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Biological reaction network

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https://www.readbyqxmd.com/read/28915649/digoxin-induced-anemia-among-patients-with-atrial-fibrillation-and-heart-failure-clinical-data-analysis-and-drug-gene-interaction-network
#1
Yubi Lin, Siqi He, Ruiling Feng, Zhe Xu, Wanqun Chen, Zifeng Huang, Yang Liu, Qianhuan Zhang, Bin Zhang, Kejian Wang, Shulin Wu
Digoxin is widely used to treat various heart conditions. In order to clarify the association between digoxin and anemia adverse reaction, we inspected case reports submitted to the FDA Adverse Event Reporting System (FAERS) between January 2004 and December 2015. These reports involved 75618 atrial fibrillation patients and 15699 heart failure patients. Compared to other therapies, digoxin treatment was significantly more likely to be concurrent with anemia adverse reaction among both atrial fibrillation patients (pooled OR = 1...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28912490/the-interdependent-network-of-gene-regulation-and-metabolism-is-robust-where-it-needs-to-be
#2
David F Klosik, Anne Grimbs, Stefan Bornholdt, Marc-Thorsten Hütt
Despite being highly interdependent, the major biochemical networks of the living cell-the networks of interacting genes and of metabolic reactions, respectively-have been approached mostly as separate systems so far. Recently, a framework for interdependent networks has emerged in the context of statistical physics. In a first quantitative application of this framework to systems biology, here we study the interdependent network of gene regulation and metabolism for the model organism Escherichia coli in terms of a biologically motivated percolation model...
September 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28901190/transcriptome-analysis-of-induced-pluripotent-stem-cell-ipsc-derived-pancreatic-%C3%AE-like-cell-differentiation
#3
Yan Huang, Jian Wan, Yibing Guo, Shajun Zhu, Yao Wang, Lei Wang, Qingsong Guo, Yuhua Lu, Zhiwei Wang
Diabetes affects millions of people worldwide, and β-cell replacement is one of the promising new strategies for treatment. Induced pluripotent stem cells (iPSCs) can differentiate into any cell type, including pancreatic β cells, providing a potential treatment for diabetes. However, the molecular mechanisms underlying the differentiation of iPSC-derived β cells have not yet been fully elucidated. Here, we generated pancreatic β-like cells from mouse iPSCs using a 3-step protocol and performed deep RNA sequencing to get a transcriptional landscape of iPSC-derived pancreatic β-like cells during the selective differentiation period...
August 2017: Cell Transplantation
https://www.readbyqxmd.com/read/28881987/efficient-simulation-of-intrinsic-extrinsic-and-external-noise-in-biochemical-systems
#4
Dennis Pischel, Kai Sundmacher, Robert J Flassig
Motivation: Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution. Results: In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881680/identification-of-dysregulated-long-non-coding-rnas-micrornas-mrnas-in-tnm-i-stage-lung-adenocarcinoma
#5
Ziqiang Tian, Shiwang Wen, Yuefeng Zhang, Xinqiang Shi, Yonggang Zhu, Yanzhao Xu, Huilai Lv, Guiying Wang
Lung adenocarcinoma (LUAD) is the primary subtype in lung cancer, which is the leading cause of cancer-related death worldwide. This study aimed to investigate the aberrant expression profiling of long non-coding RNA (lncRNA) in TNM I stage (stage I) LUAD. The lncRNA/mRNA/miRNA expression profiling of stage I LUAD and adjacent non-tumor tissues from 4 patients were measured by RNA-sequencing. Total of 175 differentially expressed lncRNAs (DELs), 1321 differentially expressed mRNAs (DEMs) and 94 differentially expressed microRNAs (DEMIs) were identified in stage I LUAD...
August 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28878200/a-protocol-for-generating-and-exchanging-genome-scale-metabolic-resource-allocation-models
#6
Alexandra-M Reimers, Henning Lindhorst, Steffen Waldherr
In this article, we present a protocol for generating a complete (genome-scale) metabolic resource allocation model, as well as a proposal for how to represent such models in the systems biology markup language (SBML). Such models are used to investigate enzyme levels and achievable growth rates in large-scale metabolic networks. Although the idea of metabolic resource allocation studies has been present in the field of systems biology for some years, no guidelines for generating such a model have been published up to now...
September 6, 2017: Metabolites
https://www.readbyqxmd.com/read/28876046/electron-bifurcation-thermodynamics-and-kinetics-of-two-electron-brokering-in-biological-redox-chemistry
#7
Peng Zhang, Jonathon L Yuly, Carolyn E Lubner, David W Mulder, Paul W King, John W Peters, David N Beratan
How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently...
September 6, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28874657/emergence-of-native-peptide-sequences-in-prebiotic-replication-networks
#8
Jayanta Nanda, Boris Rubinov, Denis Ivnitski, Rakesh Mukherjee, Elina Shtelman, Yair Motro, Yifat Miller, Nathaniel Wagner, Rivka Cohen-Luria, Gonen Ashkenasy
Biopolymer syntheses in living cells are perfected by an elaborate error correction machinery, which was not applicable during polymerization on early Earth. Scientists are consequently striving to identify mechanisms by which functional polymers were selected and further amplified from complex prebiotic mixtures. Here we show the instrumental role of non-enzymatic replication in the enrichment of certain product(s). To this end, we analyzed a complex web of reactions in β-sheet peptide networks, focusing on the formation of specific intermediate compounds and template-assisted replication...
