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Biological reaction network

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https://www.readbyqxmd.com/read/28447912/targeting-ret-in-patients-with-ret-rearranged-lung-cancers-results-from-the-global-multicenter-ret-registry
#1
Oliver Gautschi, Julie Milia, Thomas Filleron, Juergen Wolf, David P Carbone, Dwight Owen, Ross Camidge, Vignhesh Narayanan, Robert C Doebele, Benjamin Besse, Jordi Remon-Masip, Pasi A Janne, Mark M Awad, Nir Peled, Chul-Cho Byoung, Daniel D Karp, Michael Van Den Heuvel, Heather A Wakelee, Joel W Neal, Tony S K Mok, James C H Yang, Sai-Hong Ignatius Ou, Georg Pall, Patrizia Froesch, Gérard Zalcman, David R Gandara, Jonathan W Riess, Vamsidhar Velcheti, Kristin Zeidler, Joachim Diebold, Martin Früh, Sebastian Michels, Isabelle Monnet, Sanjay Popat, Rafael Rosell, Niki Karachaliou, Sacha I Rothschild, Jin-Yuan Shih, Arne Warth, Thomas Muley, Florian Cabillic, Julien Mazières, Alexander Drilon
Purpose In addition to prospective trials for non-small-cell lung cancers (NSCLCs) that are driven by less common genomic alterations, registries provide complementary information on patient response to targeted therapies. Here, we present the results of an international registry of patients with RET-rearranged NSCLCs, providing the largest data set, to our knowledge, on outcomes of RET-directed therapy thus far. Methods A global, multicenter network of thoracic oncologists identified patients with pathologically confirmed NSCLC that harbored a RET rearrangement...
May 1, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28436483/itraq-based-proteomic-analysis-reveals-key-proteins-affecting-muscle-growth-and-lipid-deposition-in-pigs
#2
Zhixiu Wang, Peng Shang, Qinggang Li, Liyuan Wang, Yangzom Chamba, Bo Zhang, Hao Zhang, Changxin Wu
Growth rate and meat quality, two economically important traits in pigs, are controlled by multiple genes and biological pathways. In the present study, we performed a proteomic analysis of longissimus dorsi muscle from six-month-old pigs from two Chinese native mini-type breeds (TP and DSP) and two introduced western breeds (YY and LL) using isobaric tag for relative and absolute quantification (iTRAQ). In total, 4,815 peptides corresponding to 969 proteins were detected. Comparison of expression patterns between TP-DSP and YY-LL revealed 288 differentially expressed proteins (DEPs), of which 169 were up-regulated and 119 were down-regulated...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28430194/engineering-genetic-circuit-interactions-within-and-between-synthetic-minimal-cells
#3
Katarzyna P Adamala, Daniel A Martin-Alarcon, Katriona R Guthrie-Honea, Edward S Boyden
Genetic circuits and reaction cascades are of great importance for synthetic biology, biochemistry and bioengineering. An open question is how to maximize the modularity of their design to enable the integration of different reaction networks and to optimize their scalability and flexibility. One option is encapsulation within liposomes, which enables chemical reactions to proceed in well-isolated environments. Here we adapt liposome encapsulation to enable the modular, controlled compartmentalization of genetic circuits and cascades...
May 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28425930/the-peculiar-glycolytic-pathway-in-hyperthermophylic-archaea-understanding-its-whims-by-experimentation-in-silico
#4
Yanfei Zhang, Theresa Kouril, Jacky L Snoep, Bettina Siebers, Matteo Barberis, Hans V Westerhoff
Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5'-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase...
April 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28420402/sser-species-specific-essential-reactions-database
#5
Abraham A Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang, Feng-Biao Guo
BACKGROUND: Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction is catalyzed by multiple enzymes, then inhibiting the reaction would be a better option than targeting the enzymes or the corresponding enzyme-encoding gene. The existing databases such as BRENDA, BiGG, KEGG, Bio-models, Biosilico, and many others offer useful and comprehensive information on biochemical reactions...
