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https://www.readbyqxmd.com/read/28423712/model-based-unsupervised-learning-informs-metformin-induced-cell-migration-inhibition-through-an-ampk-independent-mechanism-in-breast-cancer
#1
Arjun P Athreya, Krishna R Kalari, Junmei Cairns, Alan J Gaglio, Quin F Wills, Nifang Niu, Richard Weinshilboum, Ravishankar K Iyer, Liewei Wang
We demonstrate that model-based unsupervised learning can uniquely discriminate single-cell subpopulations by their gene expression distributions, which in turn allow us to identify specific genes for focused functional studies. This method was applied to MDA-MB-231 breast cancer cells treated with the antidiabetic drug metformin, which is being repurposed for treatment of triple-negative breast cancer. Unsupervised learning identified a cluster of metformin-treated cells characterized by a significant suppression of 230 genes (p-value < 2E-16)...
March 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28416775/volatile-organic-compounds-in-gastrointestinal-stromal-tumour-tissue-originating-from-patient-derived-xenografts
#2
Renata Wawrzyniak, Agnieszka Woźniak, Yemarshet Gebreyohannes, Bartosz Dykcik, Patrick Schöffski, Michal Markuszewski
Gastrointestinal stromal tumours (GIST) are the most common mesenchymal neoplasms of the gastrointestinal tract, localized mainly in the stomach or small intestine. The metabolomic signature of GIST signature associated with various mutations in KIT gene remains undiscovered and unexplored. The main aim of this pilot study was to determine and compare metabolomic profiles in GIST xenograft models with different genetic background. Metabolomic profiling using gas chromatography coupled with mass spectrometry followed by both univariate and multivariate statistical analyses was applied to select metabolites which differentiate the GIST models studied...
April 18, 2017: Journal of Breath Research
https://www.readbyqxmd.com/read/28411229/a-comprehensive-analysis-of-myocardial-substrate-preference-emphasizes-the-need-for-a-synchronized-fluxomic-metabolomic-research-design
#3
Mukundan Ragavan, Alexander Kirpich, Xiaorong Fu, Shawn C Burgess, Lauren M McIntyre, Matthew E Merritt
The heart oxidizes fatty acids, carbohydrates and ketone bodies inside the citric acid cycle (CAC) to generate the reducing equivalents needed for ATP production. Competition between these substrates makes it difficult to estimate the extent of pyruvate oxidation. Previously, hyperpolarized pyruvate detected propionate mediated activation of carbohydrate oxidation, even in the presence of acetate. In this report, the optimal concentration of propionate for activation of glucose oxidation is measured in mouse hearts perfused in Langendorff mode...
April 14, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28403831/the-role-of-tre6p-and-snrk1-in-maize-early-kernel-development-and-events-leading-to-stress-induced-kernel-abortion
#4
Samuel W Bledsoe, Clémence Henry, Cara A Griffiths, Matthew J Paul, Regina Feil, John E Lunn, Mark Stitt, L Mark Lagrimini
BACKGROUND: Drought stress during flowering is a major contributor to yield loss in maize. Genetic and biotechnological improvement in yield sustainability requires an understanding of the mechanisms underpinning yield loss. Sucrose starvation has been proposed as the cause for kernel abortion; however, potential targets for genetic improvement have not been identified. Field and greenhouse drought studies with maize are expensive and it can be difficult to reproduce results; therefore, an in vitro kernel culture method is presented as a proxy for drought stress occurring at the time of flowering in maize (3 days after pollination)...
April 12, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28380015/in-vitro-evaluation-of-modified-surface-microhardness-measurement-focus-variation-3d-microscopy-and-contact-stylus-profilometry-to-assess-enamel-surface-loss-after-erosive-abrasive-challenges
#5
Milán Gyurkovics, Tommy Baumann, Thiago Saads Carvalho, Cristiane Meira Assunção, Adrian Lussi
The aim of the study was to compare surface loss values after erosion-abrasion cycles obtained with modified surface microhardness measurement (mSMH), focus variation 3D microscopy (FVM) and contact stylus profilometry (CSP). We cut human molars into buccal and lingual halves, embedded them in resin and ground 200 μm of enamel away. The resulting surfaces were polished. To maintain a reference area, we applied Block-Out resin to partly cover the enamel surface. The samples were incubated in artificial saliva (37°C; 1 h), then rinsed in deionized water (10 s) and dried with oil-free air (5 s)...
