds in Virgin Olive Oil. Int J Mol Sci. 2016;17(10) Authors: Monasterio RP, Olmo-García L, Bajoub A, Fernández-Gutiérrez A, Carrasco-Pancorbo A Abstract A powerful chromatographic method coupled to a fluorescence detector was developed to determine the phenolic compounds present in virgin olive oil (VOO), with the aim to propose an appropriate alternative to liquid chromatography-mass spectrometry. An excitation wavelength of 285 nm was selected and four different emission wavelengths (316, 328, 350 and 450 nm) were simultaneously recorded, working therefore on "multi-emission" detection mode. With the use of commercially available standards and other standards obtained by semipreparative high performance liquid chromatography, it was possible to identify simple phenols, lignans, several complex phenols, and other phenolic compounds present in the matrix under study. A total of 26 phenolic compounds belonging to different chemical families were identified (23 of them were susceptible of being quantified). The proposed methodology provided detection and quantification limits within the ranges of 0.004-7.143 μg·mL(-1) and 0.013-23.810 μg·mL(-1), respectively. As far as the repeatability is concerned, the relative standard deviation values were below 0.43% for retention time, and 9.05% for peak area. The developed methodology was applied for the determination of phenolic compounds in ten VOOs, both monovarietals and blends. Secoiridoids were the most abundant fraction in all the samples, followed by simple phenolic alcohols, lignans, flavonoids, and phenolic acids (being the abundance order of the latter chemical classes logically depending on the variety and origin of the VOOs). PMID: 27669238 [PubMed - as supplied by publisher]

Multiplatform Mass Spectrometry-Based Approach Identifies Extracellular Glycolipids of the Yeast Rhodotorula babjevae UCDFST 04-877. J Nat Prod. 2016 Sep 26; Authors: Cajka T, Garay LA, Sitepu IR, Boundy-Mills KL, Fiehn O Abstract A multiplatform mass spectrometry-based approach was used for elucidating extracellular lipids with biosurfactant properties produced by the oleaginous yeast Rhodotorula babjevae UCDFST 04-877. This strain secreted 8.6 ± 0.1 g/L extracellular lipids when grown in a benchtop bioreactor fed with 100 g/L glucose in medium without addition of hydrophobic substrate, such as oleic acid. Untargeted reversed-phase liquid chromatography-quadrupole/time-of-flight mass spectrometry (QTOFMS) detected native glycolipid molecules with masses of 574-716 Da. After hydrolysis into the fatty acid and sugar components and hydrophilic interaction chromatography-QTOFMS analysis, the extracellular lipids were found to consist of hydroxy fatty acids and sugar alcohols. Derivatization and chiral separation gas chromatography-mass spectrometry (GC-MS) identified these components as d-arabitol, d-mannitol, (R)-3-hydroxymyristate, (R)-3-hydroxypalmitate, and (R)-3-hydroxystearate. In order to assemble these substructures back into intact glycolipids that were detected in the initial screen, potential structures were in-silico acetylated to match the observed molar masses and subsequently characterized by matching predicted and observed MS/MS fragmentation using the Mass Frontier software program. Eleven species of acetylated sugar alcohol esters of hydroxy fatty acids were characterized for this yeast strain. PMID: 27669091 [PubMed - as supplied by publisher]

Complex Mixtures by NMR and Complex NMR for Mixtures: experimental and publication challenges. Magn Reson Chem. 2016 Sep 26; Authors: Wist J Abstract Untargeted strategies have changed the rules of the game in complex mixture analysis, introducing an amazing potential for medical and biological applications that is just starting to be tapped. But with great power come great challenges; though untargeted mixture analysis opens the road for many exciting possibilities, the road is still full of perils. On the one hand, this article highlights some of the difficulties that need to be sorted for mixture analysis by NMR to fulfill its potential, along with insight on how they may be managed. Highlighted key points include the need for "computer friendly" solutions for sharing data, experimental design and algorithm to facilitate the steady growth of knowledge and modeling ability in the field, and the need for large-scale studies to improve confidence in newly identified biomarkers. On the other hand, the second part of this article presents some breakthroughs in NMR experiments that, when combined, may modify the landscape of mixture analysis. PMID: 27668407 [PubMed - as supplied by publisher]