April 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28419089/erroneous-energy-generating-cycles-in-published-genome-scale-metabolic-networks-identification-and-removal
#6
Claus Jonathan Fritzemeier, Daniel Hartleb, Balázs Szappanos, Balázs Papp, Martin J Lercher
Energy metabolism is central to cellular biology. Thus, genome-scale models of heterotrophic unicellular species must account appropriately for the utilization of external nutrients to synthesize energy metabolites such as ATP. However, metabolic models designed for flux-balance analysis (FBA) may contain thermodynamically impossible energy-generating cycles: without nutrient consumption, these models are still capable of charging energy metabolites (such as ADP→ATP or NADP+→NADPH). Here, we show that energy-generating cycles occur in over 85% of metabolic models without extensive manual curation, such as those contained in the ModelSEED and MetaNetX databases; in contrast, such cycles are rare in the manually curated models of the BiGG database...
April 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28415475/novel-non-cytotoxic-bioactive-and-biodegradable-hybrid-materials-based-on-polyurethanes-tio2-for-biomedical-applications
#7
Dulce M González-García, L Téllez Jurado, R Jiménez-Gallegos, Luis M Rodríguez-Lorenzo
Titanium compounds have demonstrated great interfacial properties with biological tissues whereas a wide variety of polyurethanes have also been successfully probed in medical applications. However, studies about hybrids based on polyurethanes/TiO2 for medical applications are scarce. The aim of this work is to design novel biodegradable hybrid materials based on polyurethanes/TiO2 (80% organic-20% inorganic) and to perform a preliminary study of the potential applications in bone regeneration. The hybrids have been prepared by a sol-gel reaction using titanium isopropoxide as precursor of the inorganic component and polyurethane as the organic one...
June 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28415301/nonlinear-signaling-on-biological-networks-the-role-of-stochasticity-and-spectral-clustering
#8
Gonzalo Hernandez-Hernandez, Jesse Myers, Enrique Alvarez-Lacalle, Yohannes Shiferaw
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different conformational states. Signaling is typically a cooperative process which requires the occurrence of multiple binding events so that reaction rates have a nonlinear dependence on the amount of signaling molecule. It is this nonlinearity that endows biological signaling networks with robust switchlike properties which are critical to their biological function...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28412017/the-endocannabinoid-system-a-novel-and-key-participant-in-acupuncture-s-multiple-beneficial-effects
#9
REVIEW
Bo Hu, Fuhai Bai, Lize Xiong, Qiang Wang
Acupuncture and its modified forms have been used to treat multiple medical conditions, but whether the diverse effects of acupuncture are intrinsically linked at the cellular and molecular level and how they might be connected have yet to be determined. Recently, an emerging role for the endocannabinoid system (ECS) in the regulation of a variety of physiological/pathological conditions has been identified. Overlap between the biological and therapeutic effects induced by ECS activation and acupuncture has facilitated investigations into the participation of ECS in the acupuncture-induced beneficial effects, which have shed light on the idea that the ECS may be a primary mediator and regulatory factor of acupuncture's beneficial effects...
April 12, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28398072/the-reactive-species-interactome-evolutionary-emergence-biological-significance-and-opportunities-for-redox-metabolomics-and-personalized-medicine
#10
Miriam Margherita Cortese-Krott, Anne Koning, Gunter Georg Kuhnle, Peter Nagy, Christopher Bianco, Andreas Pasch, David A Wink, Jon Fukuto, Alan A Jackson, Harry van Goor, Kenneth R Olson, Martin Feelisch
SIGNIFICANCE: Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not administration of antioxidants is ineffective, suggesting our current understanding of the underlying regulatory processes is incomplete. Recent Advances. Similar to reactive oxygen and nitrogen species (ROS, RNS), reactive sulfur species (RSS) are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism and mitochondrial function...
