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https://www.readbyqxmd.com/read/28814063/icave-an-open-source-tool-for-visualizing-biomolecular-networks-in-3d-stereoscopic-3d-and-immersive-3d
#1
Vaja Liluashvili, Selim Kalayci, Eugene Fluder, Manda Wilson, Aaron Gabow, Zeynep H Gümüs
Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28813715/induction-of-cyclooxygenase-2-by-streptococcus-pyogenes-is-mediated-by-cytolysins
#2
Ulrike Blaschke, Andreas Beineke, Johanna Klemens, Eva Medina, Oliver Goldmann
Prostaglandin E2 (PGE2), an arachidonic acid metabolite regulating a broad range of physiological activities, is an important modulator of the severity of infection caused by Streptococcus pyogenes. Here, we investigated the role of streptococcal cytolysin S (SLS) and streptococcal cytolysin O (SLO) in the induction of cyclooxygenase-2 (COX-2), the rate-limiting enzyme in the synthesis of prostaglandins, in in vitro cultured macrophages and during in vivo infection. Macrophages were infected with S. pyogenes wild type or with the isogenic mutant strains deficient in SLS (ΔSLS), SLO (ΔSLO), or both (ΔSLS/ΔSLO), and the expression of COX-2 was determined at the transcriptional and the protein level...
August 17, 2017: Journal of Innate Immunity
https://www.readbyqxmd.com/read/28813682/circadian-and-feeding-rhythms-orchestrate-the-diurnal-liver-acetylome
#3
Daniel Mauvoisin, Florian Atger, Loïc Dayon, Antonio Núñez Galindo, Jingkui Wang, Eva Martin, Laetitia Da Silva, Ivan Montoliu, Sebastiano Collino, Francois-Pierre Martin, Joanna Ratajczak, Carles Cantó, Martin Kussmann, Felix Naef, Frédéric Gachon
Lysine acetylation is involved in various biological processes and is considered a key reversible post-translational modification in the regulation of gene expression, enzyme activity, and subcellular localization. This post-translational modification is therefore highly relevant in the context of circadian biology, but its characterization on the proteome-wide scale and its circadian clock dependence are still poorly described. Here, we provide a comprehensive and rhythmic acetylome map of the mouse liver...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28813658/ccctc-binding-factor-translates-interleukin-2-and-%C3%AE-ketoglutarate-sensitive-metabolic-changes-in-t%C3%A2-cells-into-context-dependent-gene-programs
#4
Danielle A Chisolm, Daniel Savic, Amanda J Moore, Andre Ballesteros-Tato, Beatriz León, David K Crossman, Cornelis Murre, Richard M Myers, Amy S Weinmann
Despite considerable research connecting cellular metabolism with differentiation decisions, the underlying mechanisms that translate metabolite-sensitive activities into unique gene programs are still unclear. We found that aspects of the interleukin-2 (IL-2)-sensitive effector gene program in CD4(+) and CD8(+) T cells in type 1 conditions (Th1) were regulated by glutamine and alpha-ketoglutarate (αKG)-induced events, in part through changes in DNA and histone methylation states. We further identified a mechanism by which IL-2- and αKG-sensitive metabolic changes regulated the association of CCCTC-binding factor (CTCF) with select genomic sites...
August 15, 2017: Immunity
https://www.readbyqxmd.com/read/28813608/hot-air-treatment-induces-disease-resistance-through-activating-the-phenylpropanoid-metabolism-in-cherry-tomato-fruit
#5
Yingying Wei, Dandan Zhou, Jing Peng, Leiqing Pan, Kang Tu
To explore the effects of hot air (HA, 38 °C for 12 h) treatment on phenylpropanoid metabolism in cherry tomatoes, phenylpropanoid metabolite levels and the activities and expression of key enzymes were analyzed in HA-treated fruit. HA treatment enhanced phenylpropanoid metabolism, as evidenced by elevated levels of phenolics and flavonoids, higher activities of phenylalanine ammonia-lyase and cinnamate-4-hydroxylase, and up-regulated expression of LeCHS, LeCHI, LeF3H, and LeFLS. Levels of several phenylpropanoid metabolites were higher after HA treatment, including p-coumaric acid, caffeic acid, chlorogenic acid, isoquercitrin, quercetin, and rutin...