September 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28872145/synthesis-of-infectious-bacteriophages-in-an-e-coli-based-cell-free-expression-system
#9
Mark Rustad, Allen Eastlund, Ryan Marshall, Paul Jardine, Vincent Noireaux
A new generation of cell-free transcription-translation (TXTL) systems, engineered to have a greater versatility and modularity, provide novel capabilities to perform basic and applied sciences in test tube reactions. Over the past decade, cell-free TXTL has become a powerful technique for a broad range of novel multidisciplinary research areas related to quantitative and synthetic biology. The new TXTL platforms are particularly useful to construct and interrogate biochemical systems through the execution of synthetic or natural gene circuits...
August 17, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28858246/thirty-minutes-of-hypobaric-hypoxia-provokes-alterations-of-immune-response-haemostasis-and-metabolism-proteins-in-human-serum
#10
Jochen Hinkelbein, Stefanie Jansen, Ivan Iovino, Silvia Kruse, Moritz Meyer, Fabrizio Cirillo, Hendrik Drinhaus, Andreas Hohn, Corinna Klein, Edoardo De Robertis, Dirk Beutner
Hypobaric hypoxia (HH) during airline travel induces several (patho-) physiological reactions in the human body. Whereas severe hypoxia is investigated thoroughly, very little is known about effects of moderate or short-term hypoxia, e.g. during airline flights. The aim of the present study was to analyse changes in serum protein expression and activation of signalling cascades in human volunteers staying for 30 min in a simulated altitude equivalent to airline travel. After approval of the local ethics committee, 10 participants were exposed to moderate hypoxia (simulation of 2400 m or 8000 ft for 30 min) in a hypobaric pressure chamber...
August 31, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28846378/printable-heterostructured-bioelectronic-interfaces-with-enhanced-electrode-reaction-kinetics-by-intermicroparticle-network
#11
Rodtichoti Wannapob, Mikhail Yu Vagin, Yu Liu, Panote Thavarungkul, Proespichaya Kanatharana, Anthony P F Turner, Wing Cheung Mak
Printable organic bioelectronics provide a fast and cost-effective approach for the fabrication of novel biodevices, while the general challenge is to achieve optimized reaction kinetics at multiphase boundaries between biomolecules and electrodes. Here, we present an entirely new concept based on a modular approach for the construction of heterostructured bioelectronic interfaces by using tailored functional "biological microparticles" combined with "transducer microparticles" as modular building blocks. This approach offers high versatility for the design and fabrication of bioelectrodes with a variety of forms of interparticle spatial organization, from layered-structures to more advance bulk heterostructured architectures...
September 13, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28845192/grip-on-complexity-in-chemical-reaction-networks
#12
REVIEW
Albert S Y Wong, Wilhelm T S Huck
A new discipline of "systems chemistry" is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function...
2017: Beilstein Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28835163/an-epigenome-wide-association-study-of-inflammatory-response-to-fenofibrate-in-the-genetics-of-lipid-lowering-drugs-and-diet-network
#13
Nabiha Yusuf, Bertha Hidalgo, Marguerite R Irvin, Jin Sha, Degui Zhi, Hemant K Tiwari, Devin Absher, Donna K Arnett, Stella W Aslibekyan
AIM: Fenofibrate, a PPAR-α inhibitor used for treating dyslipidemia, has well-documented anti-inflammatory effects that vary between individuals. While DNA sequence variation explains some of the observed variability in response, epigenetic patterns present another promising avenue of inquiry due to the biological links between the PPAR-α pathway, homocysteine and S-adenosylmethionine - a source of methyl groups for the DNA methylation reaction. HYPOTHESIS: DNA methylation variation at baseline is associated with the inflammatory response to a short-term fenofibrate treatment...
September 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/28821301/space-type-radiation-induces-multimodal-responses-in-the-mouse-gut-microbiome-and-metabolome
#14
David Casero, Kirandeep Gill, Vijayalakshmi Sridharan, Igor Koturbash, Gregory Nelson, Martin Hauer-Jensen, Marjan Boerma, Jonathan Braun, Amrita K Cheema
BACKGROUND: Space travel is associated with continuous low dose rate exposure to high linear energy transfer (LET) radiation. Pathophysiological manifestations after low dose radiation exposure are strongly influenced by non-cytocidal radiation effects, including changes in the microbiome and host gene expression. Although the importance of the gut microbiome in the maintenance of human health is well established, little is known about the role of radiation in altering the microbiome during deep-space travel...
August 18, 2017: Microbiome
https://www.readbyqxmd.com/read/28812671/sulfate-radicals-enable-a-non-enzymatic-krebs-cycle-precursor
#15
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
#16
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
#17
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...
September 2017: Journal of Contaminant Hydrology
https://www.readbyqxmd.com/read/28797226/network-design-and-analysis-for-multi-enzyme-biocatalysis
#18
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
#19
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
#20
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
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