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

Biomolecular changes that occur in the antennal gland of the giant freshwater prawn (Machrobrachium rosenbergii).

Fri, 29/09/2017 - 12:24
Related Articles Biomolecular changes that occur in the antennal gland of the giant freshwater prawn (Machrobrachium rosenbergii). PLoS One. 2017;12(6):e0177064 Authors: Bose U, Kruangkum T, Wang T, Zhao M, Ventura T, Mitu SA, Hodson MP, Shaw PN, Sobhon P, Cummins SF Abstract In decapod crustaceans, the antennal gland (AnG) is a major primary source of externally secreted biomolecules, and some may act as pheromones that play a major role in aquatic animal communication. In aquatic crustaceans, sex pheromones regulate reproductive behaviours, yet they remain largely unidentified besides the N-acetylglucosamine-1,5-lactone (NAGL) that stimulates male to female attraction. In this study, we used an AnG transcriptome of the female giant freshwater prawn (Macrobrachium rosenbergii) to predict the secretion of 226 proteins, including the most abundantly expressed transcripts encoding the Spaetzle protein, a serine protease inhibitor, and an arthropodial cuticle protein AMP 8.1. A quantitative proteome analysis of the female AnG at intermolt, premolt and postmolt, identified numerous proteins of different abundances, such as the hemocyanin subunit 1 that is most abundant at intermolt. We also show that hemocyanin subunit 1 is present within water surrounding females. Of those metabolites identified, we demonstrate that the NAGL and N-acetylglucosamine (NAG) can bind with high affinity to hemocyanin subunit 1. In summary, this study has revealed components of the female giant freshwater prawn AnG that are released and contribute to further research towards understanding crustacean conspecific signalling. PMID: 28662025 [PubMed - indexed for MEDLINE]

Prognostic modeling in pediatric acute liver failure.

Fri, 29/09/2017 - 12:24
Related Articles Prognostic modeling in pediatric acute liver failure. Liver Transpl. 2016 Oct;22(10):1418-30 Authors: Jain V, Dhawan A Abstract Liver transplantation (LT) is the only proven treatment for pediatric acute liver failure (PALF). However, over a period of time, spontaneous native liver survival is increasingly reported, making us wonder if we are overtransplanting children with acute liver failure (ALF). An effective prognostic model for PALF would help direct appropriate organ allocation. Only patients who would die would undergo LT, and those who would spontaneously recover would avoid unnecessary LT. Deriving and validating such a model for PALF, however, encompasses numerous challenges. In particular, the heterogeneity of age and etiology in PALF, as well as a lack of understanding of the natural history of the disease, contributed by the availability of LT has led to difficulties in prognostic model development. Several prognostic laboratory variables have been identified, and the incorporation of these variables into scoring systems has been attempted. A reliable targeted prognostic model for ALF in Wilson's disease has been established and externally validated. The roles of physiological, immunological, and metabolomic parameters in prognosis are being investigated. This review discusses the challenges with prognostic modeling in PALF and describes predictive methods that are currently available and in development for the future. Liver Transplantation 22 1418-1430 2016 AASLD. PMID: 27343006 [PubMed - indexed for MEDLINE]

metabolomics; +43 new citations

Thu, 28/09/2017 - 14:28
43 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2017/09/28PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +19 new citations

Tue, 26/09/2017 - 13:42
19 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2017/09/26PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Effects of stimulation technique, anatomical region, and time on human sweat lipid mediator profiles.

Mon, 25/09/2017 - 15:36
Effects of stimulation technique, anatomical region, and time on human sweat lipid mediator profiles. Prostaglandins Other Lipid Mediat. 2017 Sep 20;: Authors: Agrawal K, Waller JD, Pedersen TL, Newman JW Abstract Few studies compare sampling protocol effect on sweat composition. Here we evaluate the impact of sweat stimulation mode and site of collection on lipid mediator composition. Sweat from healthy males (n=7) was collected weekly for three weeks from the volar forearm following either pilocarpine iontophoresis or exercise, and from the forearm, back and thigh following pilocarpine iontophoresis only. Sweat content of over 150 lipid mediators were measured by liquid chromatography-tandem mass spectrometry. Seventy lipid mediators were routinely detected, including prostanoids, alcohols, diols, epoxides, ketones, nitrolipids, N-acylethanolamides, monoacylglycerols, and ceramides. Detected lipid mediators appeared unaffected by sampling site, though the forearm was the most consistent source of sweat. Pilocarpine-induced sweat showed increased concentrations of most detected compounds. Moreover, lipid mediator concentrations and profiles were temporally stable over the study duration. Sweat therefore appears to be a consistent and anatomically-stable source of lipid mediators, but care must be taken in comparing results obtained from different stimulation techniques. PMID: 28942325 [PubMed - as supplied by publisher]

Immunosurveillance of Malignant Cells with Complex Karyotypes.

