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https://www.readbyqxmd.com/read/28719601/clic-a-tool-for-expanding-biological-pathways-based-on-co-expression-across-thousands-of-datasets
#1
Yang Li, Alexis A Jourdain, Sarah E Calvo, Jun S Liu, Vamsi K Mootha
In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression...
July 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28716182/atp-sensing-in-living-plant-cells-reveals-tissue-gradients-and-stress-dynamics-of-energy-physiology
#2
Valentina De Col, Philippe Fuchs, Thomas Nietzel, Marlene Elsässer, Chia Pao Voon, Alessia Candeo, Ingo Seeliger, Mark D Fricker, Christopher Grefen, Ian Max Møller, Andrea Bassi, Boon Leong Lim, Marco Zancani, Andreas J Meyer, Alex Costa, Stephan Wagner, Markus Schwarzländer
Growth and development of plants is ultimately driven by light energy captured through photosynthesis. ATP acts as universal cellular energy cofactor fuelling all life processes, including gene expression, metabolism, and transport. Despite a mechanistic understanding of ATP biochemistry, ATP dynamics in the living plant have been largely elusive. Here, we establish MgATP(2-) measurement in living plants using the fluorescent protein biosensor ATeam1.03-nD/nA. We generate Arabidopsis sensor lines and investigate the sensor in vitro under conditions appropriate for the plant cytosol...
July 18, 2017: ELife
https://www.readbyqxmd.com/read/28716092/the-role-of-microglial-p2x7-modulation-of-cell-death-and-cytokine-release
#3
Yingbo He, Natalie Taylor, Lawrence Fourgeaud, Anindya Bhattacharya
BACKGROUND: ATP-gated P2X7 is a non-selective cation channel, which participates in a wide range of cellular functions as well as pathophysiological processes including neuropathic pain, immune response, and neuroinflammation. Despite its abundant expression in microglia, the role of P2X7 in neuroinflammation still remains unclear. METHODS: Primary microglia were isolated from cortices of P0-2 C57BL/6 wild-type or P2X7 knockout (P2X7(-/-)) mouse pups. Lipopolysaccharide, lipopolysaccharide plus IFNγ, or IL4 plus IL13 were used to polarize microglia to pro-inflammatory or anti-inflammatory states...
July 17, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28715120/characterization-of-a-multiple-particle-delivery-complex-and-determination-of-cellular-photodamage-in-skin-fibroblast-and-breast-cancer-cell-lines
#4
Ivan Mfouo-Tynga, Nicolette Nadene Houreld, Heidi Abrahamse
Zinc metallized Phthalocyanine (ZnPcSmix ), a potent photosensitizer (PS), is conjugated to gold dendrimer encapsulated nanoparticles (AuDENPs) in order to improve the efficacy of Photodynamic therapy (PDT) using MCF-7 breast cancer cells and WS1 fibroblast cells as a control. Both ZnPcSmix and AuDENPs are mixed in a nitrogen atmosphere for 48 h and characterization analysis conducted using ultra violet visible (UV-vis) spectrometry for spectral properties, transmission electron microscopy (TEM) for morphological features and zeta potential measurement for surface stability and size distribution of the compound obtained or of the multiple particles delivery complex (MPDC)...
July 17, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/28714890/cardamom-cumin-and-dill-weed-essential-oils-chemical-compositions-antimicrobial-activities-and-mechanisms-of-action-against-campylobacter-spp
#5
Aysegul Mutlu-Ingok, Funda Karbancioglu-Guler
Natural antimicrobials as well as essential oils (EOs) have gained interest to inhibit pathogenic microorganisms and to control food borne diseases. Campylobacter spp. are one of the most common causative agents of gastroenteritis. In this study, cardamom, cumin, and dill weed EOs were evaluated for their antibacterial activities against Campylobacter jejuni and Campylobacter coli by using agar-well diffusion and broth microdilution methods, along with the mechanisms of antimicrobial action. Chemical compositions of EOs were also tested by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS)...
July 15, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28713932/human-trypsin-inhibitor-reduces-the-apoptosis-of-lipopolysaccharide%C3%A2-induced-human-kidney%C3%A2-2-cells-by-promoting-mitochondrial-fusion
#6
Ning Liu, Zhiyi Jiang, Yongjun Liu, Yao Nie, Juan Chen, Bin Ouyang, Xiangdong Guan, Minying Chen
Imbalance in mitochondrial fusion/fission is one of the mechanisms leading to sepsis‑induced mitochondrial dysfunction and cell apoptosis. The present study examined the effects of human trypsin inhibitor (UTI), a well‑known antioxidant and anti‑inflammatory substance, on mitochondrial dynamics and cell apoptosis in lipopolysaccharide (LPS)‑induced human kidney‑2 (HK‑2) cells. The HK‑2 cells were incubated for 24 h either with LPS (800 ng/ml) or LPS (800 ng/ml) mixed with UTI (250 U/ml). Cell viability was assessed using a3‑(4,5‑dimethyl‑2‑thiazolyl)‑2, 5‑diphenyl‑2‑H‑tetrazolium bromide assay...
