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https://www.readbyqxmd.com/read/29353021/phosphoproteomics-unveils-stable-energy-supply-as-key-to-flooding-tolerance-in-kandelia-candel
#1
Dezhuo Pan, Lingxia Wang, Fanglin Tan, Si Lu, Xiaojie Lv, Madiha Zaynab, Chi-Lien Cheng, Yakubu Saddeeq Abubakar, Shipin Chen, Wei Chen
The mangrove Kandelia candel (L.) Druce experiences daily flooding cycles. To explore the molecular mechanism underlying the physiological adaptation of K. candel to flooding, the potential role of protein phosphorylation in flooding responses was investigated by a large-scale quantitative phosphoproteomic analysis using isobaric tag for relative and absolute quantitation. Total 2141 unique phosphopeptides and 2603 non-redundant phosphorylation sites were identified from 1516 phosphoproteins in K. candel leaves...
January 15, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29349465/exploring-candidate-biomarkers-for-lung-and-prostate-cancers-using-gene-expression-and-flux-variability-analysis
#2
Yazdan Asgari, Pegah Khosravi, Zahra Zabihinpour, Mahnaz Habibi
Genome-scale metabolic models have provided valuable resources for exploring changes in metabolism under normal and cancer conditions. However, metabolism itself is strongly linked to gene expression, so integration of gene expression data into metabolic models might improve the detection of genes involved in the control of tumor progression. Herein, we considered gene expression data as extra constraints to enhance the predictive powers of metabolic models. We reconstructed genome-scale metabolic models for lung and prostate, under normal and cancer conditions to detect the major genes associated with critical subsystems during tumor development...
January 19, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29349039/engineering-escherichia-coli-for-the-production-of-terpene-mixture-enriched-in-caryophyllene-and-caryophyllene-alcohol-as-potential-aviation-fuel-compounds
#3
Weihua Wu, Fang Liu, Ryan W Davis
Recent studies have revealed that caryophyllene and its stereoisomers not only exhibit multiple biological activities but also have desired properties as renewable candidates for ground transportation and jet fuel applications. This study presents the first significant production of caryophyllene and caryolan-1-ol by an engineered E. coli with heterologous expression of mevalonate pathway genes with a caryophyllene synthase and a caryolan-1-ol synthase. By optimizing metabolic flux and fermentation parameters, the engineered strains yielded 449 mg/L of total terpene, including 406 mg/L sesquiterpene with 100 mg/L caryophyllene and 10 mg/L caryolan-1-ol...
June 2018: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29347381/maximum-entropy-modeling-of-metabolic-networks-by-constraining-growth-rate-moments-predicts-coexistence-of-phenotypes
#4
Daniele De Martino
In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347168/quantifying-the-entropic-cost-of-cellular-growth-control
#5
Daniele De Martino, Fabrizio Capuani, Andrea De Martino
Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346685/metabolic-flux-engineering-of-cembratrien-ol-production-in-both-the-glandular-trichome-and-leaf-mesophyll-in-nicotiana-tabacum
#6
Hongying Zhang, Songtao Zhang, Yongxia Yang, Hongfang Jia, Hong Cui
Cembratrien-ol synthase (CBTS) catalyses the first step in cembranoid biosynthesis, producing cembratrien-ols in plant trichomes. In our previous study, microarray transcriptomes between leaves with trichomes and leaves without trichomes showed that a NtCBTS2 gene was expressed exclusively and abundantly in trichomes. Here, two NtCBTS2 isogenes (NtCBTS2a and NtCBTS2b), derived from a diploid genome donor, N. sylvestris, were identified from N. tabacum. Both genes were expressed primarily in trichomes, with relatively decreased transcription in flowers and stems, faint expression in roots, and no expression was detected in leaves lacking trichomes...