Mon, 25/09/2017 - 15:36
Immunosurveillance of Malignant Cells with Complex Karyotypes. Trends Cell Biol. 2017 Sep 19;: Authors: López-Soto A, Gonzalez S, López-Larrea C, Kroemer G Abstract A wide array of cell-intrinsic surveillance mechanisms maintains the homeostasis of dividing cells and the integrity of the genome. Accumulating evidence also supports a role for cell-extrinsic mechanisms. Among them, the immune system, together with cell-autonomous checkpoint processes, eliminates cells that harbor unbalanced karyotypes generated by mitotic defects. PMID: 28939156 [PubMed - as supplied by publisher]

metabolomics; +24 new citations

Mon, 25/09/2017 - 12:32
24 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2017/09/25PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +18 new citations

Sun, 24/09/2017 - 15:04
18 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2017/09/24PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Strategies for the etiological therapy of cystic fibrosis.

Sat, 23/09/2017 - 14:42
Strategies for the etiological therapy of cystic fibrosis. Cell Death Differ. 2017 Sep 22;: Authors: Maiuri L, Raia V, Kroemer G Abstract Etiological therapies aim at repairing the underlying cause of cystic fibrosis (CF), which is the functional defect of the cystic fibrosis transmembrane conductance regulator (CFTR) protein owing to mutations in the CFTR gene. Among these, the F508del CFTR mutation accounts for more than two thirds of CF cases worldwide. Two somehow antinomic schools of thought conceive CFTR repair in a different manner. According to one vision, drugs should directly target the mutated CFTR protein to increase its plasma membrane expression (correctors) or improve its ion transport function (potentiators). An alternative strategy consists in modulating the cellular environment and proteostasis networks in which the mutated CFTR protein is synthesized, traffics to its final destination, the plasma membrane, and is turned over. We will analyze distinctive advantages and drawbacks of these strategies in terms of their scientific and clinical dimensions, and we will propose a global strategy for CF research and development based on a reconciliatory approach. Moreover, we will discuss the utility of preclinical biomarkers that may guide the personalized, patient-specific implementation of CF therapies.Cell Death and Differentiation advance online publication, 22 September 2017; doi:10.1038/cdd.2017.126. PMID: 28937684 [PubMed - as supplied by publisher]

Specificities of Human Hepatocellular Carcinoma Developed on Non-Alcoholic Fatty Liver Disease in Absence of Cirrhosis Revealed by Tissue Extracts ¹H-NMR Spectroscopy.

Sat, 23/09/2017 - 14:42
Specificities of Human Hepatocellular Carcinoma Developed on Non-Alcoholic Fatty Liver Disease in Absence of Cirrhosis Revealed by Tissue Extracts ¹H-NMR Spectroscopy. Metabolites. 2017 Sep 22;7(4): Authors: Teilhet C, Morvan D, Joubert-Zakeyh J, Biesse AS, Pereira B, Massoulier S, Dechelotte P, Pezet D, Buc E, Lamblin G, Peoc'h M, Porcheron J, Vasson MP, Abergel A, Demidem A Abstract There is a rising incidence of non-alcoholic fatty liver disease (NAFLD) as well as of the frequency of Hepato-Cellular Carcinoma (HCC) associated with NAFLD. To seek for putative metabolic pathways specific of the NAFLD etiology, we performed comparative metabolomics between HCC associated with NAFLD and HCC associated with cirrhosis. The study included 28 pairs of HCC tissue versus distant Non-Tumoral Tissue (NTT) collected from patients undergoing hepatectomy. HCC was associated with cirrhosis (n = 9), normal liver (n = 6) and NAFLD (n = 13). Metabolomics was performed using 1H-NMR Spectroscopy on tissue extracts and combined to multivariate statistical analysis. In HCC compared to NTT, statistical models showed high levels of lactate and phosphocholine, and low level of glucose. Shared and Unique Structures (SUS) plots were performed to remove the impact of underlying disease on the metabolic profile of HCC. HCC-cirrhosis was characterized by high levels of β-hydroxybutyrate, tyrosine, phenylalanine and histidine whereas HCC-NAFLD was characterized by high levels of glutamine/glutamate. In addition, the overexpression glutamine/glutamate on HCC-NAFLD was confirmed by both Glutamine Synthetase (GS) immuno-staining and NMR-spectroscopy glutamine quantification. This study provides evidence of metabolic specificities of HCC associated with non-cirrhotic NAFLD versus HCC associated with cirrhosis. These alterations could suggest activation of glutamine synthetase pathway in HCC-NAFLD and mitochondrial dysfunction in HCC-cirrhosis, that may be part of specific carcinogenic processes. PMID: 28937622 [PubMed]