July 5, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28711444/mitochondrial-membrane-potential
#7
Ljubava D Zorova, Vasily A Popkov, Egor Y Plotnikov, Denis N Silachev, Irina B Pevzner, Stanislovas S Jankauskas, Valentina A Babenko, Savva D Zorov, Anastasia V Balakireva, Magdalena Juhaszova, Steven J Sollott, Dmitry B Zorov
The mitochondrial membrane potential (ΔΨm) generated by proton pumps (Complexes I, III and IV) is an essential component in the process of energy storage during oxidative phosphorylation. Together with the proton gradient (ΔpH), ΔΨm forms the transmembrane potential of hydrogen ions which is harnessed to make ATP. The levels of ΔΨm and ATP in the cell are kept relatively stable although there are limited fluctuations of both these factors that can occur reflecting normal physiological activity. However, sustained changes in both factors may be deleterious...
July 12, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28708306/a-toolbox-of-chromones-and-quinolones-for-measuring-a-wide-range-of-atp-concentrations
#8
Vasyl Georgievich Pivovarenko, Oleksandra Bugera, Nicolas Humbert, Andrey Sergeevich Klymchenko, Yves Mély
A series of 26 3-hydroxychromones, three bis-flavonols and four 3-hydroxyquinolones were studied to evaluate their fluorescence response to interaction with ATP in buffer. The dyes differ by the total charge, the size and number of their aromatic units, as well as the position or electron donating ability of their substituents. All of them were suggested to form complexes with ATP of 1:1 and 1:2 stoichiometry, which can be evidenced by their bright fluorescence and their 3000-6000 cm-1 red-shifted excitation band...
July 14, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28705804/loss-of-nitric-oxide-mediated-inhibition-of-purine-neurotransmitter-release-in-the-colon-in-the-absence-of-interstitial-cells-of-cajal
#9
Leonie Durnin, Andrea Lees, Sheerien Manzoor, Kent C Sasse, Kenton M Sanders, Violeta N Mutafova-Yambolieva
Regulation of colonic motility depends upon the integrity of enteric inhibitory neurotransmission mediated by nitric oxide (NO), purine neurotransmitters, and neuropeptides. Intramuscular interstitial cells of Cajal (ICC-IM) and platelet-derived growth factor receptor α-positive (PDGFRα(+)) cells are involved in generating responses to NO and purine neurotransmitters, respectively. Previous studies have suggested a decreased nitrergic and increased purinergic neurotransmission in Kit(W)/Kit(W-v) (W/W(v) ) mice that display lesions in ICC-IM along the gastrointestinal tract...
July 13, 2017: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/28705594/induction-of-abcg2-bcrp-restricts-the-distribution-of-zidovudine-to-the-fetal-brain-in-rats
#10
María Fernanda Filia, Timoteo Marchini, Juan Mauricio Minoia, Martín Ignacio Roma, Fernanda Teresa De Fino, Modesto Carlos Rubio, Guillermo J Copello, Pablo A Evelson, Roxana Noemí Peroni
Safety concerns for fetus development of zidovudine (AZT) administration as prophylaxis of vertical transmission of HIV persist. We evaluated the participation of the ATP-binding cassette efflux transporter ABCG2 in the penetration of AZT into the fetal brain and the relevance for drug safety. Oral daily doses of AZT (60mg/kg body weight) or its vehicle were administered between post gestational days 11 (E11) and 20 (E20) to Sprague-Dawley pregnant rats. At E21, animals received an intravenous bolus of 60mg AZT/kg body weight in the presence or absence of the ABCG2 inhibitor gefitinib (20mg/kg body weight, ip) and AZT in maternal plasma and fetal brain were measured by HPLC-UV...
July 10, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28705588/elevated-uric-acid-and-adenosine-triphosphate-concentrations-in-bronchoalveolar-lavage-fluid-of-eosinophilic-pneumonia
#11
Takehito Kobayashi, Kazuyuki Nakagome, Toru Noguchi, Kiyoko Kobayashi, Yutaka Ueda, Tomoyuki Soma, Kenji Ikebuchi, Hidetomo Nakamoto, Makoto Nagata
BACKGROUND: Recent evidence has suggested that the innate immune response may play a role in the development of eosinophilic airway inflammation. We previously reported that uric acid (UA) and adenosine triphosphate (ATP), two important damage-associated molecular pattern molecules (DAMPs), activate eosinophil functions, suggesting that these molecules may be involved in the development of eosinophilic airway inflammation. The objective of this study was to measure the concentrations of DAMPs including UA and ATP in the bronchoalveolar lavage fluid (BALF) of patients with eosinophilic pneumonia (EP)...