April 11, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28392606/design-of-an-embedded-inverse-feedforward-biomolecular-tracking-controller-for-enzymatic-reaction-processes
#11
Mathias Foo, Jongrae Kim, Rucha Sawlekar, Declan G Bates
Feedback control is widely used in chemical engineering to improve the performance and robustness of chemical processes. Feedback controllers require a 'subtractor' that is able to compute the error between the process output and the reference signal. In the case of embedded biomolecular control circuits, subtractors designed using standard chemical reaction network theory can only realise one-sided subtraction, rendering standard controller design approaches inadequate. Here, we show how a biomolecular controller that allows tracking of required changes in the outputs of enzymatic reaction processes can be designed and implemented within the framework of chemical reaction network theory...
April 6, 2017: Computers & Chemical Engineering
https://www.readbyqxmd.com/read/28391052/bio-orthogonal-conjugation-and-enzymatically-triggered-release-of-proteins-within-multi-layered-hydrogels
#12
Chen Guo, Heejae Kim, Elisa M Ovadia, Christine M Mourafetis, Mingrui Yang, Wilfred Chen, April M Kloxin
Hydrogels are facile architectures for the controlled presentation of proteins with far-reaching applications, from fundamental biological studies in three-dimensional culture to new regenerative medicine and therapeutic delivery strategies. Here, we demonstrate a versatile approach for spatially-defined presentation of engineered proteins within hydrogels through i) immobilization using bio-orthogonal strain-promoted alkyne-azide click chemistry and ii) dynamic proteasedriven protein release using exogenously applied enzyme...
April 5, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28390165/default-mode-and-task-positive-networks-connectivity-during-the-n-back-task-in-remitted-depressed-patients-with-or-without-emotional-residual-symptoms
#13
Pauline Delaveau, Tiago Arruda Sanchez, Ricardo Steffen, Karine Deschet, Maritza Jabourian, Vincent Perlbarg, Emerson Leandro Gasparetto, Stéphanie Dubal, Jorge Costa E Silva, Philippe Fossati
Clinical remission of depression may be associated with emotional residual symptoms. We studied the association of emotional blunting, rumination with neural networks dynamics in remitted depressed patients and cognitive performance during an N-Back task. Twenty-six outpatients in remission of depression (Hamilton Depressive rating scale score <7) performed an N-Back task during fMRI assessment. All patients had been treated by paroxetine for a minimum of 4 months. Two subgroups of patients [Nonemotionally blunted (NEB) = 14 and emotionally blunted (EB) = 12] were determined...
April 8, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28388123/sensitivity-estimation-for-stochastic-models-of-biochemical-reaction-networks-in-the-presence-of-extrinsic-variability
#14
Jakob Ruess, Heinz Koeppl, Christoph Zechner
Determining the sensitivity of certain system states or outputs to variations in parameters facilitates our understanding of the inner working of that system and is an essential design tool for the de novo construction of robust systems. In cell biology, the output of interest is often the response of a certain reaction network to some input (e.g., stressors or nutrients) and one aims to quantify the sensitivity of this response in the presence of parameter heterogeneity. We argue that for such applications, parametric sensitivities in their standard form do not paint a complete picture of a system's robustness since one assumes that all cells in the population have the same parameters and are perturbed in the same way...
March 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28387499/versatile-bottom-up-synthesis-of-tethered-bilayer-lipid-membranes-on-nanoelectronic-biosensor-devices
#15
Weiwei Zhou, Peter J Burke
Interfacing nanoelectronic devices with cell membranes can enable multiplexed detection of fundamental biological processes (such as signal transduction, electrophysiology, and import/export control) even down to the single ion channel level, which can lead to a variety of applications in pharmacology and clinical diagnosis. Therefore, it is necessary to understand and control the chemical and electrical interface between the device and the lipid bilayer membrane. Here, we develop a simple bottom-up approach to assemble tethered bilayer lipid membranes (tBLMs) on silicon wafers and glass slides, using a covalent tether attachment chemistry based on silane functionalization, followed by step-by-step stacking of two other functional molecular building blocks (oligo-poly(ethylene glycol) (PEG) and lipid)...