Metabolite ratios as potential biomarkers for type 2 diabetes: a DIRECT study.

Sat, 23/09/2017 - 14:42
Related Articles Metabolite ratios as potential biomarkers for type 2 diabetes: a DIRECT study. Diabetologia. 2017 Sep 21;: Authors: Molnos S, Wahl S, Haid M, Eekhoff EMW, Pool R, Floegel A, Deelen J, Much D, Prehn C, Breier M, Draisma HH, van Leeuwen N, Simonis-Bik AMC, Jonsson A, Willemsen G, Bernigau W, Wang-Sattler R, Suhre K, Peters A, Thorand B, Herder C, Rathmann W, Roden M, Gieger C, Kramer MHH, van Heemst D, Pedersen HK, Gudmundsdottir V, Schulze MB, Pischon T, de Geus EJC, Boeing H, Boomsma DI, Ziegler AG, Slagboom PE, Hummel S, Beekman M, Grallert H, Brunak S, McCarthy MI, Gupta R, Pearson ER, Adamski J, 't Hart LM Abstract AIMS/HYPOTHESIS: Circulating metabolites have been shown to reflect metabolic changes during the development of type 2 diabetes. In this study we examined the association of metabolite levels and pairwise metabolite ratios with insulin responses after glucose, glucagon-like peptide-1 (GLP-1) and arginine stimulation. We then investigated if the identified metabolite ratios were associated with measures of OGTT-derived beta cell function and with prevalent and incident type 2 diabetes. METHODS: We measured the levels of 188 metabolites in plasma samples from 130 healthy members of twin families (from the Netherlands Twin Register) at five time points during a modified 3 h hyperglycaemic clamp with glucose, GLP-1 and arginine stimulation. We validated our results in cohorts with OGTT data (n = 340) and epidemiological case-control studies of prevalent (n = 4925) and incident (n = 4277) diabetes. The data were analysed using regression models with adjustment for potential confounders. RESULTS: There were dynamic changes in metabolite levels in response to the different secretagogues. Furthermore, several fasting pairwise metabolite ratios were associated with one or multiple clamp-derived measures of insulin secretion (all p < 9.2 × 10(-7)). These associations were significantly stronger compared with the individual metabolite components. One of the ratios, valine to phosphatidylcholine acyl-alkyl C32:2 (PC ae C32:2), in addition showed a directionally consistent positive association with OGTT-derived measures of insulin secretion and resistance (p ≤ 5.4 × 10(-3)) and prevalent type 2 diabetes (ORVal_PC ae C32:2 2.64 [β 0.97 ± 0.09], p = 1.0 × 10(-27)). Furthermore, Val_PC ae C32:2 predicted incident diabetes independent of established risk factors in two epidemiological cohort studies (HRVal_PC ae C32:2 1.57 [β 0.45 ± 0.06]; p = 1.3 × 10(-15)), leading to modest improvements in the receiver operating characteristics when added to a model containing a set of established risk factors in both cohorts (increases from 0.780 to 0.801 and from 0.862 to 0.865 respectively, when added to the model containing traditional risk factors + glucose). CONCLUSIONS/INTERPRETATION: In this study we have shown that the Val_PC ae C32:2 metabolite ratio is associated with an increased risk of type 2 diabetes and measures of insulin secretion and resistance. The observed effects were stronger than that of the individual metabolites and independent of known risk factors. PMID: 28936587 [PubMed - as supplied by publisher]

Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Responses.