July 10, 2017: Allergology International: Official Journal of the Japanese Society of Allergology
https://www.readbyqxmd.com/read/28705382/impact-of-cardiorespiratory-fitness-and-risk-of-systemic-hypertension-in-nonobese-versus-obese-men-who-are-metabolically-healthy-or-unhealthy
#12
Sae Young Jae, Abraham Samuel Babu, Eun Sun Yoon, Sudhir Kurl, Jari A Laukkanen, Yoon-Ho Choi, Barry A Franklin
Few data are available regarding the influence of body phenotype on systemic hypertension (SH) and whether cardiorespiratory fitness (CRF) attenuates this relation. We tested the hypothesis that obesity phenotypes and CRF would predict incident hypertension, evaluating 3,800 Korean men who participated in 2 health examinations in1998 to 2009. All participants were normotensive at baseline and were divided into 4 groups based on body mass index using the Asia-Pacific descriptors for obesity and metabolic health status and the National Cholesterol Education Program's adult treatment panel III (ATP-III) criteria...
June 15, 2017: American Journal of Cardiology
https://www.readbyqxmd.com/read/28700655/cyclophosphamide-leads-to-persistent-deficits-in-physical-performance-and-in-vivo-mitochondria-function-in-a-mouse-model-of-chemotherapy-late-effects
#13
Marie-Laure Crouch, Gary Knowels, Rudolph Stuppard, Nolan G Ericson, Jason H Bielas, David J Marcinek, Karen L Syrjala
Fatigue is the symptom most commonly reported by long-term cancer survivors and is increasingly recognized as related to skeletal muscle dysfunction. Traditional chemotherapeutic agents can cause acute toxicities including cardiac and skeletal myopathies. To investigate the mechanism by which chemotherapy may lead to persistent skeletal muscle dysfunction, mature adult mice were injected with a single cyclophosphamide dose and evaluated for 6 weeks. We found that exposed mice developed a persistent decrease in treadmill running time compared to baseline (25...
2017: PloS One
https://www.readbyqxmd.com/read/28697955/nesfatin-1-inhibits-voltage-gated-k-channels-in-pancreatic-beta-cells
#14
Yuko Maejima, Shoichiro Horita, Daisuke Kobayashi, Miho Aoki, Rie O'hashi, Ryota Imai, Kazuho Sakamoto, Masatomo Mori, Katsuya Takasu, Kazuma Ogawa, Seiichi Takenoshita, Songji Zhao, Akihiro Hazama, Kenju Shimomura
The anorexigenic neuropeptide NEFA/nucleobindin 2 (NUCB2)/nesfatin-1-containing neurons are distributed in the brain regions involved in feeding regulation. In spite of the growing knowledge of its physiological functions through extensive studies, its molecular mechanism of reaction, including its receptor, remains unknown. NUCB2/nesfatin-1 is also involved in various peripheral regulations, including glucose homeostasis. In pancreatic beta-cells, NUCB2/nesfatin-1 is reported to enhance glucose-stimulated insulin secretion (GSIS) but its exact mechanism remains unknown...
July 8, 2017: Peptides
https://www.readbyqxmd.com/read/28697441/a-novel-molecularly-imprinted-electrochemical-sensor-modified-with-carbon-dots-chitosan-gold-nanoparticles-for-the-determination-of-patulin
#15
Wei Guo, Fuwei Pi, Hongxia Zhang, Jiadi Sun, Yinzhi Zhang, Xiulan Sun
In this paper, molecular imprinting technique was applied to the electrochemical sensor. We used 2-oxindole as dummy template, ρ-Aminothiophenol (ρ-ATP) as functional monomers, combined with the high sensitivity of electrochemical detection, to achieve a specific and efficient detection of patulin in fruit juice. In addition, carbon dots and chitosan were used as the modifying material to improve electron-transfer rate, expand the electroactive surface of glassy carbon electrode and enhance strength of the signal...
July 5, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28696576/nad-p-h-and-flavin-autofluorescence-correlation-with-atp-in-rat-livers-with-different-metabolic-steady-state-conditions
#16
Anna C Croce, Andrea Ferrigno, Laura G Di Pasqua, Clarissa Berardo, Giovanni Bottiroli, Mariapia Vairetti
The monitoring of NAD(P)H and flavin autofluorescence (AF) is at the basis of numerous investigations on energy metabolism. Nevertheless, the ability of these AF biomarkers to accurately represent the energy currency, ATP, is poorly explored. Here we focused on the AF/ATP correlation in lean and fatty livers with different steady-state metabolic conditions, achieved after organ isolation, preservation and recovery, in a likely dependence on both liver intrinsic metabolic features and externally induced perturbations...
