keyword
MENU ▼
Read by QxMD icon Read
search

metabolic flux analysis

keyword
https://www.readbyqxmd.com/read/28733443/direct-metabolic-interrogation-of-dihydrotestosterone-biosynthesis-from-adrenal-precursors-in-primary-prostatectomy-tissues
#1
Charles Dai, Yoon-Mi Chung, Evan Kovac, Ziqi Zhu, Jianneng Li, Cristina Magi-Galluzzi, Andrew J Stephenson, Eric A Klein, Nima Sharifi
Purpose: A major mechanism of castration-resistant prostate cancer (CRPC) involves intratumoral biosynthesis of dihydrotestosterone (DHT) from adrenal precursors. We have previously shown that adrenal-derived androstenedione (AD) is the preferred substrate over testosterone (T) for 5α-reductase expressed in metastatic CRPC, bypassing T as an obligate precursor to DHT. However, the metabolic pathway of adrenal-derived DHT biosynthesis has not been rigorously investigated in the setting of primary disease in the prostate...
July 21, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28731563/improving-fructose-utilization-and-butanol-production-by-clostridium-acetobutylicum-via-extracellular-redox-potential-regulation-and-intracellular-metabolite-analysis
#2
Li-Jie Chen, You-Duo Wu, Chuang Xue, Feng-Wu Bai
Jerusalem artichoke (JA) can grow well in marginal lands with high biomass yield, and thus is a potential energy crop for biorefinery. The major biomass of JA is from tubers, which contain inulin that can be easily hydrolyzed into a mixture of fructose and glucose, but fructose utilization for producing butanol as an advanced biofuel is poor compared to glucose-based ABE fermentation by Clostridium acetobutylicum. In this article, the impact of extracellular redox potential (ORP) on the process was studied using a mixture of fructose and glucose to simulate the hydrolysate of JA tubers...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28727725/redgem-systematic-reduction-and-analysis-of-genome-scale-metabolic-reconstructions-for-development-of-consistent-core-metabolic-models
#3
Meric Ataman, Daniel F Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis
Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the complexity of these large metabolic networks often hinders their utility in various practical applications. Although reduced models are commonly used for modeling and in integrating experimental data, they are often inconsistent across different studies and laboratories due to different criteria and detail, which can compromise transferability of the findings and also integration of experimental data from different groups...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28727166/hepatocytes-contribute-to-residual-glucose-production-in-a-mouse-model-for-glycogen-storage-disease-type-ia
#4
Brenda S Hijmans, Andreas Boss, Theo H van Dijk, Maud Soty, Henk Wolters, Elodie Mutel, Albert K Groen, Terry G J Derks, Gilles Mithieux, Arend Heerschap, Dirk-Jan Reijngoud, Fabienne Rajas, Maaike H Oosterveer
It is a longstanding enigma how glycogen storage disease (GSD) type I patients retain a limited capacity for endogenous glucose production (EGP) despite the loss of glucose-6-phosphatase (G6Pase) activity. Insight into the source of residual EGP is of clinical importance given the risk of sudden death in these patients, but so far contradictory mechanisms have been proposed. We investigated G6Pase-independent EGP in hepatocytes isolated from a liver-specific GSD Ia mouse model (L-G6pc(-/-) mice), and performed real-time analysis of hepatic glucose fluxes and glycogen metabolism in L-G6pc(-/-) mice using state-of-the-art stable isotope methodologies...
