PubMed

Related Articles Next-Generation Breast Cancer Omics. Am J Pathol. 2017 Oct;187(10):2130-2132 Authors: Coleman WB Abstract This Editorial highlights the reviews in the Breast Cancer Theme Issue that features topics related to next-generation breast cancer omics. PMID: 28822804 [PubMed - indexed for MEDLINE]

Related Articles Lactate dehydrogenase activity drives hair follicle stem cell activation. Nat Cell Biol. 2017 Sep;19(9):1017-1026 Authors: Flores A, Schell J, Krall AS, Jelinek D, Miranda M, Grigorian M, Braas D, White AC, Zhou JL, Graham NA, Graeber T, Seth P, Evseenko D, Coller HA, Rutter J, Christofk HR, Lowry WE Abstract Although normally dormant, hair follicle stem cells (HFSCs) quickly become activated to divide during a new hair cycle. The quiescence of HFSCs is known to be regulated by a number of intrinsic and extrinsic mechanisms. Here we provide several lines of evidence to demonstrate that HFSCs utilize glycolytic metabolism and produce significantly more lactate than other cells in the epidermis. Furthermore, lactate generation appears to be critical for the activation of HFSCs as deletion of lactate dehydrogenase (Ldha) prevented their activation. Conversely, genetically promoting lactate production in HFSCs through mitochondrial pyruvate carrier 1 (Mpc1) deletion accelerated their activation and the hair cycle. Finally, we identify small molecules that increase lactate production by stimulating Myc levels or inhibiting Mpc1 carrier activity and can topically induce the hair cycle. These data suggest that HFSCs maintain a metabolic state that allows them to remain dormant and yet quickly respond to appropriate proliferative stimuli. PMID: 28812580 [PubMed - indexed for MEDLINE]

Related Articles Gene expression and metabolite profiling of gibberellin biosynthesis during induction of somatic embryogenesis in Medicago truncatula Gaertn. PLoS One. 2017;12(7):e0182055 Authors: Igielski R, Kępczyńska E Abstract Gibberellins (GAs) are involved in the regulation of numerous developmental processes in plants including zygotic embryogenesis, but their biosynthesis and role during somatic embryogenesis (SE) is mostly unknown. In this study we show that during three week- long induction phase, when cells of leaf explants from non-embryogenic genotype (M9) and embryogenic variant (M9-10a) were forming the callus, all the bioactive gibberellins from non-13-hydroxylation (GA4, GA7) and 13-hydroxylation (GA1, GA5, GA3, GA6) pathways were present, but the contents of only a few of them differed between the tested lines. The GA53 and GA19 substrates synthesized by the 13-hydroxylation pathway accumulated specifically in the M9-10a line after the first week of induction; subsequently, among the bioactive gibberellins detected, only the content of GA3 increased and appeared to be connected with acquisition of embryogenic competence. We fully annotated 20 Medicago truncatula orthologous genes coding the enzymes which catalyze all the known reactions of gibberellin biosynthesis. Our results indicate that, within all the genes tested, expression of only three: MtCPS, MtGA3ox1 and MtGA3ox2, was specific to embryogenic explants and reflected the changes observed in GA53, GA19 and GA3 contents. Moreover, by analyzing expression of MtBBM, SE marker gene, we confirmed the inhibitory effect of manipulation in GAs metabolism, applying exogenous GA3, which not only impaired the production of somatic embryos, but also significantly decreased expression of this gene. PMID: 28750086 [PubMed - indexed for MEDLINE]