Normal-Gamma-Bernoulli Peak Detection for Analysis of Comprehensive Two-Dimensional Gas Chromatography Mass Spectrometry Data. Comput Stat Data Anal. 2017 Jan;105:96-111 Authors: Kim S, Jang H, Koo I, Lee J, Zhang X Abstract Compared to other analytical platforms, comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC×GC-MS) has much increased separation power for analysis of complex samples and thus is increasingly used in metabolomics for biomarker discovery. However, accurate peak detection remains a bottleneck for wide applications of GC×GC-MS. Therefore, the normal-exponential-Bernoulli (NEB) model is generalized by gamma distribution and a new peak detection algorithm using the normal-gamma-Bernoulli (NGB) model is developed. Unlike the NEB model, the NGB model has no closed-form analytical solution, hampering its practical use in peak detection. To circumvent this difficulty, three numerical approaches, which are fast Fourier transform (FFT), the first-order and the second-order delta methods (D1 and D2), are introduced. The applications to simulated data and two real GC×GC-MS data sets show that the NGB-D1 method performs the best in terms of both computational expense and peak detection performance. PMID: 27667882 [PubMed - as supplied by publisher]

MALDI-TOF-MS reveals differential N-linked plasma- and IgG-glycosylation profiles between mothers and their newborns. Sci Rep. 2016;6:34001 Authors: Jansen BC, Bondt A, Reiding KR, Scherjon SA, Vidarsson G, Wuhrer M Abstract During pregnancy, the mother provides multiple nutrients and substances to the foetus, with maternal immunoglobulin G (IgG) being actively transported to the foetus. Newborns depend on maternal IgG for immune-protection in their first months. The glycosylation of IgG has been shown to influence its dynamics, e.g. receptor binding. While minor differences in IgG glycosylation have been found between IgG derived from maternal blood and umbilical cord blood (UC) of newborn children, the differential glycosylation of maternal and UC plasma has hitherto not been studied. Here, we studied the N-glycosylation of IgG and total plasma proteome of both maternal and UC plasma of 42 pairs of mothers and newborn children. A total of 37 N-glycans were quantified for IgG and 45 for the total plasma N-glycome (TPNG). The study showed slightly higher levels of galactosylation for UC IgG than maternal IgG, confirming previous results, as well as lower bisection and sialylation. Furthermore, the TPNG results showed lower values for galactosylation and sialylation, and higher values for fucosylation in the UC plasma. In conclusion, this study presents some novel insights into IgG glycosylation differences as well as the first broad overview of the differential plasma glycosylation between mothers and newborns. PMID: 27666402 [PubMed - as supplied by publisher]

Metabolomic Profiling in Relation to New-Onset Atrial Fibrillation (from the Framingham Heart Study). Am J Cardiol. 2016 Aug 24; Authors: Ko D, Riles EM, Marcos EG, Magnani JW, Lubitz SA, Lin H, Long MT, Schnabel RB, McManus DD, Ellinor PT, Ramachandran VS, Wang TJ, Gerszten RE, Benjamin EJ, Yin X, Rienstra M Abstract Previous studies have shown several metabolic biomarkers to be associated with prevalent and incident atrial fibrillation (AF), but the results have not been replicated. We investigated metabolite profiles of 2,458 European ancestry participants from the Framingham Heart Study without AF at the index examination and followed them for 10 years for new-onset AF. Amino acids, organic acids, lipids, and other plasma metabolites were profiled by liquid chromatography-tandem mass spectrometry using fasting plasma samples. We conducted Cox proportional hazard analyses for association between metabolites and new-onset AF. We performed hypothesis-generating analysis to identify novel metabolites and hypothesis-testing analysis to confirm the previously reported associations between metabolites and AF. Mean age was 55.1 ± 9.9 years, and 53% were women. Incident AF developed in 156 participants (6.3%) in 10 years of follow-up. A total of 217 metabolites were examined, consisting of 54 positively charged metabolites, 59 negatively charged metabolites, and 104 lipids. None of the 217 metabolites met our a priori specified Bonferroni corrected level of significance in the multivariate analyses. We were unable to replicate previous results demonstrating associations between metabolites that we had measured and AF. In conclusion, in our metabolomics approach, none of the metabolites we tested were significantly associated with the risk of future AF. PMID: 27666170 [PubMed - as supplied by publisher]