Sat, 23/09/2017 - 14:42
Related Articles Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Responses. Front Plant Sci. 2017;8:1486 Authors: Serrano A, Espinoza C, Armijo G, Inostroza-Blancheteau C, Poblete E, Meyer-Regueiro C, Arce A, Parada F, Santibáñez C, Arce-Johnson P Abstract Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I), lag (II), and ripening (III), in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process. In this review, we focus on the integration of global approaches, including proteomics, metabolomics, and especially transcriptomics, to understand grape berry development. Several aspects will be considered, including seed development and the production of seedless fruits; veraison, at which anthocyanin accumulation begins in the berry skin of colored varieties; and hormonal regulation of berry development and signaling throughout ripening, focusing on the transcriptional regulation of hormone receptors, protein kinases, and genes related to secondary messenger sensing. Finally, berry responses to different environmental factors, including abiotic (temperature, water-related stress and UV-B radiation) and biotic (fungi and viruses) stresses, and how they can significantly modify both, development and composition of vine fruit, will be discussed. Until now, advances have been made due to the application of Omics tools at different molecular levels. However, the potential of these technologies should not be limited to the study of single-level questions; instead, data obtained by these platforms should be integrated to unravel the molecular aspects of grapevine development. Therefore, the current challenge is the generation of new tools that integrate large-scale data to assess new questions in this field, and to support agronomical practices. PMID: 28936215 [PubMed]

Metabolic status of CSF distinguishes rats with tauopathy from controls.

Sat, 23/09/2017 - 14:42
Related Articles Metabolic status of CSF distinguishes rats with tauopathy from controls. Alzheimers Res Ther. 2017 Sep 21;9(1):78 Authors: Karlíková R, Mičová K, Najdekr L, Gardlo A, Adam T, Majerová P, Friedecký D, Kováč A Abstract BACKGROUND: Tauopathies represent heterogeneous groups of neurodegenerative diseases that are characterised by abnormal deposition of the microtubule-associated protein tau. Alzheimer's disease is the most prevalent tauopathy, affecting more than 35 million people worldwide. In this study we investigated changes in metabolic pathways associated with tau-induced neurodegeneration. METHODS: Cerebrospinal fluid (CSF), plasma and brain tissue were collected from a transgenic rat model for tauopathies and from age-matched control animals. The samples were analysed by targeted and untargeted metabolomic methods using high-performance liquid chromatography coupled to mass spectrometry. Unsupervised and supervised statistical analysis revealed biochemical changes associated with the tauopathy process. RESULTS: Energy deprivation and potentially neural apoptosis were reflected in increased purine nucleotide catabolism and decreased levels of citric acid cycle intermediates and glucose. However, in CSF, increased levels of citrate and aconitate that can be attributed to glial activation were observed. Other significant changes were found in arginine and phosphatidylcholine metabolism. CONCLUSIONS: Despite an enormous effort invested in development of biomarkers for tauopathies during the last 20 years, there is no clinically used biomarker or assay on the market. One of the most promising strategies is to create a panel of markers (e.g., small molecules, proteins) that will be continuously monitored and correlated with patients' clinical outcome. In this study, we identified several metabolic changes that are affected during the tauopathy process and may be considered as potential markers of tauopathies in humans. PMID: 28934963 [PubMed - in process]

(1)H NMR spectroscopy-based metabolomics analysis for the diagnosis of symptomatic E. coli-associated urinary tract infection (UTI).