January 15, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29345370/inhibition-of-soluble-epoxide-hydrolase-attenuates-eosinophil-recruitment-and-food-allergen-induced-gastrointestinal-inflammation
#7
Idil Bastan, Xiao Na Ge, Mythili Dileepan, Yana G Greenberg, Alonso G Guedes, Sung Hee Hwang, Bruce D Hammock, Robert J Washabau, Savita P Rao, P Sriramarao
Prevalence of food allergies in the United States is on the rise. Eosinophils are recruited to the intestinal mucosa in substantial numbers in food allergen-driven gastrointestinal (GI) inflammation. Soluble epoxide hydrolase (sEH) is known to play a pro-inflammatory role during inflammation by metabolizing anti-inflammatory epoxyeicosatrienoic acids (EETs) to pro-inflammatory diols. We investigated the role of sEH in a murine model of food allergy and evaluated the potential therapeutic effect of a highly selective sEH inhibitor (trans-4-{4-[3-(4-trifluoromethoxyphenyl)-ureido]-cyclohexyloxy}-benzoic acid [t-TUCB])...
January 17, 2018: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/29344310/drug-repurposing-screening-identifies-tioconazole-as-an-atg4-inhibitor-that-suppresses-autophagy-and-sensitizes-cancer-cells-to-chemotherapy
#8
Pei-Feng Liu, Kun-Lin Tsai, Chien-Jen Hsu, Wei-Lun Tsai, Jin-Shiung Cheng, Hsueh-Wei Chang, Chung-Wai Shiau, Yih-Gang Goan, Ho-Hsing Tseng, Chih-Hsuan Wu, John C Reed, Lee-Wei Yang, Chih-Wen Shu
Background: Tumor cells require proficient autophagy to meet high metabolic demands and resist chemotherapy, which suggests that reducing autophagic flux might be an attractive route for cancer therapy. However, this theory in clinical cancer research remains controversial due to the limited number of drugs that specifically inhibit autophagy-related (ATG) proteins. Methods: We screened FDA-approved drugs using a novel platform that integrates computational docking and simulations as well as biochemical and cellular reporter assays to identify potential drugs that inhibit autophagy-required cysteine proteases of the ATG4 family...
2018: Theranostics
https://www.readbyqxmd.com/read/29343967/indoleamine-2-3-dioxygenase-activity-increases-nad-production-in-ifn-%C3%AE-stimulated-human-primary-mononuclear-cells
#9
Ross S Grant
IFN-γ activation of mononuclear phagocytes significantly increases indoleamine 2,3-dioxygenase (IDO) and flux through the kynurenine pathway (KP). However, the effect of IDO on NAD+ synthesis, the end product of KP metabolism, is unknown. To investigate this, primary human peripheral blood mononuclear cells were cultured up to 10 days and activated with IFN-γ in the presence or absence of a poly(ADP-ribose) polymerase (PARP) inhibitor. Day 10 macrophages had significantly higher NAD+ levels compared with monocytes...
2018: International Journal of Tryptophan Research: IJTR
https://www.readbyqxmd.com/read/29343830/biological-rejuvenation-of-iron-oxides-in-bioturbated-marine-sediments
#10
Jacob P Beam, Jarrod J Scott, Sean M McAllister, Clara S Chan, James McManus, Filip J R Meysman, David Emerson
The biogeochemical cycle of iron is intricately linked to numerous element cycles. Although biological processes that catalyze the reductive side of the iron cycle are established, little is known about microbial oxidative processes on iron cycling in sedimentary environments-resulting in the formation of iron oxides. Here we show that a potential source of sedimentary iron oxides originates from the metabolic activity of iron-oxidizing bacteria from the class Zetaproteobacteria, presumably enhanced by burrowing animals in coastal sediments...
January 17, 2018: ISME Journal
https://www.readbyqxmd.com/read/29337084/a-graph-based-approach-to-analyze-flux-balanced-pathways-in-metabolic-networks
#11
Mona Arabzadeh, Morteza Saheb Zamani, Mehdi Sedighi, Sayed-Amir Marashi
An Elementary Flux Mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find these flux-balanced pathways. In this paper, an approach to find a subset of EFMs is proposed based on a graph data model. The given metabolic network is mapped to the graph model and decisions for reaction inclusion can be made based on metabolites and their associated reactions...