Related Articles In vitro, in vivo and in silico metabolic profiling of α-pyrrolidinopentiothiophenone, a novel thiophene stimulant. Bioanalysis. 2016;8(1):65-82 Authors: Swortwood MJ, Carlier J, Ellefsen KN, Wohlfarth A, Diao X, Concheiro-Guisan M, Kronstrand R, Huestis MA Abstract BACKGROUND: Little or no pharmacological or toxicological data are available for novel psychoactive substances when they first emerge, making their identification and interpretation in biological matrices challenging. MATERIALS & METHODS: A new synthetic cathinone, α-pyrrolidinopentiothiophenone (α-PVT), was incubated with hepatocytes and samples were analyzed using liquid chromatography coupled to a Q Exactive™ Orbitrap mass spectrometer. Authentic urine specimens from suspected α-PVT cases were also analyzed. Scans were data mined with Compound Discoverer™ for identification and structural elucidation of metabolites. RESULTS/CONCLUSION: Seven α-PVT metabolites were identified in hepatocyte incubations, and in the authentic urine samples, also with an additional monohydroxylated product and a glucuronide of low intensity. α-PVT dihydroxypyrrolidinyl, α-PVT 2-ketopyrrolidinyl, α-PVT hydroxythiophenyl and α-PVT thiophenol had the most intense in vivo signals. PMID: 26648097 [PubMed - indexed for MEDLINE]

Related Articles Highly-accurate metabolomic detection of early-stage ovarian cancer. Sci Rep. 2015;5:16351 Authors: Gaul DA, Mezencev R, Long TQ, Jones CM, Benigno BB, Gray A, Fernández FM, McDonald JF Abstract High performance mass spectrometry was employed to interrogate the serum metabolome of early-stage ovarian cancer (OC) patients and age-matched control women. The resulting spectral features were used to establish a linear support vector machine (SVM) model of sixteen diagnostic metabolites that are able to identify early-stage OC with 100% accuracy in our patient cohort. The results provide evidence for the importance of lipid and fatty acid metabolism in OC and serve as the foundation of a clinically significant diagnostic test. PMID: 26573008 [PubMed - indexed for MEDLINE]

Related Articles Identification of a Cyanobacterial RND-Type Efflux System Involved in Export of Free Fatty Acids. Plant Cell Physiol. 2015 Dec;56(12):2467-77 Authors: Kato A, Takatani N, Use K, Uesaka K, Ikeda K, Chang Y, Kojima K, Aichi M, Ihara K, Nakahigashi K, Maeda S, Omata T Abstract An RND (resistance-nodulation-division)-type transporter having the capacity to export free fatty acids (FFAs) was identified in the cyanobacterium Synechococcus elongatus strain PCC 7942 during characterization of a mutant strain engineered to produce FFAs. The basic strategy for construction of the FFA-producing mutant was a commonly used one, involving inactivation of the endogenous acyl-acyl carrier protein synthetase gene (aas) and introduction of a foreign thioesterase gene ('tesA), but a nitrate transport mutant NA3 was used as the parental strain to achieve slow, nitrate-limited growth in batch cultures. Also, a nitrogen-regulated promoter PnirA was used to drive 'tesA to maximize thioesterase expression during the nitrate-limited growth. The resulting mutant (dAS2T) was, however, incapable of growth under the conditions of nitrate limitation, presumably due to toxicity associated with FFA overproduction. Incubation of the mutant culture under the non-permissive conditions allowed for isolation of a pseudorevertant (dAS2T-pr1) capable of growth on nitrate. Genome sequence and gene expression analyses of this strain suggested that expression of an RND-type efflux system had rescued growth on nitrate. Targeted inactivation of the RND-type transporter genes in the wild-type strain resulted in loss of tolerance to exogenously added FFAs including capric, lauric, myristic, oleic and linolenic acids. Overexpression of the genes in dAS2T, on the other hand, enhanced FFA excretion and cell growth in nitrate-containing medium, verifying that the genes encode an efflux pump for FFAs. These results demonstrate the importance of the efflux system in efficient FFA production using genetically engineered cyanobacteria. PMID: 26468506 [PubMed - indexed for MEDLINE]