Sat, 23/09/2017 - 14:42
Related Articles (1)H NMR spectroscopy-based metabolomics analysis for the diagnosis of symptomatic E. coli-associated urinary tract infection (UTI). BMC Microbiol. 2017 Sep 21;17(1):201 Authors: Lussu M, Camboni T, Piras C, Serra C, Del Carratore F, Griffin J, Atzori L, Manzin A Abstract BACKGROUND: Urinary tract infection (UTI) is one of the most common diagnoses in girls and women, and to a lesser extent in boys and men younger than 50 years. Escherichia coli, followed by Klebsiella spp. and Proteus spp., cause 75-90% of all infections. Infection of the urinary tract is identified by growth of a significant number of a single species in the urine, in the presence of symptoms. Urinary culture is an accurate diagnostic method but takes several hours or days to be carried out. Metabolomics analysis aims to identify biomarkers that are capable of speeding up diagnosis. METHODS: Urine samples from 51 patients with a prior diagnosis of Escherichia coli-associated UTI, from 21 patients with UTI caused by other pathogens (bacteria and fungi), and from 61 healthy controls were analyzed. The (1)H-NMR spectra were acquired and processed. Multivariate statistical models were applied and their performance was validated using permutation test and ROC curve. RESULTS: Orthogonal Partial Least Squares-discriminant Analysis (OPLS-DA) showed good separation (R(2)Y = 0.76, Q2=0.45, p < 0.001) between UTI caused by Escherichia coli and healthy controls. Acetate and trimethylamine were identified as discriminant metabolites. The concentrations of both metabolites were calculated and used to build the ROC curves. The discriminant metabolites identified were also evaluated in urine samples from patients with other pathogens infections to test their specificity. CONCLUSIONS: Acetate and trimethylamine were identified as optimal candidates for biomarkers for UTI diagnosis. The conclusions support the possibility of a fast diagnostic test for Escherichia coli-associated UTI using acetate and trimethylamine concentrations. PMID: 28934947 [PubMed - in process]

Peripheral blood mitochondrial DNA content in relation to circulating metabolites and inflammatory markers: A population study.

Sat, 23/09/2017 - 14:42
Related Articles Peripheral blood mitochondrial DNA content in relation to circulating metabolites and inflammatory markers: A population study. PLoS One. 2017;12(7):e0181036 Authors: Knez J, Marrachelli VG, Cauwenberghs N, Winckelmans E, Zhang Z, Thijs L, Brguljan-Hitij J, Plusquin M, Delles C, Monleon D, Redón J, Staessen JA, Nawrot TS, Kuznetsova T Abstract Mitochondrial DNA (mtDNA) content might undergo significant changes caused by metabolic derangements, oxidative stress and inflammation that lead to development and progression of cardiovascular diseases. We, therefore, investigated in a general population the association of peripheral blood mtDNA content with circulating metabolites and inflammatory markers. We examined 310 subjects (50.6% women; mean age, 53.3 years) randomly selected from a Flemish population. Relative mtDNA content was measured by quantitative real-time PCR in peripheral blood cells. Peak circulating metabolites were quantified using nuclear magnetic resonance spectroscopy. The level of inflammation was assessed via established inflammatory markers. Using Partial Least Squares analysis, we constructed 3 latent factors from the 44 measured metabolites that explained 62.5% and 8.5% of the variance in the contributing metabolites and the mtDNA content, respectively. With adjustments applied, mtDNA content was positively associated with the first latent factor (P = 0.002). We identified 6 metabolites with a major impact on the construction of this latent factor including HDL3 apolipoproteins, tyrosine, fatty acid with αCH2, creatinine, β-glucose and valine. We summarized them into a single composite metabolite score. We observed a negative association between the composite metabolic score and mtDNA content (P = 0.001). We also found that mtDNA content was inversely associated with inflammatory markers including hs-CRP, hs-IL6, white blood cell and neutrophil counts as well as neutrophil-to-lymphocyte ratio (P≤0.0024). We demonstrated that in a general population relative peripheral blood mtDNA content was associated with circulating metabolites indicative of perturbed lipid metabolism and with inflammatory biomarkers. PMID: 28704533 [PubMed - indexed for MEDLINE]

Comparing the impact of ultrafine particles from petrodiesel and biodiesel combustion to bacterial metabolism by targeted HPLC-MS/MS metabolic profiling.

