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Biological reaction network

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https://www.readbyqxmd.com/read/28812671/sulfate-radicals-enable-a-non-enzymatic-krebs-cycle-precursor
#1
Markus A Keller, Domen Kampjut, Stuart A Harrison, Markus Ralser
The evolutionary origins of the Krebs cycle (tricarboxylic acid cycle) are not currently clear. Despite the existence of a simple non-enzymatic Krebs cycle catalyst being dismissed only a few years ago as 'an appeal to magic', citrate and other intermediates have since been discovered on a carbonaceous meteorite and do interconvert non-enzymatically. To identify a metabolism-like non-enzymatic Krebs cycle catalyst, we used combinatorial, quantitative high-throughput metabolomics to systematically screen iron and sulfate compounds in a reaction mixture that orients on the typical components of Archaean sediment...
March 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811624/pupil-size-tracks-attentional-performance-in-attention-deficit-hyperactivity-disorder
#2
G Wainstein, D Rojas-Líbano, N A Crossley, X Carrasco, F Aboitiz, T Ossandón
Attention-deficit/hyperactivity disorder (ADHD) diagnosis is based on reported symptoms, which carries the potential risk of over- or under-diagnosis. A biological marker that helps to objectively define the disorder, providing information about its pathophysiology, is needed. A promising marker of cognitive states in humans is pupil size, which reflects the activity of an 'arousal' network, related to the norepinephrine system. We monitored pupil size from ADHD and control subjects, during a visuo-spatial working memory task...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28802767/real-rock-microfluidic-flow-cell-a-test-bed-for-real-time-in-situ-analysis-of-flow-transport-and-reaction-in-a-subsurface-reactive-transport-environment
#3
Rajveer Singh, Mayandi Sivaguru, Glenn A Fried, Bruce W Fouke, Robert A Sanford, Martin Carrera, Charles J Werth
Physical, chemical, and biological interactions between groundwater and sedimentary rock directly control the fundamental subsurface properties such as porosity, permeability, and flow. This is true for a variety of subsurface scenarios, ranging from shallow groundwater aquifers to deeply buried hydrocarbon reservoirs. Microfluidic flow cells are now commonly being used to study these processes at the pore scale in simplified pore structures meant to mimic subsurface reservoirs. However, these micromodels are typically fabricated from glass, silicon, or polydimethylsiloxane (PDMS), and are therefore incapable of replicating the geochemical reactivity and complex three-dimensional pore networks present in subsurface lithologies...
August 4, 2017: Journal of Contaminant Hydrology
https://www.readbyqxmd.com/read/28797226/network-design-and-analysis-for-multi-enzyme-biocatalysis
#4
Lisa Katharina Blaß, Christian Weyler, Elmar Heinzle
BACKGROUND: As more and more biological reaction data become available, the full exploration of the enzymatic potential for the synthesis of valuable products opens up exciting new opportunities but is becoming increasingly complex. The manual design of multi-step biosynthesis routes involving enzymes from different organisms is very challenging. To harness the full enzymatic potential, we developed a computational tool for the directed design of biosynthetic production pathways for multi-step catalysis with in vitro enzyme cascades, cell hydrolysates and permeabilized cells...