Related Articles Functional Characterization and Substrate Promiscuity of UGT71 Glycosyltransferases from Strawberry (Fragaria × ananassa). Plant Cell Physiol. 2015 Dec;56(12):2478-93 Authors: Song C, Gu L, Liu J, Zhao S, Hong X, Schulenburg K, Schwab W Abstract Glycosylation determines the complexity and diversity of plant natural products. To characterize fruit ripening-related UDP-dependent glycosyltransferases (UGTs) functionally in strawberry, we mined the publicly available Fragaria vesca genome sequence and found 199 putative UGT genes. Candidate UGTs whose expression levels were strongly up-regulated during fruit ripening were cloned from F.×ananassa and six were successfully expressed in Escherichia coli and biochemically characterized. UGT75T1 showed very strict substrate specificity and glucosylated only galangin out of 33 compounds. The other recombinant enzymes exhibited broad substrate tolerance, accepting numerous flavonoids, hydroxycoumarins, naphthols and the plant hormone, (+)-S-abscisic acid (ABA). UGT71W2 showed the highest activity towards 1-naphthol, while UGT71A33, UGT71A34a/b and UGT71A35 preferred 3-hydroxycoumarin and formed 3- and 7-O-glucosides as well as a diglucoside from flavonols. Screening of a strawberry physiological aglycone library identified kaempferol, quercetin, ABA and three unknown natural compounds as putative in planta substrates of UGT71A33, UGT71A34a and UGT71W2. Metabolite analyses of RNA interference (RNAi)-mediated silenced fruits demonstrated that UGT71W2 contributes to the glycosylation of flavonols, xenobiotics and, to a minor extent, of ABA, in planta. The study showed that both specialist and generalist UGTs were expressed during strawberry fruit ripening and the latter were probably not restricted to only one function in plants. PMID: 26454881 [PubMed - indexed for MEDLINE]

Human Serum Metabolites Associate With Severity and Patient Outcomes in Traumatic Brain Injury. EBioMedicine. 2016 Jul 15; Authors: Orešič M, Posti JP, Kamstrup-Nielsen MH, Takala RS, Lingsma HF, Mattila I, Jäntti S, Katila AJ, Carpenter KL, Ala-Seppälä H, Kyllönen A, Maanpää HR, Tallus J, Coles JP, Heino I, Frantzén J, Hutchinson PJ, Menon DK, Tenovuo O, Hyötyläinen T Abstract Traumatic brain injury (TBI) is a major cause of death and disability worldwide, especially in children and young adults. TBI is an example of a medical condition where there are still major lacks in diagnostics and outcome prediction. Here we apply comprehensive metabolic profiling of serum samples from TBI patients and controls in two independent cohorts. The discovery study included 144 TBI patients, with the samples taken at the time of hospitalization. The patients were diagnosed as severe (sTBI; n=22), moderate (moTBI; n=14) or mild TBI (mTBI; n=108) according to Glasgow Coma Scale. The control group (n=28) comprised of acute orthopedic non-brain injuries. The validation study included sTBI (n=23), moTBI (n=7), mTBI (n=37) patients and controls (n=27). We show that two medium-chain fatty acids (decanoic and octanoic acids) and sugar derivatives including 2,3-bisphosphoglyceric acid are strongly associated with severity of TBI, and most of them are also detected at high concentrations in brain microdialysates of TBI patients. Based on metabolite concentrations from TBI patients at the time of hospitalization, an algorithm was developed that accurately predicted the patient outcomes (AUC=0.84 in validation cohort). Addition of the metabolites to the established clinical model (CRASH), comprising clinical and computed tomography data, significantly improved prediction of patient outcomes. The identified 'TBI metabotype' in serum, that may be indicative of disrupted blood-brain barrier, of protective physiological response and altered metabolism due to head trauma, offers a new avenue for the development of diagnostic and prognostic markers of broad spectrum of TBIs. PMID: 27665050 [PubMed - as supplied by publisher]