April 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28387237/decoding-network-structure-in-on-chip-integrated-flow-cells-with-synchronization-of-electrochemical-oscillators
#16
Yanxin Jia, István Z Kiss
The analysis of network interactions among dynamical units and the impact of the coupling on self-organized structures is a challenging task with implications in many biological and engineered systems. We explore the coupling topology that arises through the potential drops in a flow channel in a lab-on-chip device that accommodates chemical reactions on electrode arrays. The networks are revealed by analysis of the synchronization patterns with the use of an oscillatory chemical reaction (nickel electrodissolution) and are further confirmed by direct decoding using phase model analysis...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28378986/neurophysiological-maturation-in-adolescence-vulnerability-and-counteracting-addiction-to-alcohol
#17
Roman Chwedorowicz, Henryk Skarżyński, Weronika Pucek, Tadeusz Studziński
The results of contemporary studies confirm the formation of two neural networks in the brain during the period of adolescence. The first is defined as emotional, located in the limbic system, develops earlier, quicker, and more intensively than the second one in the prefrontal cortex, called the judgement network, which fulfils the role of control and inhibition of emotional reactions. The domination of the emotional network in adolescence is manifested by hyperactivity of the limbic system, accompanied by intensified undertaking of courageous, reckless, risky, or even sometimes dangerous actions, so very characteristic in the maturation...
March 22, 2017: Annals of Agricultural and Environmental Medicine: AAEM
https://www.readbyqxmd.com/read/28374495/genome-wide-expression-profiling-and-bioinformatics-analysis-of-deregulated-genes-in-human-gastric-cancer-tissue-after-gastroscopy
#18
Yudi Mao, Qihong Zhao, Shi Yin, Xiping Ding, Hua Wang
AIM: The aim of this study was to analyze the gene expression profile and biological processes enriched in gastric cancer. METHODS: We collected five human advanced gastric cancer tissues by gastroscopy and five peritumor normal tissues as controls and examined the gene expression changes by microarray. KEGG Orthology Based Annotation System annotation was used to identify pathways and biological processes regulated by the deregulated genes. Protein-protein interaction network analysis identified protein complex and functional modules...
April 4, 2017: Asia-Pacific Journal of Clinical Oncology
https://www.readbyqxmd.com/read/28372523/in-vivo-ros-production-and-use-of-oxidative-stress-derived-biomarkers-to-detect-the-onset-of-diseases-such-as-alzheimer-s-disease-parkinson-s-disease-and-diabetes
#19
Aya Umeno, Vasudevanpillai Biju, Yasukazu Yoshida
Breakthroughs in biochemistry have furthered our understanding of the onset and progression of various diseases, and have advanced the development of new therapeutics. Oxidative stress and reactive oxygen species (ROS) are ubiquitous in biological systems. ROS can be formed non-enzymatically by chemical, photochemical and electron transfer reactions, or as the byproducts of endogenous enzymatic reactions, phagocytosis, and inflammation. Imbalances in ROS homeostasis, caused by impairments in antioxidant enzymes or non-enzymatic antioxidant networks, increase oxidative stress, leading to the deleterious oxidation and chemical modification of biomacromolecules such as lipids, DNA, and proteins...
April 3, 2017: Free Radical Research
https://www.readbyqxmd.com/read/28367572/a-systematic-reconstruction-and-constraint-based-analysis-of-leishmania-donovani-metabolic-network-identification-of-potential-antileishmanial-drug-targets
#20
Mahesh Sharma, Naeem Shaikh, Shailendra Yadav, Sushma Singh, Prabha Garg
Visceral leishmaniasis, a lethal parasitic disease, is caused by the protozoan parasite Leishmania donovani. The absence of an effective vaccine, drug toxicity and parasite resistance necessitates the identification of novel drug targets. Reconstruction of genome-scale metabolic models and their simulation has been established as an important tool for systems-level understanding of a microorganism's metabolism. In this work, amalgamating the tools and techniques of computational systems biology with rigorous manual curation, a constraint-based metabolic model for Leishmania donovani BPK282A1 has been developed...
April 3, 2017: Molecular BioSystems
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