August 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28793226/signaling-architectures-that-transmit-unidirectional-information-despite-retroactivity
#5
Rushina Shah, Domitilla Del Vecchio
A signaling pathway transmits information from an upstream system to downstream systems, ideally in a unidirectional fashion. A key obstacle to unidirectional transmission is retroactivity, the additional reaction flux that affects a system once its species interact with those of downstream systems. This raises the fundamental question of whether signaling pathways have developed specialized architectures that overcome retroactivity and transmit unidirectional signals. Here, we propose a general procedure based on mathematical analysis that provides an answer to this question...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28793223/constraint-and-contingency-pervade-the-emergence-of-novel-phenotypes-in-complex-metabolic-systems
#6
Sayed-Rzgar Hosseini, Andreas Wagner
An evolutionary constraint is a bias or limitation in phenotypic variation that a biological system produces. We know examples of such constraints, but we have no systematic understanding about their extent and causes for any one biological system. We here study metabolisms, genomically encoded complex networks of enzyme-catalyzed biochemical reactions, and the constraints they experience in bringing forth novel phenotypes that allow survival on novel carbon sources. Our computational approach does not limit us to analyzing constrained variation in any one organism, but allows us to quantify constraints experienced by any metabolism...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28782551/operating-regimes-of-covalent-modification-cycles-at-high-enzyme-concentrations
#7
Ronny Straube
The Goldbeter-Koshland model has been a paradigm for ultrasensitivity in biological networks for more than 30 years. Despite its simplicity the validity of this model is restricted to conditions when the substrate is in excess over the converter enzymes - a condition that is easy to satisfy in vitro, but which is rarely satisfied in vivo. Here, we analyze the Goldbeter-Koshland model by means of the total quasi-steady state approximation which yields a comprehensive classification of the steady state operating regimes under conditions when the enzyme concentrations are comparable to or larger than that of the substrate...
August 4, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28782515/stochastic-simulation-of-biochemical-reactions-with-partial-propensity-and-rejection-based-approaches
#8
Vo Hong Thanh
We present in this paper a new exact algorithm for improving performance of exact stochastic simulation algorithm. The algorithm is developed on concepts of the partial-propensity and the rejection-based approaches. It factorizes the propensity bounds of reactions and groups factors by common reactant species for selecting next reaction firings. Our algorithm provides favorable computational advantages for simulating of biochemical reaction networks by reducing the cost for selecting the next reaction firing to scale with the number of chemical species and avoiding expensive propensity updates during the simulation...
August 4, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28774651/microarray-profiling-of-circular-rnas-and-the-potential-regulatory-role-of-hsa_circ_0071410-in-the-activated-human-hepatic-stellate-cell-induced-by-irradiation
#9
Yuhan Chen, Baoying Yuan, Zhifeng Wu, Yinying Dong, Li Zhang, Zhaochong Zeng
Radiation-induced liver fibrosis (RILF) is considered as a major complication of radiation therapy for liver cancer. Circular RNA (circRNA) has been recently identified as a functional noncoding RNA involving in various biological processes. However, the expression pattern and regulatory capacity of circRNA in the irradiated hepatic stellate cell (HSC), the main fibrogenic cell type, still remain unclear. A circRNA microarray was used to identify circRNA expression profiles in irradiated and normal HSC. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to confirm the dysregulated circRNAs...
July 31, 2017: Gene
https://www.readbyqxmd.com/read/28771719/the-aberrantly-expressed-long-noncoding-rna-in-the-substantia-nigra-and-corpus-striatum-of-nrf2-knockout-mice
#10
Jian Liu, Yali Xu, Yunxiao Kang, Shanhu Cao, Geming Shi, Huixian Cui, Shaoguang Sun, Lei Wang
Nuclear factor erythroid 2 like 2 (Nrf2) functions as a neuroprotective agent in Parkinson's disease (PD). The present study aimed to investigate the key long noncoding RNAs (lncRNAs) correlated with Nrf2, which might provide valuable information for the exploration of pathogenesis of PD. The lncRNA and mRNA expression profiling of substantia nigra and corpus striatum of Nrf2 (-/-) mice model was obtained from microarray analysis. The animal experiments conducted for this study were approved by the ethics committee of Hebei Medical University...
August 3, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28765971/identification-of-key-genes-and-pathways-in-parkinson-s-disease-through-integrated-analysis
#11
Jingru Wang, Yining Liu, Tuanzhi Chen
Parkinson's disease (PD) is a progressive, degene-rative neurological disease, typically characterized by tremors and muscle rigidity. The present study aimed to identify differe-ntially expressed genes (DEGs) between patients with PD and healthy patients, and clarify their association with additional biological processes that may regulate factors that lead to PD. An integrated analysis of publicly available Gene Expression Omnibus datasets of PD was performed. DEGs were identified between PD and normal blood samples...