Proteomic comparison of near-isogenic barley (Hordeum vulgare L.) germplasm differing in the allelic state of a major senescence QTL identifies numerous proteins involved in plant pathogen defense. Plant Physiol Biochem. 2016 Sep 14;109:114-127 Authors: Mason KE, Hilmer JK, Maaty WS, Reeves BD, Grieco PA, Bothner B, Fischer AM Abstract Senescence is the last developmental phase of plant tissues, organs and, in the case of monocarpic senescence, entire plants. In monocarpic crops such as barley, it leads to massive remobilization of nitrogen and other nutrients to developing seeds. To further investigate this process, a proteomic comparison of flag leaves of near-isogenic late- and early-senescing barley germplasm was performed. Protein samples at 14 and 21 days past anthesis were analyzed using both two-dimensional gel-based and label-free quantitative mass spectrometry-based ('shotgun') proteomic techniques. This approach identified >9000 barley proteins, and one-third of them were quantified. Analysis focused on proteins that were significantly (p < 0.05; difference ≥1.5-fold) upregulated in early-senescing line '10_11' as compared to late-senescing variety 'Karl', as these may be functionally important for senescence. Proteins in this group included family 1 pathogenesis-related proteins, intracellular and membrane receptors or co-receptors (NBS-LRRs, LRR-RLKs), enzymes involved in attacking pathogen cell walls (glucanases), enzymes with possible roles in cuticle modification, and enzymes involved in DNA repair. Additionally, proteases and elements of the ubiquitin-proteasome system were upregulated in line '10_11', suggesting involvement of nitrogen remobilization and regulatory processes. Overall, the proteomic data highlight a correlation between early senescence and upregulated defense functions. This correlation emerges more clearly from the current proteomic data than from a previously performed transcriptomic comparison of 'Karl' and '10_11'. Our findings stress the value of studying biological systems at both the transcript and protein levels, and point to the importance of pathogen defense functions during developmental leaf senescence. PMID: 27665045 [PubMed - as supplied by publisher]

Related Articles Accumulation of guaiacol glycoconjugates in fruit, leaves and shoots of Vitis vinifera cv. Monastrell following foliar applications of guaiacol or oak extract to grapevines. Food Chem. 2017 Feb 15;217:782-789 Authors: Pardo-Garcia AI, Wilkinson KL, Culbert JA, Lloyd ND, Alonso GL, Salinas MR Abstract Previous studies have shown that volatile compounds present within a vineyard during the growing season can be absorbed by grapevines, assimilated within grapes, and then released during fermentation to influence the final aroma of wine. For example, the accumulation of volatile phenols in glycoconjugate forms following grapevine exposure to bushfire smoke, and their subsequent release during winemaking. This study investigated the accumulation of guaiacol glycoconjugates in the fruit, shoots and leaves of Monastrell grapevines following foliar applications (at veraison) of either an aqueous solution of guaiacol or an aqueous oak extract. Fruit, shoot and leaf samples were then collected at 3 time points between veraison and maturity, and analysed by gas chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry, to quantify guaiacol and its glycoconjugates, respectively. Guaiacol glycoconjugates were observed in fruit and leaves in particular, demonstrating glycosylation occurred after grapevine treatment; however, different glycoconjugate profiles were apparent. PMID: 27664698 [PubMed - as supplied by publisher]

Related Articles Comparison of gravimetric, creamatocrit and esterified fatty acid methods for determination of total fat content in human milk. Food Chem. 2017 Feb 15;217:505-510 Authors: Du J, Gay MC, Lai CT, Trengove RD, Hartmann PE, Geddes DT Abstract The gravimetric method is considered the gold standard for measuring the fat content of human milk. However, it is labor intensive and requires large volumes of human milk. Other methods, such as creamatocrit and esterified fatty acid assay (EFA), have also been used widely in fat analysis. However, these methods have not been compared concurrently with the gravimetric method. Comparison of the three methods was conducted with human milk of varying fat content. Correlations between these methods were high (r(2)=0.99). Statistical differences (P<0.001) were observed in the overall fat measurements and within each group (low, medium and high fat milk) using the three methods. Overall, stronger correlation with lower mean (4.73g/L) and percentage differences (5.16%) was observed with the creamatocrit than the EFA method when compared to the gravimetric method. Furthermore, the ease of operation and real-time analysis make the creamatocrit method preferable. PMID: 27664665 [PubMed - as supplied by publisher]