July 20, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28724354/novel-plasmodium-falciparum-metabolic-network-reconstruction-identifies-shifts-associated-with-clinical-antimalarial-resistance
#5
Maureen A Carey, Jason A Papin, Jennifer L Guler
BACKGROUND: Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing experimental knowledge and further understanding of these mechanisms. RESULTS: Here, we developed a novel genome-scale metabolic network reconstruction, iPfal17, of the asexual blood-stage P...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28720902/comparative-genomic-analysis-of-paenibacillus-sp-ssg-1-and-its-closely-related-strains-reveals-the-effect-of-glycometabolism-on-environmental-adaptation
#6
Hui Xu, Shishang Qin, Yanhong Lan, Mengjia Liu, Xiyue Cao, Dairong Qiao, Yu Cao, Yi Cao
The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716914/metabolic-profiles-of-exercise-in-patients-with-mcardle-disease-or-mitochondrial-myopathy
#7
Nigel F Delaney, Rohit Sharma, Laura Tadvalkar, Clary B Clish, Ronald G Haller, Vamsi K Mootha
McArdle disease and mitochondrial myopathy impair muscle oxidative phosphorylation (OXPHOS) by distinct mechanisms: the former by restricting oxidative substrate availability caused by blocked glycogen breakdown, the latter because of intrinsic respiratory chain defects. We applied metabolic profiling to systematically interrogate these disorders at rest, when muscle symptoms are typically minimal, and with exercise, when symptoms of premature fatigue and potential muscle injury are unmasked. At rest, patients with mitochondrial disease exhibit elevated lactate and reduced uridine; in McArdle disease purine nucleotide metabolites, including xanthine, hypoxanthine, and inosine are elevated...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28715411/a-curated-genome-scale-metabolic-model-of-bordetella-pertussis-metabolism
#8
Nick Fyson, Jerry King, Thomas Belcher, Andrew Preston, Caroline Colijn
The Gram-negative bacterium Bordetella pertussis is the causative agent of whooping cough, a serious respiratory infection causing hundreds of thousands of deaths annually worldwide. There are effective vaccines, but their production requires growing large quantities of B. pertussis. Unfortunately, B. pertussis has relatively slow growth in culture, with low biomass yields and variable growth characteristics. B. pertussis also requires a relatively expensive growth medium. We present a new, curated flux balance analysis-based model of B...
July 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28710856/quantitative-intracellular-flux-modeling-and-applications-in-biotherapeutic-development-and-production-using-cho-cell-cultures
#9
REVIEW
Zhuangrong Huang, Dong-Yup Lee, Seongkyu Yoon
Chinese hamster ovary (CHO) cells have been widely used for producing many recombinant therapeutic proteins. Constraint-based modeling, such as flux balance analysis (FBA) and metabolic flux analysis (MFA), has been developing rapidly for the quantification of intracellular metabolic flux distribution at a systematic level. Such methods would produce detailed maps of flows through metabolic networks, which contribute significantly to better understanding of metabolism in cells. Although these approaches have been extensively established in microbial systems, their application to mammalian cells is sparse...
July 15, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28706006/integration-of-flux-measurements-to-resolve-changes-in-anabolic-and-catabolic-metabolism-in-cardiac-myocytes
#10
Andrew A Gibb, Pawel K Lorkiewicz, Yu-Ting Zheng, Xiang Zhang, Aruni Bhatnagar, Steven P Jones, Bradford G Hill
Although ancillary pathways of glucose metabolism are critical for synthesizing cellular building blocks and modulating stress responses, how they are regulated remains unclear.  In this study, we used radiometric glycolysis assays, [(13)C6]-glucose isotope tracing, and extracellular flux analysis to understand how phosphofructokinase (PFK)-mediated changes in glycolysis regulate glucose carbon partitioning into catabolic and anabolic pathways. Expression of kinase-deficient or phosphatase-deficient 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase in rat neonatal cardiomyocytes coordinately regulated glycolytic rate and lactate production...