Related Articles Longer sleep is associated with lower BMI and favorable metabolic profiles in UK adults: Findings from the National Diet and Nutrition Survey. PLoS One. 2017;12(7):e0182195 Authors: Potter GDM, Cade JE, Hardie LJ Abstract Ever more evidence associates short sleep with increased risk of metabolic diseases such as obesity, which may be related to a predisposition to non-homeostatic eating. Few studies have concurrently determined associations between sleep duration and objective measures of metabolic health as well as sleep duration and diet, however. We therefore analyzed associations between sleep duration, diet and metabolic health markers in UK adults, assessing associations between sleep duration and 1) adiposity, 2) selected metabolic health markers and 3) diet, using National Diet and Nutrition Survey data. Adults (n = 1,615, age 19-65 years, 57.1% female) completed questions about sleep duration and 3 to 4 days of food diaries. Blood pressure and waist circumference were recorded. Fasting blood lipids, glucose, glycated haemoglobin (HbA1c), thyroid hormones, and high-sensitivity C-reactive protein (CRP) were measured in a subset of participants. We used regression analyses to explore associations between sleep duration and outcomes. After adjustment for age, ethnicity, sex, smoking, and socioeconomic status, sleep duration was negatively associated with body mass index (-0.46 kg/m2 per hour, 95% CI -0.69 to -0.24 kg/m2, p < 0.001) and waist circumference (-0.9 cm per hour, 95% CI -1.5 to -0.3cm, p = 0.004), and positively associated with high-density lipoprotein cholesterol (0.03 mmol/L per hour, 95% CI 0.00 to 0.05, p = 0.03). Sleep duration tended to be positively associated with free thyroxine levels and negatively associated with HbA1c and CRP (p = 0.09 to 0.10). Contrary to our hypothesis, sleep duration was not associated with any dietary measures (p ≥ 0.14). Together, our findings show that short-sleeping UK adults are more likely to have obesity, a disease with many comorbidities. PMID: 28750055 [PubMed - indexed for MEDLINE]

Related Articles The Evolving Role of Companion Diagnostics for Breast Cancer in an Era of Next-Generation Omics. Am J Pathol. 2017 Oct;187(10):2185-2198 Authors: Rosenbaum JN, Weisman P Abstract A companion diagnostic is a test for a specific biomarker-approved by the United States Food and Drug Administration-qualifying a patient to receive a specific, associated therapy. As interest has grown in precision medicine over the past decade, the principle of companion diagnostics has gained increasing purchase among laboratory professionals, clinicians, regulators, and even patients. The evolution of the biomarkers used to stratify and treat breast cancer illustrates the history of companion diagnostics and provides a lens through which to examine potential challenges. As new targeted therapies and corresponding biomarkers accumulate, algorithms for diagnosis and treatment necessarily become lengthier and more complex. To accommodate future needs of breast cancer patients, the companion diagnostic model will continue to adapt and evolve. PMID: 28733195 [PubMed - indexed for MEDLINE]

Related Articles An engineered photoswitchable mammalian pyruvate kinase. FEBS J. 2017 Sep;284(18):2955-2980 Authors: Gehrig S, Macpherson JA, Driscoll PC, Symon A, Martin SR, MacRae JI, Kleinjung J, Fraternali F, Anastasiou D Abstract Changes in allosteric regulation of glycolytic enzymes have been linked to metabolic reprogramming involved in cancer. Remarkably, allosteric mechanisms control enzyme function at significantly shorter time-scales compared to the long-term effects of metabolic reprogramming on cell proliferation. It remains unclear if and how the speed and reversibility afforded by rapid allosteric control of metabolic enzymes is important for cell proliferation. Tools that allow specific, dynamic modulation of enzymatic activities in mammalian cells would help address this question. Towards this goal, we have used molecular dynamics simulations to guide the design of mPKM2 internal light/oxygen/voltage-sensitive domain 2 (LOV2) fusion at position D24 (PiL[D24]), an engineered pyruvate kinase M2 (PKM2) variant that harbours an insertion of the light-sensing LOV2 domain from Avena Sativa within a region implicated in allosteric regulation by fructose 1,6-bisphosphate (FBP). The LOV2 photoreaction is preserved in the PiL[D24] chimera and causes secondary structure changes that are associated with a 30% decrease in the Km of the enzyme for phosphoenolpyruvate resulting in increased pyruvate kinase activity after light exposure. Importantly, this change in activity is reversible upon light withdrawal. Expression of PiL[D24] in cells leads to light-induced increase in labelling of pyruvate from glucose. PiL[D24] therefore could provide a means to modulate cellular glucose metabolism in a remote manner and paves the way for studying the importance of rapid allosteric phenomena in the regulation of metabolism and enzyme control. PMID: 28715126 [PubMed - indexed for MEDLINE]