Related Articles Geoclimatic, morphological, and temporal effects on Lebanese olive oils composition and classification: A (1)H NMR metabolomic study. Food Chem. 2017 Feb 15;217:379-388 Authors: Merchak N, El Bacha E, Bou Khouzam R, Rizk T, Akoka S, Bejjani J Abstract Two hundred and thirty-four Lebanese olive samples were collected from different regions and the corresponding oils were analysed by (1)H NMR spectroscopy. The variables obtained, related to fatty acids and minor components, were used as inputs in univariate and multivariate analyses aiming to characterize and classify the oils according to geographical, morphological, and temporal factors. Samples were sorted according to the colour, size, and shape of olives, which allowed statistically significant classifications to be achieved. A sequential strategy was developed to discriminate among samples from different altitudes and latitudes. Following this strategy, obvious trends and classifications were obtained at subregional level. Furthermore, the shift in the harvest date within a range of three weeks was considered and its effect on the classification models was investigated. Likewise, the harvest year effect was evaluated; the precipitation level in April and May had a significant impact on the characteristics of the oils. PMID: 27664649 [PubMed - as supplied by publisher]

Related Articles Mass-based metabolomic analysis of soybean sprouts during germination. Food Chem. 2017 Feb 15;217:311-319 Authors: Gu EJ, Kim DW, Jang GJ, Song SH, Lee JI, Lee SB, Kim BM, Cho Y, Lee HJ, Kim HJ Abstract We investigated the metabolite profile of soybean sprouts at 0, 1, 2, 3, and 4days after germination using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-MS (LC-MS) to understand the relationship between germination and nutritional quality. Data were analyzed by partial least squares-discriminant analysis (PLS-DA), and sprout samples were separated successfully using their PLS-DA scores. Fifty-eight metabolites, including macromolecular derivatives related to energy production, amino acids, myo-inositol metabolites, phytosterols, antioxidants, isoflavones, and soyasaponins, contributed to the separation. Amino acids, myo-inositol metabolites, isoflavone aglycones, B soyasaponins, antioxidants, and phytosterols, associated with health benefits and/or taste quality, increased with germination time while isoflavone glycosides and DDMP soyasaponins decreased. Based on these metabolites, the metabolomic pathway associated with energy production in soybean sprouts is suggested. Our data suggest that sprouting is a useful processing step to improve soybean nutritional quality, and metabolomic analysis is useful in understanding nutritional change during sprouting. PMID: 27664639 [PubMed - as supplied by publisher]

Related Articles High resolution magic angle spinning NMR spectroscopy reveals that pectoralis muscle dystrophy in chicken is associated with reduced muscle content of anserine and carnosine. Food Chem. 2017 Feb 15;217:151-154 Authors: Sundekilde UK, Rasmussen MK, Young JF, Bertram HC Abstract Increased incidences of pectoralis muscle dystrophy are observed in commercial chicken products, but the muscle physiological causes for the condition remain to be identified. In the present study a high-resolution magic angle spinning (HR-MAS) proton ((1)H) NMR spectroscopic examination of intact pectoralis muscle samples (n=77) were conducted to explore metabolite perturbations associated with the muscle dystrophy condition for the very first time. Both in chicken with an age of 21 and 31days, respectively, pectoralis muscle dystrophy was associated with a significantly lower content of anserine (p=0.034), carnosine (p=0.019) and creatine (p=0.049). These findings must be considered intriguing as they corroborate that characteristic muscle di-peptides composed of β-alanine and histidine derivatives such as anserine are extremely important in homeostasis of contractile muscles as a results of their role as buffering, anti-oxidative, and anti-glycation capacities. PMID: 27664620 [PubMed - as supplied by publisher]