July 31, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28763026/genome-wide-analysis-reveals-extensive-changes-in-lncrnas-during-skeletal-muscle-development-in-hu-sheep
#12
Caifang Ren, Mingtian Deng, Yixuan Fan, Hua Yang, Guomin Zhang, Xu Feng, Fengzhe Li, Dan Wang, Feng Wang, Yanli Zhang
As an important type of noncoding RNA molecules, long non-coding RNAs (lncRNAs) act as versatile players in various biological processes. However, little is known about lncRNA regulators during sheep muscle growth. To explore functional lncRNAs during sheep muscle growth, we systematically investigated lncRNAs using strand-specific Ribo-Zero RNA sequencing at three key developmental stages in Hu sheep. A total of 6924 lncRNAs were obtained, and the differentially expressed lncRNAs and genes were screened from (control vs...
August 1, 2017: Genes
https://www.readbyqxmd.com/read/28762750/genome-scale-modeling-of-nadph-driven-%C3%AE-lapachone-sensitization-in-head-and-neck-squamous-cell-carcinoma
#13
Joshua E Lewis, Francesco Costantini, Jade Mims, Xiaofei Chen, Cristina Furdui, David A Boothman, Melissa L Kemp
AIMS: The purpose of this study was to investigate differential NADPH production between radiation-sensitive and -resistant head and neck squamous cell carcinoma (HNSCC) cell lines, and whether these differences are predictive of sensitivity to the chemotherapeutic ß-lapachone. RESULTS: We have developed a novel human genome-scale metabolic modeling platform that combines transcriptomic, kinetic, thermodynamic, and metabolite concentration data. Upon incorporation of this information into cell-line specific models, we observed that the radiation-resistant HNSCC model redistributed flux through several major NADPH producing reactions...
August 1, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28761373/chronic-constriction-injury-of-sciatic-nerve-changes-circular-rna-expression-in-rat-spinal-dorsal-horn
#14
Song Cao, Wenwen Deng, Ying Li, Bangyong Qin, Lin Zhang, Shouyang Yu, Peng Xie, Zhi Xiao, Tian Yu
BACKGROUND: Mechanisms of neuropathic pain are still largely unknown. Molecular changes in spinal dorsal horn may contribute to the initiation and development of neuropathic pain. Circular RNAs (circRNAs) have been identified as microRNA sponges and involved in various biological processes, but whether their expression profile changes in neuropathic pain condition is not reported. METHODS: To test whether neuropathic pain influences circRNA expression, we developed a sciatic chronic constriction injury (CCI) model in rats...
2017: Journal of Pain Research
https://www.readbyqxmd.com/read/28755503/spectrum-evaluation-assisted-eicosanoid-metabolomics-for-global-eicosanoid-profiling-in-human-vascular-endothelial-cells
#15
Qiankun Bao, Yajin Liu, Hao Song, Nan Yang, Ding Ai, Yi Zhu, Xu Zhang
Eicosanoids are hundreds of metabolites derived from poly-unsaturated fatty acids (PUFAs), which regulate biological processes from multiple angles via a complex metabolic network. Targeted eicosanoid metabolomics is used to study the eicosanoid profile in biological samples but only for eicosanoids with available standards. To expand the coverage of eicosanoids detected, we identified the eicosanoids without available standards by estimation of the retention time and comparison of the MS/MS spectra with the reference ones which was collected in a database from literature...