August 16, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28813537/metabolite-patterns-predicting-sex-and-age-in-participants-of-the-karlsruhe-metabolomics-and-nutrition-karmen-study
#6
Manuela J Rist, Alexander Roth, Lara Frommherz, Christoph H Weinert, Ralf Krüger, Benedikt Merz, Diana Bunzel, Carina Mack, Björn Egert, Achim Bub, Benjamin Görling, Pavleta Tzvetkova, Burkhard Luy, Ingrid Hoffmann, Sabine E Kulling, Bernhard Watzl
Physiological and functional parameters, such as body composition, or physical fitness are known to differ between men and women and to change with age. The goal of this study was to investigate how sex and age-related physiological conditions are reflected in the metabolome of healthy humans and whether sex and age can be predicted based on the plasma and urine metabolite profiles. In the cross-sectional KarMeN (Karlsruhe Metabolomics and Nutrition) study 301 healthy men and women aged 18-80 years were recruited...
2017: PloS One
https://www.readbyqxmd.com/read/28813487/effect-of-masticatory-stimulation-on-the-quantity-and-quality-of-saliva-and-the-salivary-metabolomic-profile
#7
Nobuyuki Okuma, Makiko Saita, Noriyuki Hoshi, Tomoyoshi Soga, Masaru Tomita, Masahiro Sugimoto, Katsuhiko Kimoto
BACKGROUND: This study characterized the changes in quality and quantity of saliva, and changes in the salivary metabolomic profile, to understand the effects of masticatory stimulation. METHODS: Stimulated and unstimulated saliva samples were collected from 55 subjects and salivary hydrophilic metabolites were comprehensively quantified using capillary electrophoresis-time-of-flight mass spectrometry. RESULTS: In total, 137 metabolites were identified and quantified...
2017: PloS One
https://www.readbyqxmd.com/read/28813145/selective-uptake-and-bioaccumulation-of-antidepressants-in-fish-from-effluent-impacted-niagara-river
#8
Prapha Arnnok, Randolph Reyes Singh, Rodjana Burakham, Alicia Pérez-Fuentetaja, Diana S Aga
The continuous release of pharmaceuticals and personal care products (PPCPs) into freshwater systems impacts the health of aquatic organisms. This study evaluates the concentrations and bioaccumulation of PPCPs and the selective uptake of antidepressants in fish from the Niagara River, which connects two of the North American Great lakes (Erie and Ontario). The Niagara River receives PPCPs from different wastewater treatment plants (WWTPs) situated along the river and Lake Erie. Of the 22 targeted PPCPs, 11 were found at part-per-billion levels in WWTP effluents and at part-per-trillion levels in river water samples...
August 16, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28812315/metabolite-cycled-steam-and-semi-laser-localization-for-mr-spectroscopy-of-the-human-brain-at-9-4t
#9
Ioannis-Angelos Giapitzakis, Tingting Shao, Nikolai Avdievich, Ralf Mekle, Roland Kreis, Anke Henning
PURPOSE: Metabolite cycling (MC) is an MRS technique for the simultaneous acquisition of water and metabolite spectra that avoids chemical exchange saturation transfer effects and for which water may serve as a reference signal or contain additional information in functional or diffusion studies. Here, MC was developed for human investigations at ultrahigh field. METHODS: MC-STEAM and MC-semi-LASER are introduced at 9.4T with an optimized inversion pulse and elaborate coil setup...
August 15, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28812298/a-gata-type-transcription-factor-acareb-for-nitrogen-metabolism-is-involved-in-regulation-of-cephalosporin-biosynthesis-in-acremonium-chrysogenum
#10
Feifei Guan, Yuanyuan Pan, Jinyang Li, Gang Liu
In filamentous fungi, nitrogen metabolism is repressed by GATA-type zinc finger transcription factors. Nitrogen metabolite repression has been found to affect antibiotic production, but the mechanism is still poorly understood. AcareB, encoding a homologue of fungal GATA-type regulatory protein, was cloned from Acremonium chrysogenum. Gene disruption and genetic complementation demonstrated that AcareB plays a key role in utilization of ammonium, glutamine and urea. In addition, significant reduction of cephalosporin production in the AcareB disruption mutant indicated that AcareB is important for cephalosporin production...