Related Articles Glycolysis and pyrimidine biosynthesis are required for replication of adherent-invasive Escherichia coli in macrophages. Microbiology. 2016 Jun;162(6):954-65 Authors: Thompson AP, O'Neill I, Smith EJ, Catchpole J, Fagan A, Burgess KE, Carmody RJ, Clarke DJ Abstract Adherent-invasive Escherichia coli (AIEC) have been implicated in the aetiology of Crohn's disease (CD), a chronic inflammatory bowel condition. It has been proposed that AIEC-infected macrophages produce high levels of pro-inflammatory cytokines thus contributing to the inflammation observed in CD. AIEC can replicate in macrophages and we wanted to determine if bacterial replication was linked to the high level of cytokine production associated with AIEC-infected macrophages. Therefore, we undertook a genetic analysis of the metabolic requirements for AIEC replication in the macrophage and we show that AIEC replication in this niche is dependent on bacterial glycolysis. In addition, our analyses indicate that AIEC have access to a wide range of nutrients in the macrophage, although the levels of purines and pyrimidines do appear to be limiting. Finally, we show that the macrophage response to AIEC infection is indistinguishable from the response to the non-replicating glycolysis mutant (ΔpfkAB) and a non-pathogenic strain of E. coli, MG1655. Therefore, AIEC does not appear to subvert the normal macrophage response to E. coli during infection. PMID: 27058922 [PubMed - indexed for MEDLINE]

26 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 2017/10/04PubMed 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.

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. Bioinformatics. 2017 Sep 14;: Authors: Wandy J, Zhu Y, van der Hooft JJJ, Daly R, Barrett MP, Rogers S Abstract Motivation: We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualisations. Results: Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a dataset onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service. Availability and Implementation: The website can be found at http://ms2lda.org , while the source code is available at https://github.com/sdrogers/ms2ldaviz under the MIT license. Contact: simon.rogers@glasgow.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online. PMID: 28968802 [PubMed - as supplied by publisher]

A sensitive and accurate method to simultaneously measure uric acid and creatinine in human saliva by using LC-MS/MS. Bioanalysis. 2017 Oct 02;: Authors: Liu XY, Luo Y, Zhou CY, Peng A, Liu JY Abstract AIM: To establish a method to simultaneously measure uric acid (UA) and creatinine (Cr) in human saliva. MATERIALS & METHODS: By using HPLC-MS/MS, we developed and validated a fast, sensitive and accurate method to simultaneously determine UA and Cr in human saliva. The determination range for Cr and UA is of 10-5000 ng/ml with the R(2) for both calibration curves over 0.999. The accuracy, precision and recovery of Cr and UA were all acceptable. By using the established method, the Cr and UA levels in saliva from 28 healthy volunteers were measured as 2.9 ± 0.8 µM and 46.8 ± 18.2 µM, respectively. CONCLUSION: This method can simultaneously determine Cr and UA in saliva for clinical and translational study. PMID: 28967800 [PubMed - as supplied by publisher]

The hypoglycemic and antioxidant effects of polysaccharides from the petioles and pedicels of Euryale ferox Salisb. on alloxan-induced hyperglycemic mice. Food Funct. 2017 Oct 02;: Authors: Wu CY, Wang H, He XX, Wu DW, Yue W, Wu QN Abstract The present study investigated the potential hypoglycemic and antioxidant effects of polysaccharides extracted from the petioles and pedicels of Euryale ferox Salisb. (EFPP) on alloxan-induced hyperglycemic mice. The EFPP had a total carbohydrate of 65.72 ± 2.81%, uronic acid of 4.56 ± 0.62% and protein of 0.58 ± 0.12%, with an average molecular weight from 1.02 kDa to 11.45 kDa and monosaccharide composition of Man, GlcA, Rha, Glc, Gal and Ara at a molar ratio of 0.12 : 0.01 : 9.57 : 0.41 : 1.00 : 0.24. Administration with EFPP, especially high dose EFPP, was beneficial to reverse body weight loss, reduce blood glucose levels, enhance serum insulin levels, improve oral glucose tolerance, increase hepatic glycogen content and GCK activity, and modulate the mRNA expression of GCK in the liver. Meanwhile, EFPP had protective effects against alloxan-induced oxidative injury in mice, via increasing the activities of SOD, CAT and GSH-Px and decreasing the MDA contents in the liver and kidney of the mice. EFPP ameliorated the damage in pancreas, kidney and liver tissues, which was confirmed by histopathological observation. The results suggested that EFPP possess hypoglycemic and antioxidant activities, and could be a potential source of natural hypoglycemic and antioxidant agents for functional foods or complementary medicines. PMID: 28967662 [PubMed - as supplied by publisher]