July 29, 2017: Clinical and Experimental Pharmacology & Physiology
https://www.readbyqxmd.com/read/28754122/snoopy-s-hybrid-simulator-a-tool-to-construct-and-simulate-hybrid-biological-models
#16
Mostafa Herajy, Fei Liu, Christian Rohr, Monika Heiner
BACKGROUND: Hybrid simulation of (computational) biochemical reaction networks, which combines stochastic and deterministic dynamics, is an important direction to tackle future challenges due to complex and multi-scale models. Inherently hybrid computational models of biochemical networks entail two time scales: fast and slow. Therefore, it is intricate to efficiently and accurately analyse them using only either deterministic or stochastic simulation. However, there are only a few software tools that support such an approach...
July 28, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28749683/control-of-surface-localized-enzyme-assisted-self-assembly-of-peptides-through-catalyzed-oligomerization
#17
Cécile Vigier-Carrière, Déborah Wagner, Alain Chaumont, Baptiste Durr, Paolo Lupattelli, Christophe Lambour, Marc Schmutz, Joseph Hemmerlé, Bernard Senger, Pierre Schaaf, Fouzia Boulmedais, Loïc Jierry
Localized self-assembly allowing both spatial and temporal control over the assembly process is essential in many biological systems. This can be achieved through localized enzyme-assisted self-assembly (LEASA), also called enzyme-instructed self-assembly, where enzymes present on a substrate catalyze a reaction that transforms noninteracting species into self-assembling ones. Very few LEASA systems have been reported so far, and the control of the self-assembly process through the surface properties represents one essential step toward their use, for example, in artificial cell mimicry...
August 7, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28744146/rna-sequencing-identifies-gene-expression-profile-changes-associated-with-%C3%AE-estradiol-treatment-in-u2os-osteosarcoma-cells
#18
Bin Chen, Zude Liu, Jidong Zhang, Hantao Wang, Bo Yu
This study was conducted to identify gene expression profile changes associated with β-estradiol (E2) treatment in U2OS osteosarcoma cells by high-throughput RNA sequencing (RNA-seq). Two U2OS cell samples treated with E2 (15 μmol/L) and two untreated control U2OS cell samples were subjected to RNA-seq. Differentially expressed genes (DEGs) between the groups were identified, and main biological process enrichment was performed using gene ontology (GO) analysis. A protein-protein interaction (PPI) network was constructed using Cytoscape based on the Human Protein Reference Database...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28744139/the-long-noncoding-rna-tincr-functions-as-a-competing-endogenous-rna-to-regulate-pdk1-expression-by-sponging-mir-375-in-gastric-cancer
#19
Zhaoliang Chen, Hong Liu, Huili Yang, Yukai Gao, Gongwen Zhang, Jiaojiao Hu
BACKGROUND: Accumulating evidence indicates that the long noncoding RNA, TINCR, plays a critical role in cancer progression and metastasis. However, the overall biological role and mechanisms of TINCR that were involved in human gastric cancer (GC) progression remain largely unknown. METHODS: TINCR expression was measured in 56 paired tumor and adjacent nontumor tissue samples by real-time polymerase chain reaction (PCR). Insights of the mechanism of competitive endogenous RNAs (ceRNAs) were gained from bioinformatic analysis, luciferase assays...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28733280/construction-and-optimization-of-a-heterologous-pathway-for-protocatechuate-catabolism-in-escherichia-coli-enables-bioconversion-of-model-aromatic-compounds
#20
Sonya M Clarkson, Richard J Giannone, Donna M Kridelbaugh, James G Elkins, Adam M Guss, Joshua K Michener
The production of biofuels from lignocellulose yields a substantial lignin byproduct stream that currently has few applications. Biological conversion of lignin-derived compounds into chemicals and fuels has the potential to improve the economics of lignocellulose-derived biofuels, but few microbes are able both to catabolize lignin-derived aromatic compounds and generate valuable products. While Escherichia coli has been engineered to produce a variety of fuels and chemicals, it is incapable of catabolizing most aromatic compounds...
July 21, 2017: Applied and Environmental Microbiology
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