2017: PloS One
https://www.readbyqxmd.com/read/28366720/brain-energy-metabolism-spurns-fatty-acids-as-fuel-due-to-their-inherent-mitotoxicity-and-potential-capacity-to-unleash-neurodegeneration
#6
REVIEW
Peter Schönfeld, Georg Reiser
The brain uses long-chain fatty acids (LCFAs) to a negligible extent as fuel for the mitochondrial energy generation, in contrast to other tissues that also demand high energy. Besides this generally accepted view, some studies using cultured neural cells or whole brain indicate a moderately active mitochondrial β-oxidation. Here, we corroborate the conclusion that brain mitochondria are unable to oxidize fatty acids. In contrast, the combustion of liver-derived ketone bodies by neural cells is long-known...
March 30, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28356562/proteomic-analysis-reveals-a-role-of-melatonin-in-promoting-cucumber-seed-germination-under-high-salinity-by-regulating-energy-production
#7
Na Zhang, Hai-Jun Zhang, Qian-Qian Sun, Yun-Yun Cao, Xingsheng Li, Bing Zhao, Ping Wu, Yang-Dong Guo
Seed germination is a critical and complex process in the plant life cycle. Although previous studies have found that melatonin can promote seed germination under salt stress, the involvement of melatonin in the regulation of proteomic changes remains poorly understood. In this study, a total of 157 proteins were significantly influenced (ratio ≥ 2 or ≤ -2) by melatonin during seed germination under salt stress using a label-free quantitative technique. Our GO analysis revealed that several pathways were obviously regulated by melatonin, including ribosome biosynthesis, lipid metabolism, carbohydrate metabolism, and storage protein degradation...
March 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28351018/profiles-of-amino-acids-and-biogenic-amines-in-the-plasma-of-cri-du-chat-patients
#8
Danielle Zildeana Sousa Furtado, Fernando Brunale Vilela de Moura Leite, Cleber Nunes Barreto, Bernadete Faria, Leticia Dias Lima Jedlicka, Elisângela de Jesus Silva, Heron Dominguez Torres da Silva, Etelvino Jose Henriques Bechara, Nilson Antonio Assunção
Cri-du-chat syndrome (CDCS) is a rare innate disease attributed to chromosome 5p deletion characterized by a cat-like cry, craniofacial malformation, and altered behavior of affected children. Metabolomic analysis and a chemometric approach allow description of the metabolic profile of CDCS as compared to normal subjects. In the present work, UHPLC/MS was employed to analyze blood samples withdrawn from CDCS carriers (n=18) and normal parental subjects (n=18), all aged 0-34 years, aiming to set up a representative CDCS profile constructed from 33 targeted amino acids and biogenic amines...
March 21, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28343573/metabolic-and-cellular-stress-responses-of-catfish-horabagrus-brachysoma-g%C3%A3-nther-acclimated-to-increasing-temperatures
#9
Rishikesh S Dalvi, Tilak Das, Dipesh Debnath, Sona Yengkokpam, Kartik Baruah, Lalchand R Tiwari, Asim K Pal
We investigated the metabolic and cellular stress responses in an endemic catfish Horabagrus brachysoma acclimated to ambient (26°C), 31, 33 and 36°C for 30 days. After acclimation, fish were sampled to investigate changes in the levels of blood glucose, tissue glycogen and ascorbic acid, activities of enzymes involved in glycolysis (LDH), citric acid cycle (MDH), gluconeogenesis (FBPase and G6Pase), pentose phosphate pathway (G6PDH), protein metabolism (AST and ALT), phosphate metabolism (ACP and ALP) and energy metabolism (ATPase), and HSP70 levels in various tissues...
April 2017: Journal of Thermal Biology
https://www.readbyqxmd.com/read/28331816/inhibition-of-fat-cell-differentiation-in-3t3-l1-pre-adipocytes-by-all-trans-retinoic-acid-integrative-analysis-of-transcriptomic-and-phenotypic-data
#10
Katharina Stoecker, Steffen Sass, Fabian J Theis, Hans Hauner, Michael W Pfaffl
The process of adipogenesis is controlled in a highly orchestrated manner, including transcriptional and post-transcriptional events. In developing 3T3-L1 pre-adipocytes, this program can be interrupted by all-trans retinoic acid (ATRA). To examine this inhibiting impact by ATRA, we generated large-scale transcriptomic data on the microRNA and mRNA level. Non-coding RNAs such as microRNAs represent a field in RNA turnover, which is very important for understanding the regulation of mRNA gene expression. High throughput mRNA and microRNA expression profiling was performed using mRNA hybridisation microarray technology and multiplexed expression assay for microRNA quantification...