July 11, 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28696376/lack-of-additive-effects-of-resveratrol-and-energy-restriction-in-the-treatment-of-hepatic-steatosis-in-rats
#17
Iñaki Milton-Laskibar, Leixuri Aguirre, Alfredo Fernández-Quintela, Anabela P Rolo, João Soeiro Teodoro, Carlos M Palmeira, María P Portillo
The aims of the present study were to analyze the effect of resveratrol on liver steatosis in obese rats, to compare the effects induced by resveratrol and energy restriction and to research potential additive effects. Rats were initially fed a high-fat high-sucrose diet for six weeks and then allocated in four experimental groups fed a standard diet: a control group, a resveratrol-treated group, an energy restricted group and a group submitted to energy restriction and treated with resveratrol. We measured liver triacylglycerols, transaminases, FAS, MTP, CPT1a, CS, COX, SDH and ATP synthase activities, FATP2/FATP5, DGAT2, PPARα, SIRT1, UCP2 protein expressions, ACC and AMPK phosphorylation and PGC1α deacetylation...
July 11, 2017: Nutrients
https://www.readbyqxmd.com/read/28695448/mitochondrial-atp-mg-phosphate-carriers-transport-divalent-inorganic-cations-in-complex-with-atp
#18
Magnus Monné, Lucia Daddabbo, Lorena Carla Giannossa, Maria Cristina Nicolardi, Luigi Palmieri, Daniela Valeria Miniero, Annarosa Mangone, Ferdinando Palmieri
The ATP-Mg/phosphate carriers (APCs) modulate the intramitochondrial adenine nucleotide pool size. In this study the concentration-dependent effects of Mg(2+) and other divalent cations (Me(2+)) on the transport of [(3)H]ATP in liposomes reconstituted with purified human and Arabidopsis APCs (hAPCs and AtAPCs, respectively, including some lacking their N-terminal domains) have been investigated. The transport of Me(2+) mediated by these proteins was also measured. In the presence of a low external concentration of [(3)H]ATP (12 μM) and increasing concentrations of Me(2+), Mg(2+) stimulated the activity (measured as initial transport rate of [(3)H]ATP) of hAPCs and decreased that of AtAPCs; Fe(2+) and Zn(2+) stimulated markedly hAPCs and moderately AtAPCs; Ca(2+) and Mn(2+) markedly AtAPCs and moderately hAPCs; and Cu(2+) decreased the activity of both hAPCs and AtAPCs...
July 10, 2017: Journal of Bioenergetics and Biomembranes
https://www.readbyqxmd.com/read/28695314/bacterial-production-and-reconstitution-in-proteoliposomes-of-solanum-lycopersicum-cat2-a-transporter-of-basic-amino-acids-and-organic-cations
#19
Teresa Maria Rosaria Regina, Michele Galluccio, Mariafrancesca Scalise, Lorena Pochini, Cesare Indiveri
The vacuolar SlCAT2 was cloned, over-produced in E. coli and reconstituted in proteoliposomes. Arg, Ornithine and Lys were identified as substrates. Unexpectedly, also the organic cations Tetraethylammonium and Acetylcholine were transported indicating involvement of SlCAT2 in signaling. In land plants several transporters are involved in ion and metabolite flux across membranes of cells or intracellular organelles. The vacuolar amino acid transporter CAT2 from Solanum lycopersicum was investigated in this work...
July 10, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28694661/relevance-of-proteolysis-and-proteasome-activation-in-fatty-liver-graft-preservation-an-institut-georges-lopez-1-vs-university-of-wisconsin-appraisal
#20
Mohamed Amine Zaouali, Arnau Panisello-Roselló, Alexandre Lopez, Carlos Castro Benítez, Emma Folch-Puy, Agustín García-Gil, Teresa Carbonell, René Adam, Joan Roselló-Catafau
AIM: To compare liver proteolysis and proteasome activation in steatotic liver grafts conserved in University of Wisconsin (UW) and Institut Georges Lopez-1 (IGL-1) solutions. METHODS: Fatty liver grafts from male obese Zücker rats were conserved in UW and IGL-1 solutions for 24 h at 4 °Cand subjected to "ex vivo" normo-thermic perfusion (2 h; 37 °C). Liver proteolysis in tissue specimens and perfusate was measured by reverse-phase high performance liquid chromatography...
June 21, 2017: World Journal of Gastroenterology: WJG
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