Sat, 23/09/2017 - 14:42
Related Articles Comparing the impact of ultrafine particles from petrodiesel and biodiesel combustion to bacterial metabolism by targeted HPLC-MS/MS metabolic profiling. Ecotoxicol Environ Saf. 2017 Aug;142:164-170 Authors: Zhong F, Xu M, Schelli K, Rutowski J, Holmén BA, Zhu J Abstract Alterations of gut bacterial metabolism play an important role in their host metabolism, and can result in diseases such as obesity and diabetes. While many factors were discovered influencing the gut bacterial metabolism, exposure to ultrafine particles (UFPs) from engine combustions were recently proposed to be a potential risk factor for the perturbation of gut bacterial metabolism, and consequentially to obesity and diabetes development. This study focused on evaluation of how UFPs from diesel engine combustions impact gut bacterial metabolism. We hypothesize that UFPs from different type of diesel (petrodiesel vs. biodiesel) will both impact bacterial metabolism, and the degree of impact is also diesel type-dependent. Targeted metabolic profiling of 221 metabolites were applied to three model gut bacteria in vitro, Streptococcus salivarius, Lactobacillus acidophilus and Lactobacillus fermentum. UFPs from two types of fuels, petrodiesel (B0) and a biodiesel blend (B20: 20% soy biodiesel/80% B0 by volume), were exposed to the bacteria and their metabolic changes were compared. For each bacterial strain, metabolites with significantly changed abundance were observed in both perturbations, and all three strains have increased number of altered metabolites detected from B20 UFPs perturbation in comparison to B0 UFPs. Multivariate statistical analysis further confirmed that the metabolic profiles were clearly different between testing groups. Metabolic pathway analyses also demonstrated several important metabolic pathways, including pathways involves amino acids biosynthesis and sugar metabolism, were significantly impacted by UFPs exposure. PMID: 28410499 [PubMed - indexed for MEDLINE]

Cytosolic malate dehydrogenase activity helps support glycolysis in actively proliferating cells and cancer.

Sat, 23/09/2017 - 14:42
Related Articles Cytosolic malate dehydrogenase activity helps support glycolysis in actively proliferating cells and cancer. Oncogene. 2017 Jul 06;36(27):3915-3924 Authors: Hanse EA, Ruan C, Kachman M, Wang D, Lowman XH, Kelekar A Abstract Increased glucose consumption is a hallmark of cancer cells. The increased consumption and subsequent metabolism of glucose during proliferation creates the need for a constant supply of NAD, a co-factor in glycolysis. Regeneration of the NAD required to support enhanced glycolysis has been attributed to the terminal glycolytic enzyme, lactate dehydrogenase (LDH). However, loss of glucose carbons to biosynthetic pathways early in glycolysis reduces the carbon supply to LDH. Thus, alternative routes for NAD regeneration must exist to support the increased glycolytic rate while allowing for the diversion of glucose to generate biomass and support proliferation. Here we demonstrate, using a variety of cancer cell lines as well as activated primary T cells, that cytosolic malate dehydrogenase 1 (MDH1) is an alternative to LDH as a supplier of NAD. Moreover, our results indicate that MDH1 generates malate with carbons derived from glutamine, thus enabling utilization of glucose carbons for glycolysis and for biomass. Amplification of MDH1 occurs at an impressive frequency in human tumors and correlates with poor prognosis. Together, our findings suggest that proliferating cells rely on both MDH1 and LDH to replenish cytosolic NAD, and that therapies designed at targeting glycolysis must consider both dehydrogenases. PMID: 28263970 [PubMed - indexed for MEDLINE]

Systems biotechnology for protein production in Pichia pastoris.

Fri, 22/09/2017 - 14:37
Related Articles Systems biotechnology for protein production in Pichia pastoris. FEMS Yeast Res. 2017 Nov 01;17(7): Authors: Zahrl RJ, Peña DA, Mattanovich D, Gasser B Abstract The methylotrophic yeast Pichia pastoris (syn. Komagataella spp.) is one of the most important production systems for heterologous proteins. After the first genome sequences were published in 2009, tremendous effort was made to establish systems-level analytical methods. Methylotrophic lifestyle was one of the most thoroughly investigated topics, studied at the levels of transcriptome, proteome and metabolic flux. Also the responses of P. pastoris to environmental stress conditions experienced during high cell density production processes were studied. Metabolomics and flux analysis revealed the plasticity of the cellular metabolism in its adaption to the production of foreign proteins and served as blueprints for subsequent cell engineering and/or process design. The transcriptional response elicited by overexpression of heterologous proteins seems to depend on the nature and complexity of the recombinant product. Based on these data, novel targets for strain engineering could be deduced from transcriptomics and proteomics data mining and effectively enhanced protein secretion. Transcriptional regulation data also served as a valuable resource to identify novel promoters with the desired regulatory characteristics. This review aims to provide a comprehensive overview of systems biology applications in P. pastoris ranging from increased understanding of cell physiology to improving recombinant protein production in this cell factory. PMID: 28934418 [PubMed - in process]

Metabolomics and cognition in African American adults in midlife: the atherosclerosis risk in communities study.