July 13, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28701793/the-mir-29-transcriptome-in-endocrine-sensitive-and-resistant-breast-cancer-cells
#11
Penn Muluhngwi, Negin Alizadeh-Rad, Stephany L Vittitow, Ted S Kalbfleisch, Carolyn M Klinge
Aberrant microRNA expression contributes to breast cancer progression and endocrine resistance. We reported that although tamoxifen stimulated miR-29b-1/a transcription in tamoxifen (TAM)-resistant breast cancer cells, ectopic expression of miR-29b-1/a did not drive TAM-resistance in MCF-7 breast cancer cells. However, miR-29b-1/a overexpression significantly repressed TAM-resistant LCC9 cell proliferation, suggesting that miR-29b-1/a is not mediating TAM resistance but acts as a tumor suppressor in TAM-resistant cells...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28695999/to-be-certain-about-the-uncertainty-bayesian-statistics-for-13-c-metabolic-flux-analysis
#12
Axel Theorell, Samuel Leweke, Wolfgang Wiechert, Katharina Nöh
(13) C Metabolic Fluxes Analysis ((13) C MFA) remains to be the most powerful approach to determine intracellular metabolic reaction rates. Decisions on strain engineering and experimentation heavily rely upon the certainty with which these fluxes are estimated. For uncertainty quantification, the vast majority of (13) C MFA studies relies on confidence intervals from the paradigm of Frequentist statistics. However, it is well known that the confidence intervals for a given experimental outcome are not uniquely defined...
July 11, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28695583/quantitative-13-c-isotope-labelling-based-analysis-to-elucidate-the-influence-of-environmental-parameters-on-the-production-of-fermentative-aromas-during-wine-fermentation
#13
Stéphanie Rollero, Jean-Roch Mouret, Audrey Bloem, Isabelle Sanchez, Anne Ortiz-Julien, Jean-Marie Sablayrolles, Sylvie Dequin, Carole Camarasa
Nitrogen and lipids are key nutrients of grape must that influence the production of fermentative aromas by wine yeast, and we have previously shown that a strong interaction exists between these two nutrients. However, more than 90% of the acids and higher alcohols (and their acetate ester derivatives) were derived from intermediates produced by the carbon central metabolism (CCM). The objective of this study was to determine how variations in nitrogen and lipid resources can modulate the contribution of nitrogen and carbon metabolisms for the production of fermentative aromas...
July 11, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28695065/-13-c-based-proteinogenic-amino-acid-paa-and-metabolic-flux-ratio-analysis-of-lactococcus-lactis-reveals-changes-in-pentose-phosphate-pp-pathway-in-response-to-agitation-and-temperature-related-stresses
#14
Kamalrul Azlan Azizan, Habtom W Ressom, Eduardo R Mendoza, Syarul Nataqain Baharum
Lactococcus lactis subsp. cremoris MG1363 is an important starter culture for dairy fermentation. During industrial fermentations, L. lactis is constantly exposed to stresses that affect the growth and performance of the bacterium. Although the response of L. lactis to several stresses has been described, the adaptation mechanisms at the level of in vivo fluxes have seldom been described. To gain insights into cellular metabolism, (13)C metabolic flux analysis and gas chromatography mass spectrometry (GC-MS) were used to measure the flux ratios of active pathways in the central metabolism of L...
2017: PeerJ
https://www.readbyqxmd.com/read/28690597/close-to-the-edge-growth-restrained-by-the-nad-p-h-atp-formation-flux-ratio
#15
Ed W J van Niel, Basti Bergdahl, Bärbel Hahn-Hägerdal
Most fermentative microorganisms grow well-under anaerobic conditions managing a balanced redox and appropriate energy metabolism, but a few species do exist in which cells have to cope with inadequate energy recovery or capture and/or redox balancing. Two cases of these species, i.e., the metabolically engineered Saccharomyces cerevisiae enabling it to ferment xylose and Lactobacillus reuteri fermenting glucose via the phosphoketolase pathway, are here used to introduce a quantification parameter to capture what limits the growth rate of these microorganisms under anaerobic conditions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28686599/flux-balance-analysis-predicts-warburg-like-effects-of-mouse-hepatocyte-deficient-in-mir-122a
#16
Hua-Qing Wu, Mei-Ling Cheng, Jin-Mei Lai, Hsuan-Hui Wu, Meng-Chun Chen, Wen-Huan Liu, Wu-Hsiung Wu, Peter Mu-Hsin Chang, Chi-Ying F Huang, Ann-Ping Tsou, Ming-Shi Shiao, Feng-Sheng Wang
The liver is a vital organ involving in various major metabolic functions in human body. MicroRNA-122 (miR-122) plays an important role in the regulation of liver metabolism, but its intrinsic physiological functions require further clarification. This study integrated the genome-scale metabolic model of hepatocytes and mouse experimental data with germline deletion of Mir122a (Mir122a-/-) to infer Warburg-like effects. Elevated expression of MiR-122a target genes in Mir122a-/-mice, especially those encoding for metabolic enzymes, was applied to analyze the flux distributions of the genome-scale metabolic model in normal and deficient states...