Related Articles A plasma metabonomic analysis on potential biomarker in pyrexia induced by three methods using ultra high performance liquid chromatography coupled with Fourier transform ion cyclotron resonance mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2017 Sep 15;1063:214-225 Authors: Liu T, Li S, Tian X, Li Z, Cui Y, Han F, Zhao Y, Yu Z Abstract Pyrexia usually is a systemic pathological process that can lead to metabolic disorders. Metabonomics as a powerful tool not only can reveal the pathological mechanisms, but also can give insight into the progression of pyrexia from another angle. Thus, an ultra high performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry (UHPLC-FT-ICR-MS) metabonomic approach was employed for the first time to investigate the plasma biochemical characteristics of pyrexia induced by three methods and to reveal subtle metabolic changes under the condition of pyrexia so as to explore its mechanism. The acquired metabolic data of the models were subjected to principal component analysis (PCA) for allowing the clear separation of the pyrexia rats from the control rats. Variable importance for project values (VIP) and Student's t-test were used to screen the significant metabolic changes caused by pyrexia. Fifty-two endogenous metabolites were identified and putatively identified as potential biomarkers primarily associated with phospholipid metabolism, sphingolipid metabolism, fatty acid oxidation metabolism, fatty acid amides metabolism and amino acid metabolism, and related to bile acid biosynthesis and glycerolipid catabolism. LysoPC (14:0), LysoPC (18:3), LysoPC (20:4), LysoPC (16:0), phytosphingosine, Cer (d18:0/12:0), N-[(4E,8E)-1,3-dihydroxyoctadeca-4,8-dien-2-yl]hexadecanamide, oleamide, fatty acid amide C22:1, tryptophan, acetylcarnitine, palmitoylcarnitine and stearoylcarnitine were considered as common potential biomarkers of pyrexia rats induced by three methods: Our results revealed that the UHPLC-FT-ICR-MS-based metabolomic method is helpful for finding new potential metabolic markers for pyrexia detection and offers a good perspective in pyrexia research. PMID: 28886580 [PubMed - indexed for MEDLINE]

Related Articles Oxidative Stickland reactions in an obligate aerobic organism - amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus. FEBS J. 2017 Jul;284(13):2078-2095 Authors: Stark H, Wolf J, Albersmeier A, Pham TK, Hofmann JD, Siebers B, Kalinowski J, Wright PC, Neumann-Schaal M, Schomburg D Abstract The thermoacidophilic Crenarchaeon Sulfolobus solfataricus is a model organism for archaeal adaptation to extreme environments and renowned for its ability to degrade a broad variety of substrates. It has been well characterised concerning the utilisation of numerous carbohydrates as carbon source. However, its amino acid metabolism, especially the degradation of single amino acids, is not as well understood. In this work, we performed metabolic modelling as well as metabolome, transcriptome and proteome analysis on cells grown on caseinhydrolysate as carbon source in order to draw a comprehensive picture of amino acid metabolism in S. solfataricus P2. We found that 10 out of 16 detectable amino acids are imported from the growth medium. Overall, uptake of glutamate, methionine, leucine, phenylalanine and isoleucine was the highest of all observed amino acids. Our simulations predict an incomplete degradation of leucine and tyrosine to organic acids, and in accordance with this, we detected the export of branched-chain and aromatic organic acids as well as amino acids, ammonium and trehalose into the culture supernatants. The branched-chain amino acids as well as phenylalanine and tyrosine are degraded to organic acids via oxidative Stickland reactions. Such reactions are known for prokaryotes capable of anaerobic growth, but so far have never been observed in an obligate aerobe. Also, 3-methyl-2-butenoate and 2-methyl-2-butenoate are for the first time found as products of modified Stickland reactions for the degradation of branched-chain amino acids. This work presents the first detailed description of branched-chain and aromatic amino acid catabolism in S. solfataricus. PMID: 28497654 [PubMed - indexed for MEDLINE]