Fri, 22/09/2017 - 14:37
Related Articles Metabolomics and cognition in African American adults in midlife: the atherosclerosis risk in communities study. Transl Psychiatry. 2017 Jul 18;7(7):e1173 Authors: Bressler J, Yu B, Mosley TH, Knopman DS, Gottesman RF, Alonso A, Sharrett AR, Wruck LM, Boerwinkle E Abstract Clinical studies have shown alterations in metabolic profiles when patients with mild cognitive impairment and Alzheimer's disease dementia were compared to cognitively normal subjects. Associations between 204 serum metabolites measured at baseline (1987-1989) and cognitive change were investigated in 1035 middle-aged community-dwelling African American participants in the biracial Atherosclerosis Risk in Communities (ARIC) Study. Cognition was evaluated using the Delayed Word Recall Test (DWRT; verbal memory), the Digit Symbol Substitution Test (DSST; processing speed) and the Word Fluency Test (WFT; verbal fluency) at visits 2 (1990-1992) and 4 (1996-1998). In addition, Cox regression was used to analyze the metabolites as predictors of incident hospitalized dementia between baseline and 2011. There were 141 cases among 1534 participants over a median 17.1-year follow-up period. After adjustment for established risk factors, one standard deviation increase in N-acetyl-1-methylhistidine was significantly associated with greater 6-year change in DWRT scores (β=-0.66 words; P=3.65 × 10(-4)). Two metabolites (one unnamed and a long-chain omega-6 polyunsaturated fatty acid found in vegetable oils (docosapentaenoate (DPA, 22:5 n-6)) were significantly associated with less decline on the DSST (DPA: β=1.25 digit-symbol pairs, P=9.47 × 10(-5)). Two unnamed compounds and three sex steroid hormones were associated with an increased risk of dementia (all P<3.9 × 10(-4)). The association of 4-androstene-3beta, 17beta-diol disulfate 1 with dementia was replicated in European Americans. These results demonstrate that screening the metabolome in midlife can detect biologically plausible biomarkers that may improve risk stratification for cognitive impairment at older ages. PMID: 28934192 [PubMed - in process]

Gas Chromatography-Mass Spectrometry for Metabolite Profiling of Japanese Black Cattle Naturally Contaminated with Zearalenone and Sterigmatocystin.

Fri, 22/09/2017 - 14:37
Related Articles Gas Chromatography-Mass Spectrometry for Metabolite Profiling of Japanese Black Cattle Naturally Contaminated with Zearalenone and Sterigmatocystin. Toxins (Basel). 2017 Sep 21;9(10): Authors: Toda K, Kokushi E, Uno S, Shiiba A, Hasunuma H, Fushimi Y, Wijayagunawardane MPB, Zhang C, Yamato O, Taniguchi M, Fink-Gremmels J, Takagi M Abstract The objective of this study was to evaluate the metabolic profile of cattle fed with or without zearalenone (ZEN) and sterigmatocystin (STC)-contaminated diets using a gas chromatography-mass spectrometry metabolomics approach. Urinary samples were collected from individual animals (n = 6 per herd) from fattening female Japanese Black (JB) cattle herds (23 months old, 550-600 kg). Herd 1 had persistently high urinary ZEN and STC concentrations due to the presence of contaminated rice straw. Herd 2, the second female JB fattening herd (23 months old, 550-600 kg), received the same dietary feed as Herd 1, with non-contaminated rice straw. Urine samples were collected from Herd 1, two weeks after the contaminated rice straw was replaced with uncontaminated rice straw (Herd 1N). Identified metabolites were subjected to principal component analysis (PCA) and ANOVA. The PCA revealed that the effects on cattle metabolites depended on ZEN and STC concentrations. The contamination of cattle feed with multiple mycotoxins may alter systemic metabolic processes, including metabolites associated with ATP generation, amino acids, glycine-conjugates, organic acids, and purine bases. The results obtained from Herd 1N indicate that a two-week remedy period was not sufficient to improve the levels of urinary metabolites, suggesting that chronic contamination with mycotoxins may have long-term harmful effects on the systemic metabolism of cattle. PMID: 28934162 [PubMed - in process]

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