August 14, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28812002/image-guided-thermal-ablation-with-mr-based-thermometry
#11
REVIEW
Mingming Zhu, Ziqi Sun, Chin K Ng
Thermal ablation techniques such as radiofrequency, microwave, high intensity focused ultrasound (HIFU) and laser have been used as minimally invasive strategies for the treatment of variety of cancers. MR thermometry methods are readily available for monitoring thermal distribution and deposition in real time, leading to decrease of incidents of normal tissue damage around targeted lesion. HIFU and laser-induced thermal therapy (LITT) are the two widely accepted tumor ablation techniques because of their compatibility with MR systems...
June 2017: Quantitative Imaging in Medicine and Surgery
https://www.readbyqxmd.com/read/28811909/a-fourth-subtype-of-retinoic-acid-receptor-related-orphan-receptors-is-activated-by-oxidized-all-trans-retinoic-acid-in-medaka-oryzias-latipes
#12
Kotowa Sakai, Haruka Fukushima, Yuya Yamamoto, Toshitaka Ikeuchi
BACKGROUND: The three known subtypes of the retinoic acid receptor-related orphan receptor (ROR) have been implicated in the control of immunity, brain function, and circadian rhythm in mammals. Here, we demonstrate by phylogenetic analysis that there were originally four subtypes of RORs in vertebrates. One of the novel ror paralogs, rord1 (rorca in the Ensembl database), is conserved among teleosts, but absent in mammals. Using medaka (Oryzias latipes) as a model teleost, we evaluated the expression pattern of this gene, its transactivational properties for endogenic chemicals, and its ability to activate the promoters of putative target genes...
2017: Zoological Letters
https://www.readbyqxmd.com/read/28811829/metabolomics-analysis-for-defining-serum-biochemical-markers-in-colorectal-cancer-patients-with-qi-deficiency-syndrome-or-yin-deficiency-syndrome
#13
Fangfang Tao, Ping Lü, Chunbo Xu, Mengmeng Zheng, Wenhong Liu, Minhe Shen, Shanming Ruan
Colorectal cancer is one of the leading causes of tumor-associated death, and traditional Chinese medicine (TCM) classifies colorectal cancer into various subtypes mainly according to the symptomatic pattern identification (ZHENG). Here, we investigated the difference in metabolic profiles of serum by comparing colorectal cancer subjects with Nondeficiency (ND), Qi deficiency (QD), and Yin deficiency (YD). The ratio of subjects with carcinoembryonic antigen (CEA) was higher in YD pattern, and the ratio of subjects with carbohydrate antigen 19-9 (CA19-9) was higher both in YD and in QD, compared with ND...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/28811657/colorimetric-fingerprints-of-gold-nanorods-for-discriminating-catecholamine-neurotransmitters-in-urine-samples
#14
Somayeh Jafarinejad, Mahmoud Ghazi-Khansari, Forough Ghasemi, Pezhman Sasanpour, M Reza Hormozi-Nezhad
Catecholamine neurotransmitters, generally including dopamine (DA), epinephrine (EP) and norepinephrine (NE) are known as substantial indicators of various neurological diseases. Simultaneous detection of these compounds and their metabolites is highly recommended in early clinical diagnosis. To this aim, in the present contribution, a high performance colorimetric sensor array has been proposed for the detection and discrimination of catecholamines based on their reducing ability to deposit silver on the surface of gold nanorods (AuNRs)...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811620/a-new-anthracycline-type-metabolite-from-streptomyces-sp-neau-l3
#15
Chang Lu, Yue Zhao, Wei-Qi Jia, Hui Zhang, Huan Qi, Wen-Sheng Xiang, Ji-Dong Wang, Xiang-Jing Wang
A new anthracycline-type metabolite, designated as tetracenoquinocin A (1), was isolated from the fermentation broth of Streptomyces sp. NEAU-L3. Its structure was determined on the basis of spectroscopic analysis, including 1D and 2D NMR techniques as well as ESI-MS and comparison with data from the literature. Compound 1 showed potent cytotoxic activity against three cancer cell lines (HepG2, A549, HCT-116) with IC50 values of 5.57, 24.30 and 20.82 μM, respectively.The Journal of Antibiotics advance online publication, 16 August 2017; doi:10...