July 7, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28680442/perspectives-and-challenges-in-microbial-communities-metabolic-modeling
#17
Emanuele Bosi, Giovanni Bacci, Alessio Mengoni, Marco Fondi
Bacteria have evolved to efficiently interact each other, forming complex entities known as microbial communities. These "super-organisms" play a central role in maintaining the health of their eukaryotic hosts and in the cycling of elements like carbon and nitrogen. However, despite their crucial importance, the mechanisms that influence the functioning of microbial communities and their relationship with environmental perturbations are obscure. The study of microbial communities was boosted by tremendous advances in sequencing technologies, and in particular by the possibility to determine genomic sequences of bacteria directly from environmental samples...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28680072/-arman-archaea-depend-on-association-with-euryarchaeal-host-in-culture-and-in-situ
#18
Olga V Golyshina, Stepan V Toshchakov, Kira S Makarova, Sergey N Gavrilov, Aleksei A Korzhenkov, Violetta La Cono, Erika Arcadi, Taras Y Nechitaylo, Manuel Ferrer, Ilya V Kublanov, Yuri I Wolf, Michail M Yakimov, Peter N Golyshin
Intriguing, yet uncultured 'ARMAN'-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0...
July 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28677677/marine-viruses-discovered-via-metagenomics-shed-light-on-viral-strategies-throughout-the-oceans
#19
Felipe H Coutinho, Cynthia B Silveira, Gustavo B Gregoracci, Cristiane C Thompson, Robert A Edwards, Corina P D Brussaard, Bas E Dutilh, Fabiano L Thompson
Marine viruses are key drivers of host diversity, population dynamics and biogeochemical cycling and contribute to the daily flux of billions of tons of organic matter. Despite recent advancements in metagenomics, much of their biodiversity remains uncharacterized. Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes. These outnumber all currently known phage genomes in marine habitats and include members of previously uncharacterized lineages. We designed a new method for host prediction based on co-occurrence associations that reveals these viruses infect dominant members of the marine microbiome such as Prochlorococcus and Pelagibacter...
July 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28674555/a-design-build-test-cycle-using-modeling-and-experiments-reveals-interdependencies-between-upper-glycolysis-and-xylose-uptake-in-recombinant-s-cerevisiae-and-improves-predictive-capabilities-of-large-scale-kinetic-models
#20
Ljubisa Miskovic, Susanne Alff-Tuomala, Keng Cher Soh, Dorothee Barth, Laura Salusjärvi, Juha-Pekka Pitkänen, Laura Ruohonen, Merja Penttilä, Vassily Hatzimanikatis
BACKGROUND: Recent advancements in omics measurement technologies have led to an ever-increasing amount of available experimental data that necessitate systems-oriented methodologies for efficient and systematic integration of data into consistent large-scale kinetic models. These models can help us to uncover new insights into cellular physiology and also to assist in the rational design of bioreactor or fermentation processes. Optimization and Risk Analysis of Complex Living Entities (ORACLE) framework for the construction of large-scale kinetic models can be used as guidance for formulating alternative metabolic engineering strategies...
2017: Biotechnology for Biofuels
keyword
keyword
65140
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"