Related Articles Hemorrhagic shock and tissue injury drive distinct plasma metabolome derangements in swine. J Trauma Acute Care Surg. 2017 Oct;83(4):635-642 Authors: Clendenen N, Nunns GR, Moore EE, Reisz JA, Gonzalez E, Peltz E, Silliman CC, Fragoso M, Nemkov T, Wither MJ, Hansen K, Banerjee A, Moore HB, DʼAlessandro A Abstract BACKGROUND: Tissue injury and hemorrhagic shock induce significant systemic metabolic reprogramming in animal models and critically injured patients. Recent expansions of the classic concepts of metabolomic aberrations in tissue injury and hemorrhage opened the way for novel resuscitative interventions based on the observed abnormal metabolic demands. We hypothesize that metabolic demands and resulting metabolic signatures in pig plasma will vary in response to isolated or combined tissue injury and hemorrhagic shock. METHODS: A total of 20 pigs underwent either isolated tissue injury, hemorrhagic shock, or combined tissue injury and hemorrhagic shock referenced to a sham protocol (n = 5/group). Plasma samples were analyzed by UHPLC-MS. RESULTS: Hemorrhagic shock promoted a hypermetabolic state. Tissue injury alone dampened metabolic responses in comparison to sham and hemorrhagic shock, and attenuated the hypermetabolic state triggered by shock with respect to energy metabolism (glycolysis, glutaminolysis, and Krebs cycle). Tissue injury and hemorrhagic shock had a more pronounced effect on nitrogen metabolism (arginine, polyamines, and purine metabolism) than hemorrhagic shock alone. CONCLUSION: Isolated or combined tissue injury and hemorrhagic shock result in distinct plasma metabolic signatures. These findings indicate that optimized resuscitative interventions in critically ill patients are possible based on identifying the severity of tissue injury and hemorrhage. PMID: 28463938 [PubMed - indexed for MEDLINE]

Related Articles Integrative FourD omics approach profiles the target network of the carbon storage regulatory system. Nucleic Acids Res. 2017 Feb 28;45(4):1673-1686 Authors: Sowa SW, Gelderman G, Leistra AN, Buvanendiran A, Lipp S, Pitaktong A, Vakulskas CA, Romeo T, Baldea M, Contreras LM Abstract Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network. Using this approach, we profiled the targets and potential regulatory mechanisms of a global regulatory system, the well-studied carbon storage regulatory (Csr) system of Escherichia coli, which is widespread among bacteria. Using 126 sets of proteomics and transcriptomics data, we identified 136 potential direct CsrA targets, including 50 novel ones, categorized their behaviors into distinct regulatory patterns, and performed in vivo fluorescence-based follow up experiments. The results of this work validate 17 novel mRNAs as authentic direct CsrA targets and demonstrate a generalizable strategy to integrate multiple lines of omics data to identify a core pool of regulator targets. PMID: 28126921 [PubMed - indexed for MEDLINE]

Related Articles Cell-Type-Specific H+-ATPase Activity in Root Tissues Enables K+ Retention and Mediates Acclimation of Barley (Hordeum vulgare) to Salinity Stress. Plant Physiol. 2016 Dec;172(4):2445-2458 Authors: Shabala L, Zhang J, Pottosin I, Bose J, Zhu M, Fuglsang AT, Velarde-Buendia A, Massart A, Hill CB, Roessner U, Bacic A, Wu H, Azzarello E, Pandolfi C, Zhou M, Poschenrieder C, Mancuso S, Shabala S Abstract While the importance of cell type specificity in plant adaptive responses is widely accepted, only a limited number of studies have addressed this issue at the functional level. We have combined electrophysiological, imaging, and biochemical techniques to reveal the physiological mechanisms conferring higher sensitivity of apical root cells to salinity in barley (Hordeum vulgare). We show that salinity application to the root apex arrests root growth in a highly tissue- and treatment-specific manner. Although salinity-induced transient net Na(+) uptake was about 4-fold higher in the root apex compared with the mature zone, mature root cells accumulated more cytosolic and vacuolar Na(+), suggesting that the higher sensitivity of apical cells to salt is not related to either enhanced Na(+) exclusion or sequestration inside the root. Rather, the above differential sensitivity between the two zones originates from a 10-fold difference in K(+) efflux between the mature zone and the apical region (much poorer in the root apex) of the root. Major factors contributing to this poor K(+) retention ability are (1) an intrinsically lower H(+)-ATPase activity in the root apex, (2) greater salt-induced membrane depolarization, and (3) a higher reactive oxygen species production under NaCl and a larger density of reactive oxygen species-activated cation currents in the apex. Salinity treatment increased (2- to 5-fold) the content of 10 (out of 25 detected) amino acids in the root apex but not in the mature zone and changed the organic acid and sugar contents. The causal link between the observed changes in the root metabolic profile and the regulation of transporter activity is discussed. PMID: 27770060 [PubMed - indexed for MEDLINE]