Related Articles Identification and characterization of a fusarium head blight resistance gene TaACT in wheat QTL-2DL. Plant Biotechnol J. 2016 Sep 24; Authors: Kage U, Karre S, Kushalappa AC, McCartney C Abstract Fusarium head blight (FHB) resistance in wheat is considered to be polygenic in nature. Cell wall fortification is one of the best resistance mechanisms in wheat against Fusarium graminearum which causes FHB. Metabolomics approach in our study led to the identification of a wide array of resistance related (RR) metabolites, among which hydroxycinnamic acid amides (HCAAs), such as, coumaroylagmatine and coumaroylputrescine were the highest fold-change RR metabolites in the rachis of a resistant near-isogenic line (NIL-R) upon F. graminearum infection. Placement of these metabolites in the secondary metabolic pathway led to the identification of a gene encoding agmatinecoumaroyl transferase, herein referred to as TaACT, as a candidate gene. Based on wheat survey sequence TaACT was located within a FHB quantitative trait loci on chromosome 2DL (FHB QTL-2DL) between the flanking markers WMC245 and GWM608. Phylogenetic analysis suggested that TaACT shared closest phylogenetic relationship with an ACT ortholog in barley. Sequence analysis of TaACT in resistant and susceptible NILs, with contrasting levels of resistance to FHB, led to the identification of several single nucleotide polymorphisms (SNPs) and two inversions that may be important for gene function. Further, a role for TaACT in FHB resistance was functionally validated by virus induced gene silencing (VIGS) in wheat NIL-R and based on complementation studies in Arabidopsis with act mutant background. The disease severity, fungal biomass, and RR metabolite analysis confirmed TaACT as an important gene in wheat FHB QTL-2DL, conferring resistance to F. graminearum. This article is protected by copyright. All rights reserved. PMID: 27663684 [PubMed - as supplied by publisher]

Related Articles Using reverse-phase protein arrays as pharmacodynamic assays for functional proteomics, biomarker discovery, and drug development in cancer. Semin Oncol. 2016 Aug;43(4):476-83 Authors: Lu Y, Ling S, Hegde AM, Byers LA, Coombes K, Mills GB, Akbani R Abstract The majority of the targeted therapeutic agents in clinical use target proteins and protein function. Although DNA and RNA analyses have been used extensively to identify novel targets and patients likely to benefit from targeted therapies, these are indirect measures of the levels and functions of most therapeutic targets. More importantly, DNA and RNA analysis is ill-suited for determining the pharmacodynamic effects of target inhibition. Assessing changes in protein levels and function is the most efficient way to evaluate the mechanisms underlying sensitivity and resistance to targeted agents. Understanding these mechanisms is necessary to identify patients likely to benefit from treatment and to develop rational drug combinations to prevent or bypass therapeutic resistance. There is an urgent need for a robust approach to assess protein levels and protein function in model systems and across patient samples. While "shot gun" mass spectrometry can provide in-depth analysis of proteins across a limited number of samples, and emerging approaches such as multiple reaction monitoring have the potential to analyze candidate markers, mass spectrometry has not entered into general use because of the high cost, requirement of extensive analysis and support, and relatively large amount of material needed for analysis. Rather, antibody-based technologies, including immunohistochemistry, radioimmunoassays, enzyme-linked immunosorbent assays (ELISAs), and more recently protein arrays, remain the most common approaches for multiplexed protein analysis. Reverse-phase protein array (RPPA) technology has emerged as a robust, sensitive, cost-effective approach to the analysis of large numbers of samples for quantitative assessment of key members of functional pathways that are affected by tumor-targeting therapeutics. The RPPA platform is a powerful approach for identifying and validating targets, classifying tumor subsets, assessing pharmacodynamics, and identifying prognostic and predictive markers, adaptive responses and rational drug combinations in model systems and patient samples. Its greatest utility has been realized through integration with other analytic platforms such as DNA sequencing, transcriptional profiling, epigenomics, mass spectrometry, and metabolomics. The power of the technology is becoming apparent through its use in pathology laboratories and integration into trial design and implementation. PMID: 27663479 [PubMed - in process]