August 16, 2017: Journal of Antibiotics
https://www.readbyqxmd.com/read/28811533/plasma-metabolomics-profiling-of-maintenance-hemodialysis-based-on-capillary-electrophoresis-time-of-flight-mass-spectrometry
#16
Shuxin Liu, Lichao Wang, Chunxiu Hu, Xin Huang, Hong Liu, Qiuhui Xuan, Xiaohui Lin, Xiaojun Peng, Xin Lu, Ming Chang, Guowang Xu
Uremia has been a rapidly increasing health problem in China. Hemodialysis (HD) is the main renal replacement therapy for uremia. The results of large-scale clinical trials have shown that the HD pattern is crucial for long-term prognosis of maintenance hemodialysis (MHD) in uremic patients. Plasma metabolism is very important for revealing the biological insights linked to the therapeutic effects of the HD pattern on uremia. Alteration of plasma metabolites in uremic patients in response to HD therapy has been reported...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811529/disturbance-of-plasma-lipid-metabolic-profile-in-guillain-barre-syndrome
#17
Hsiang-Yu Tang, Daniel Tsun-Yee Chiu, Jui-Fen Lin, Cheng-Yu Huang, Kuo-Hsuan Chang, Rong-Kuo Lyu, Long-Sun Ro, Hung-Chou Kuo, Mei-Ling Cheng, Chiung-Mei Chen
Guillain-Barre Syndrome (GBS) is an inflammatory disease of the peripheral nervous system. Given that plasma metabolic profiles in GBS patients have never been explored, plasma samples of 38 GBS patients, 22 multiple sclerosis (MS) patients, and 40 healthy controls were analyzed by using untargeted and targeted metabolomics analysis. The untargeted analysis showed that levels of a set of plasma lipid metabolites were significantly decreased in GBS patients compared to the controls. Furthermore, the targeted analysis demonstrated that levels of 41 metabolites in GBS patients were significantly changed compared to either the controls or MS patients...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811522/the-lichen-secondary-metabolite-atranorin-suppresses-lung-cancer-cell-motility-and-tumorigenesis
#18
Rui Zhou, Yi Yang, So-Yeon Park, Thanh Thi Nguyen, Young-Woo Seo, Kyung Hwa Lee, Jae Hyuk Lee, Kyung Keun Kim, Jae-Seoun Hur, Hangun Kim
Lichens are symbiotic organisms that produce various secondary metabolites. Here, different lichen extracts were examined to identify secondary metabolites with anti-migratory activity against human lung cancer cells. Everniastrum vexans had the most potent inhibitory activity, and atranorin was identified as an active subcomponent of this extract. Atranorin suppressed β-catenin-mediated TOPFLASH activity by inhibiting the nuclear import of β-catenin and downregulating β-catenin/LEF and c-jun/AP-1 downstream target genes such as CD44, cyclin-D1 and c-myc...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811513/altered-cerebellar-biochemical-profiles-in-infants-born-prematurely
#19
Marie Brossard-Racine, Jonathan Murnick, Marine Bouyssi-Kobar, Janie Coulombe, Taeun Chang, Catherine Limperopoulos
This study aims to compare the cerebellar biochemical profiles in preterm (PT) infants evaluated at term equivalent age (TEA) and healthy full-term newborns using proton magnetic resonance spectroscopy ((1)H-MRS). We explore the associations between altered cerebellar metabolite profiles and brain injury topography, severity of injury, and prematurity-related clinical complications. We prospectively collected high quality (1)H-MRS in 59 premature infants born ≤32 weeks and 61 healthy full term controls. (1)H-MRS data were processed using LCModel software to calculate absolute metabolite concentration for N-acetyl-aspartate (NAA), choline (Cho) and creatine (Cr)...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811511/from-metabolome-to-phenotype-gc-ms-metabolomics-of-developing-mutant-barley-seeds-reveals-effects-of-growth-temperature-and-genotype
#20
Bekzod Khakimov, Morten Arendt Rasmussen, Rubini Maya Kannangara, Birthe Møller Jespersen, Lars Munck, Søren Balling Engelsen
The development of crop varieties tolerant to growth temperature fluctuations and improved nutritional value is crucial due to climate change and global population growth. This study investigated the metabolite patterns of developing barley seed as a function of genotype and growth temperature for ideal vegetable protein production and for augmented β-glucan production. Seeds from three barley lines (Bomi, lys3.a and lys5.f) were sampled eight times during grain filling and analysed for metabolites using gas chromatography-mass spectrometry (GC-MS)...
August 15, 2017: Scientific Reports
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