Related Articles Impaired Cyclic Electron Flow around Photosystem I Disturbs High-Light Respiratory Metabolism. Plant Physiol. 2016 Dec;172(4):2176-2189 Authors: Florez-Sarasa I, Noguchi K, Araújo WL, Garcia-Nogales A, Fernie AR, Flexas J, Ribas-Carbo M Abstract The cyclic electron flow around photosystem I (CEF-PSI) increases ATP/NADPH production in the chloroplast, acting as an energy balance mechanism. Higher export of reducing power from the chloroplast in CEF-PSI mutants has been correlated with higher mitochondrial alternative oxidase (AOX) capacity and protein amount under high-light (HL) conditions. However, in vivo measurements of AOX activity are still required to confirm the exact role of AOX in dissipating the excess of reductant power from the chloroplast. Here, CEF-PSI single and double mutants were exposed to short-term HL conditions in Arabidopsis (Arabidopsis thaliana). Chlorophyll fluorescence, in vivo activities of the cytochrome oxidase (νcyt) and AOX (νalt) pathways, levels of mitochondrial proteins, metabolite profiles, and pyridine nucleotide levels were determined under normal growth and HL conditions. νalt was not increased in CEF-PSI mutants, while AOX capacity was positively correlated with photoinhibition, probably due to a reactive oxygen species-induced increase of AOX protein. The severe metabolic impairment observed in CEF-PSI mutants, as indicated by the increase in photoinhibition and changes in the levels of stress-related metabolites, can explain their lack of νalt induction. By contrast, νcyt was positively correlated with photosynthetic performance. Correlations with metabolite changes suggest that νcyt is coordinated with sugar metabolism and stress-related amino acid synthesis. Furthermore, changes in glycine-serine and NADH-NAD(+) ratios were highly correlated to νcyt Taken together, our results suggest that νcyt can act as a sink for the excess of electrons from the chloroplast, probably via photorespiratory glycine oxidation, thus improving photosynthetic performance when νalt is not induced under severe HL stress. PMID: 27760881 [PubMed - indexed for MEDLINE]

Related Articles Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence. Plant Physiol. 2016 Dec;172(4):2132-2153 Authors: Chrobok D, Law SR, Brouwer B, Lindén P, Ziolkowska A, Liebsch D, Narsai R, Szal B, Moritz T, Rouhier N, Whelan J, Gardeström P, Keech O Abstract The functions of mitochondria during leaf senescence, a type of programmed cell death aimed at the massive retrieval of nutrients from the senescing organ to the rest of the plant, remain elusive. Here, combining experimental and analytical approaches, we showed that mitochondrial integrity in Arabidopsis (Arabidopsis thaliana) is conserved until the latest stages of leaf senescence, while their number drops by 30%. Adenylate phosphorylation state assays and mitochondrial respiratory measurements indicated that the leaf energy status also is maintained during this time period. Furthermore, after establishing a curated list of genes coding for products targeted to mitochondria, we analyzed in isolation their transcript profiles, focusing on several key mitochondrial functions, such as the tricarboxylic acid cycle, mitochondrial electron transfer chain, iron-sulfur cluster biosynthesis, transporters, as well as catabolic pathways. In tandem with a metabolomic approach, our data indicated that mitochondrial metabolism was reorganized to support the selective catabolism of both amino acids and fatty acids. Such adjustments would ensure the replenishment of α-ketoglutarate and glutamate, which provide the carbon backbones for nitrogen remobilization. Glutamate, being the substrate of the strongly up-regulated cytosolic glutamine synthase, is likely to become a metabolically limiting factor in the latest stages of developmental leaf senescence. Finally, an evolutionary age analysis revealed that, while branched-chain amino acid and proline catabolism are very old mitochondrial functions particularly enriched at the latest stages of leaf senescence, auxin metabolism appears to be rather newly acquired. In summation, our work shows that, during developmental leaf senescence, mitochondria orchestrate catabolic processes by becoming increasingly central energy and metabolic hubs. PMID: 27744300 [PubMed - indexed for MEDLINE]