March 2017: Biomolecular Detection and Quantification
https://www.readbyqxmd.com/read/28322963/the-effect-of-oxaloacetic-acid-on-tyrosinase-activity-and-structure-integration-of-inhibition-kinetics-with-docking-simulation
#11
Lin Gou, Jinhyuk Lee, Hao Hao, Yong-Doo Park, Yi Zhan, Zhi-Rong Lü
Oxaloacetic acid (OA) is naturally found in organisms and well known as an intermediate of citric acid cycle producing ATP. We evaluated the effects of OA on tyrosinase activity and structure via integrating methods of enzyme kinetics and computational simulations. OA was found to be a reversible inhibitor of tyrosinase and its induced mechanism was the parabolic non-competitive inhibition type (IC50=17.5±0.5mM and Ki=6.03±1.36mM). Kinetic measurements by real-time interval assay showed that OA induced multi-phasic inactivation process composing with fast (k1) and slow (k2) phases...
March 16, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28317951/facile-synthesis-of-nanoporous-li1-xv1-xo2-c-composites-as-promising-anode-materials-for-lithium-ion-batteries
#12
Peng Mei, Malay Pramanik, Jaewoo Lee, Toshiaki Takei, Yusuke Ide, Md Shahriar A Hossain, Jung Ho Kim, Yusuke Yamauchi
Recently, a layered material with composition Li1+xV1-xO2 has been discovered as a promising alternative anode material to graphite due to its high volumetric capacity and low operation potential. Herein, we demonstrate a mild and cost-effective synthetic methodology to construct a novel nanoporous anode material (P-LVO@C), comprising Li1+xV1-xO2 nanocrystals embedded in a porous carbon matrix. The thermal decomposition of organic materials, including a triblock copolymer (P123) and citric acid, in a N2 atmosphere is the source of the nanoporous carbon in the porous composite material, while citric acid also plays a crucial role in maintaining the reductive environment of the synthetic medium...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28300620/catabolism-of-gaba-succinic-semialdehyde-or-gamma-hydroxybutyrate-through-the-gaba-shunt-impair-mitochondrial-substrate-level-phosphorylation
#13
Dora Ravasz, Gergely Kacso, Viktoria Fodor, Kata Horvath, Vera Adam-Vizi, Christos Chinopoulos
GABA is catabolized in the mitochondrial matrix through the GABA shunt, encompassing transamination to succinic semialdehyde followed by oxidation to succinate by the concerted actions of GABA transaminase (GABA-T) and succinic semialdehyde dehydrogenase (SSADH), respectively. Gamma-hydroxybutyrate (GHB) is a neurotransmitter and a psychoactive drug that could enter the citric acid cycle through transhydrogenation with α-ketoglutarate to succinic semialdehyde and d-hydroxyglutarate, a reaction catalyzed by hydroxyacid-oxoacid transhydrogenase (HOT)...
March 11, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28290889/-platelet-metabolism-in-clopidogrel-resistant-and-sensitive-patients-with-ischemic-heart-disease
#14
I Yu Grinshtein, A A Savchenko, Yu I Grinshtein, I V Filonenko, A A Kosinova
OBJECTIVE: to investigate relationship between activity of platelet nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) dependent dehydrogenases in patients with ischemic heart disease (IHD) after coronary artery bypass grafting (CABG) and their sensitivity to clopidogrel. MATERIAL AND METHODS: We studied 51 male patients with chronic IHD before and after CABG. Control group comprised 35 healthy men. In IHD patients spontaneous and induced platelet aggregation was measured by aggregometry before CABG (in 2 weeks after cessation of antiplatelet drugs), after CABG during therapy with clopidogrel (75 mg/day), and in 6 months after surgery...