January 11, 2018: Bio Systems
https://www.readbyqxmd.com/read/29335637/expression-profiling-of-host-and-virus-during-a-coccolithophore-bloom-provides-insights-into-the-role-of-viral-infection-in-promoting-carbon-export
#12
Uri Sheyn, Shilo Rosenwasser, Yoav Lehahn, Noa Barak-Gavish, Ron Rotkopf, Kay D Bidle, Ilan Koren, Daniella Schatz, Assaf Vardi
The cosmopolitan coccolithophore Emiliania huxleyi is a unicellular eukaryotic alga that forms vast blooms in the oceans impacting large biogeochemical cycles. These blooms are often terminated due to infection by the large dsDNA virus, E. huxleyi virus (EhV). It was recently established that EhV-induced modulation of E. huxleyi metabolism is a key factor for optimal viral infection cycle. Despite the huge ecological importance of this host-virus interaction, the ability to assess its spatial and temporal dynamics and its possible impact on nutrient fluxes is limited by current approaches that focus on quantification of viral abundance and biodiversity...
January 15, 2018: ISME Journal
https://www.readbyqxmd.com/read/29334655/how-yeast-coordinates-metabolism-growth-and-division
#13
REVIEW
Jennifer C Ewald
All cells, especially single cell organisms, need to adapt their metabolism, growth and division coordinately to the available nutrients. This coordination is mediated by extensive cross-talk between nutrient signaling, metabolism, growth, and the cell division cycle, which is only gradually being uncovered: Nutrient signaling not only controls entry into the cell cycle at the G1/S transition, but all phases of the cell cycle. Metabolites are even sensed directly by cell cycle regulators to prevent cell cycle progression in absence of sufficient metabolic fluxes...
January 12, 2018: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29334372/pharmacological-blockade-of-asct2-dependent-glutamine-transport-leads-to-antitumor-efficacy-in-preclinical-models
#14
Michael L Schulte, Allie Fu, Ping Zhao, Jun Li, Ling Geng, Shannon T Smith, Jumpei Kondo, Robert J Coffey, Marc O Johnson, Jeffrey C Rathmell, Joe T Sharick, Melissa C Skala, Jarrod A Smith, Jordan Berlin, M Kay Washington, Michael L Nickels, H Charles Manning
The unique metabolic demands of cancer cells underscore potentially fruitful opportunities for drug discovery in the era of precision medicine. However, therapeutic targeting of cancer metabolism has led to surprisingly few new drugs to date. The neutral amino acid glutamine serves as a key intermediate in numerous metabolic processes leveraged by cancer cells, including biosynthesis, cell signaling, and oxidative protection. Herein we report the preclinical development of V-9302, a competitive small molecule antagonist of transmembrane glutamine flux that selectively and potently targets the amino acid transporter ASCT2...
January 15, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29333574/unique-metabolic-activation-of-adipose-tissue-macrophages-in-obesity-promotes-inflammatory-responses
#15
Lily Boutens, Guido J Hooiveld, Sourabh Dhingra, Robert A Cramer, Mihai G Netea, Rinke Stienstra
AIMS/HYPOTHESIS: Recent studies have identified intracellular metabolism as a fundamental determinant of macrophage function. In obesity, proinflammatory macrophages accumulate in adipose tissue and trigger chronic low-grade inflammation, that promotes the development of systemic insulin resistance, yet changes in their intracellular energy metabolism are currently unknown. We therefore set out to study metabolic signatures of adipose tissue macrophages (ATMs) in lean and obese conditions...