Related Articles Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue. Proteomics. 2017 Apr;17(7): Authors: Percy AJ, Michaud SA, Jardim A, Sinclair NJ, Zhang S, Mohammed Y, Palmer AL, Hardie DB, Yang J, LeBlanc AM, Borchers CH Abstract The mouse is the most commonly used laboratory animal, with more than 14 million mice being used for research each year in North America alone. The number and diversity of mouse models is increasing rapidly through genetic engineering strategies, but detailed characterization of these models is still challenging because most phenotypic information is derived from time-consuming histological and biochemical analyses. To expand the biochemists' toolkit, we generated a set of targeted proteomic assays for mouse plasma and heart tissue, utilizing bottom-up LC/MRM-MS with isotope-labeled peptides as internal standards. Protein quantitation was performed using reverse standard curves, with LC-MS platform and curve performance evaluated by quality control standards. The assays comprising the final panel (101 peptides for 81 proteins in plasma; 227 peptides for 159 proteins in heart tissue) have been rigorously developed under a fit-for-purpose approach and utilize stable-isotope labeled peptides for every analyte to provide high-quality, precise relative quantitation. In addition, the peptides have been tested to be interference-free and the assay is highly multiplexed, with reproducibly determined protein concentrations spanning >4 orders of magnitude. The developed assays have been used in a small pilot study to demonstrate their application to molecular phenotyping or biomarker discovery/verification studies. PMID: 27688154 [PubMed - indexed for MEDLINE]

Related Articles Defective postreperfusion metabolic recovery directly associates with incident delayed graft function. Kidney Int. 2016 Jul;90(1):181-91 Authors: Wijermars LG, Schaapherder AF, de Vries DK, Verschuren L, Wüst RC, Kostidis S, Mayboroda OA, Prins F, Ringers J, Bierau J, Bakker JA, Kooistra T, Lindeman JH Abstract Delayed graft function (DGF) following kidney transplantation affects long-term graft function and survival and is considered a manifestation of ischemia reperfusion injury. Preclinical studies characterize metabolic defects resulting from mitochondrial damage as primary driver of ischemia reperfusion injury. In a comprehensive approach that included sequential establishment of postreperfusion arteriovenous concentration differences over the human graft, metabolomic and genomic analysis in tissue biopsies taken before and after reperfusion, we tested whether the preclinical observations translate to the context of clinical DGF. This report is based on sequential studies of 66 eligible patients of which 22 experienced DGF. Grafts with no DGF immediately recovered aerobic respiration as indicated by prompt cessation of lactate release following reperfusion. In contrast, grafts with DGF failed to recover aerobic respiration and showed persistent adenosine triphosphate catabolism indicated by a significant persistently low post reperfusion tissue glucose-lactate ratio and continued significant post-reperfusion lactate and hypoxanthine release (net arteriovenous difference for lactate and hypoxanthine at 30 minutes). The metabolic data for the group with DGF point to a persistent post reperfusion mitochondrial defect, confirmed by functional (respirometry) and morphological analyses. The archetypical mitochondrial stabilizing peptide SS-31 significantly preserved mitochondrial function in human kidney biopsies following simulated ischemia reperfusion. Thus, development of DGF is preceded by a profound post-reperfusion metabolic deficit resulting from severe mitochondrial damage. Strategies aimed at preventing DGF should be focused on safeguarding a minimally required post-reperfusion metabolic competence. PMID: 27188504 [PubMed - indexed for MEDLINE]