October 2016: Kardiologiia
https://www.readbyqxmd.com/read/28283247/environmentally-friendly-and-non-polluting-solvent-pretreatment-of-palm-samples-for-polyphenol-analysis-using-choline-chloride-deep-eutectic-solvents
#15
Najing Fu, Runqiu Lv, Zhixin Guo, Yiwei Guo, Xiaoyu You, Baokun Tang, Dandan Han, Hongyuan Yan, Kyung Ho Row
In this work, choline chloride (ChCl) deep eutectic solvents (DESs) were evaluated for the pretreatment of palm samples in the analysis of polyphenols, such as protocatechuic acid, catechins, epicatechin, and caffeic acid. During the enrichment step of the pretreatment, eight DESs comprising ChCl with ethylene glycol (EG), glycerol (Gly), xylitol (Xyl), phenol (Ph), formic acid (FA), citric acid (CiA), oxalic acid (OA), or malonic acid (MA), were prepared and applied to the reflux extraction of polyphenols from palm samples...
February 21, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28271489/the-pyruvate-dehydrogenase-complex-and-related-assemblies-in-health-and-disease
#16
Olwyn Byron, John Gordon Lindsay
The family of 2-oxoacid dehydrogenase complexes (2-OADC), typified by the pyruvate dehydrogenase multi-enzyme complex (PDC) as its most prominent member, are massive molecular machines (Mr, 4-10 million) controlling key steps in glucose homeostasis (PDC), citric acid cycle flux (OGDC, 2-oxoglutarate dehydrogenase) and the metabolism of the branched-chain amino acids, leucine, isoleucine and valine (BCOADC, branched-chain 2-OADC). These highly organised mitochondrial arrays, composed of multiple copies of three separate enzymes, have been widely studied as paradigms for the analysis of enzyme cooperativity, substrate channelling, protein-protein interactions and the regulation of activity by phosphorylation ...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28262773/metabolomics-for-clinical-use-and-research-in-chronic-kidney-disease
#17
REVIEW
Berthold Hocher, Jerzy Adamski
Chronic kidney disease (CKD) has a high prevalence in the general population and is associated with high mortality; a need therefore exists for better biomarkers for diagnosis, monitoring of disease progression and therapy stratification. Moreover, very sensitive biomarkers are needed in drug development and clinical research to increase understanding of the efficacy and safety of potential and existing therapies. Metabolomics analyses can identify and quantify all metabolites present in a given sample, covering hundreds to thousands of metabolites...
May 2017: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/28259101/mitochondrial-composition-and-function-under-the-control-of-hypoxia
#18
REVIEW
Dominik C Fuhrmann, Bernhard Brüne
Hypoxia triggers several mechanisms to adapt cells to a low oxygen environment. Mitochondria are major consumers of oxygen and a potential source of reactive oxygen species (ROS). In response to hypoxia they exchange or modify distinct subunits of the respiratory chain and adjust their metabolism, especially lowering the citric acid cycle. Intermediates of the citric acid cycle participate in regulating hypoxia inducible factors (HIF), the key mediators of adaptation to hypoxia. Here we summarize how hypoxia conditions mitochondria with consequences for ROS-production and the HIF-pathway...
February 24, 2017: Redox Biology
https://www.readbyqxmd.com/read/28256132/facile-synthesis-of-nanosized-lithium-ion-conducting-solid-electrolyte-li1-4al0-4ti1-6-po4-3-and-its-mechanical-nanocomposites-with-limn2o4-for-enhanced-cyclic-performance-in-lithium-ion-batteries
#19
Xingang Liu, Jiang Tan, Ju Fu, Ruoxin Yuan, Hao Wen, Chuhong Zhang
Nanoparticles of fast lithium-ion-conducting solid electrolyte Li1.4Al0.4Ti1.6(PO4)3 (LATP) are prepared by a modified citric-acid-assisted sol-gel method that involves a two-step heat treatment in which the dry gel is calcined first in argon and then in air. The obtained LATP exhibits smaller particle size (down to 40 nm) with a narrower size distribution and less aggregation than LATP prepared by a conventional sol-gel method because of a polymeric network that preserves during LATP crystallization. It has a high relative density of 97...
March 27, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28224688/liver-tissue-metabolic-profiling-and-pathways-of-nonalcoholic-steatohepatitis-in-rats
#20
Suwen Qi, Si Huang, Xin Chen, Qin Huo, Ni Xie, Jun Xia
AIM: The mechanisms of nonalcoholic steatohepatitis (NASH) in hepatocytes is unknown, and our aim is to study the tissue metabolic profiling and pathways of NASH. METHODS: We built rat models for simple steatosis and NASH and analyzed the liver extract using a liquid chromatograph-mass spectrometer (LC-MS). The acquired data were processed by multivariate principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) to obtain metabolic profiling...
February 22, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
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