January 14, 2018: Diabetologia
https://www.readbyqxmd.com/read/29330693/the-enhanced-biomass-and-lipid-accumulation-in-coccomyxa-subellipsoidea-with-an-integrated-treatment-strategy-initiated-by-brewery-effluent-and-phytohormones
#16
Tingting Liu, Fei Luo, Zhenyao Wang, Yuqin Li
Brewery effluent (BE) as an appreciable and sustainable resource presented new possibilities in low-cost algal biomass production, whereas the relatively low essential macronutrients hindered extensive applications as growth medium for microalgae cultivation. The objective of this study was to investigate the feasibility of an integrated treatment strategy initiated by BE coupling phytohormones in augmenting biomass and lipid accumulation in Coccomyxa subellipsoidea. Results revealed that BE coupling synthetic 1-naphthaleneacetic acid (NAA) accomplished the favorable lipid productivity of 481...
January 12, 2018: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29330665/a-synthetic-pathway-for-the-production-of-2-hydroxyisovaleric-acid-in-escherichia-coli
#17
Seokjung Cheong, James M Clomburg, Ramon Gonzalez
Synthetic biology, encompassing the design and construction of novel artificial biological pathways and organisms and the redesign of existing natural biological systems, is rapidly expanding the number of applications for which biological systems can play an integral role. In the context of chemical production, the combination of synthetic biology and metabolic engineering approaches continues to unlock the ability to biologically produce novel and complex molecules from a variety of feedstocks. Here, we utilize a synthetic approach to design and build a pathway to produce 2-hydroxyisovaleric acid in Escherichia coli and demonstrate how pathway design can be supplemented with metabolic engineering approaches to improve pathway performance from various carbon sources...
January 12, 2018: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29326166/a-skeletal-muscle-l-type-ca2-channel-with-a-mutation-in-the-selectivity-filter-cav1-1-e1014k-conducts-k
#18
Donald Beqollari, Karen Dockstader, Roger A Bannister
A glutamate to lysine substitution at position 1014 within the selectivity filter of the skeletal muscle L-type Ca2+ channel (CaV1.1) abolishes Ca2+ flux through the channel pore. Mice engineered to exclusively express the mutant channel display accelerated muscle fatigue, changes in muscle composition and altered metabolism relative to wild-type littermates. By contrast, mice expressing another mutant CaV1.1 channel that is impermeable to Ca2+ (CaV1.1 N617D) have shown no detectable phenotypic differences from wild-type mice to date...
January 11, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29323106/sequential-forward-and-reverse-transport-of-the-na-ca2-exchanger-generates-ca2-oscillations-within-mitochondria
#19
Krishna Samanta, Gary R Mirams, Anant B Parekh
Mitochondrial Ca2+ homoeostasis regulates aerobic metabolism and cell survival. Ca2+ flux into mitochondria is mediated by the mitochondrial calcium uniporter (MCU) channel whereas Ca2+ export is often through an electrogenic Na+-Ca2+ exchanger. Here, we report remarkable functional versatility in mitochondrial Na+-Ca2+ exchange under conditions where mitochondria are depolarised. Following physiological stimulation of cell-surface receptors, mitochondrial Na+-Ca2+ exchange initially operates in reverse mode, transporting cytosolic Ca2+ into the matrix...
January 11, 2018: Nature Communications
https://www.readbyqxmd.com/read/29321350/neuro-fuzzy-model-of-homocysteine-metabolism
#20
Shaik Mohammad Naushad, Akella Radha Rama Devi, Sriraman Nivetha, Ganapathy Lakshmitha, Alex Balraj Stanley, Tajamul Hussain, Vijay Kumar Kutala
In view of well-documented association of hyperhomocysteinaemia with a wide spectrum of diseases and higher incidence of vitamin deficiencies in Indians, we proposed a mathematical model to forecast the role of demographic and genetic variables in influencing homocysteinemetabolism and investigated the influence of life style modulations in controlling homocysteine levels. Total plasma homocysteine levels were measured in fasting samples using reverse phase HPLC. Multiple linear regression (MLR) and neuro-fuzzy models were developed...
December 2017: Journal of Genetics
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