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Biological reaction network

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https://www.readbyqxmd.com/read/28107392/upon-accounting-for-the-impact-of-isoenzyme-loss-gene-deletion-costs-anticorrelate-with-their-evolutionary-rates
#1
Christopher Jacobs, Luke Lambourne, Yu Xia, Daniel Segrè
System-level metabolic network models enable the computation of growth and metabolic phenotypes from an organism's genome. In particular, flux balance approaches have been used to estimate the contribution of individual metabolic genes to organismal fitness, offering the opportunity to test whether such contributions carry information about the evolutionary pressure on the corresponding genes. Previous failure to identify the expected negative correlation between such computed gene-loss cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae has been ascribed to a real biological gap between a gene's fitness contribution to an organism "here and now" and the same gene's historical importance as evidenced by its accumulated mutations over millions of years of evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28103880/the-use-of-genome-scale-metabolic-network-reconstruction-to-predict-fluxes-and-equilibrium-composition-of-n-fixing-versus-c-fixing-cells-in-a-diazotrophic-cyanobacterium-trichodesmium-erythraeum
#2
Joseph J Gardner, Nanette R Boyle
BACKGROUND: Computational, genome based predictions of organism phenotypes has enhanced the ability to investigate the biological phenomena that help organisms survive and respond to their environments. In this study, we have created the first genome-scale metabolic network reconstruction of the nitrogen fixing cyanobacterium T. erythraeum and used genome-scale modeling approaches to investigate carbon and nitrogen fluxes as well as growth and equilibrium population composition. RESULTS: We created a genome-scale reconstruction of T...
January 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28098890/characterization-of-the-microrna-profile-in-early-stage-cervical-squamous-cell-carcinoma-by-next-generation-sequencing
#3
Wansong Lin, Mei Feng, Guilin Chen, Zhifeng Zhou, Jieyu Li, Yunbin Ye
Squamous cell carcinoma (SCC) is histologically the most prominent type of cervical cancer. There is accumulating evidence suggesting that microRNAs (miRNAs) play important regulatory roles in the biological processes of cervical squamous cell carcinoma (CSCC). Deciphering the miRNA regulatory network in CSCC could deepen our understanding at the molecular level of CSCC initiation and progression. In the present study, we performed next‑generation sequencing (NGS) to profile miRNA expression in 3 pairs of early-stage CSCC samples...
January 16, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28094815/drd2-co-expression-network-and-a-related-polygenic-index-predict-imaging-behavioral-and-clinical-phenotypes-linked-to-schizophrenia
#4
G Pergola, P Di Carlo, E D'Ambrosio, B Gelao, L Fazio, M Papalino, A Monda, G Scozia, B Pietrangelo, M Attrotto, J A Apud, Q Chen, V S Mattay, A Rampino, G Caforio, D R Weinberger, G Blasi, A Bertolino
Genetic risk for schizophrenia (SCZ) is determined by many genetic loci whose compound biological effects are difficult to determine. We hypothesized that co-expression pathways of SCZ risk genes are associated with system-level brain function and clinical phenotypes of SCZ. We examined genetic variants related to the dopamine D2 receptor gene DRD2 co-expression pathway and associated them with working memory (WM) behavior, the related brain activity and treatment response. Using two independent post-mortem prefrontal messenger RNA (mRNA) data sets (total N=249), we identified a DRD2 co-expression pathway enriched for SCZ risk genes...
January 17, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28071851/preprogramming-complex-hydrogel-responses-using-enzymatic-reaction-networks
#5
Sjoerd G J Postma, Ilia N Vialshin, Casper Y Gerritsen, Min Bao, Wilhelm T S Huck
The creation of adaptive matter is heavily inspired by biological systems. However, it remains challenging to design complex material responses that are governed by reaction networks, which lie at the heart of cellular complexity. The main reason for this slow progress is the lack of a general strategy to integrate reaction networks with materials. Herein we use a systematic approach to preprogram the response of a hydrogel to a trigger, in this case the enzyme trypsin, which activates a reaction network embedded within the hydrogel...
January 10, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28065897/trfba-an-algorithm-to-integrate-genome-scale-metabolic-and-transcriptional-regulatory-networks-with-incorporation-of-expression-data
#6
Ehsan Motamedian, Maryam Mohammadi, Seyed Abbas Shojaosadati, Mona Heydari
MOTIVATION: Integration of different biological networks and data-types has been a major challenge in systems biology. The present study introduces the transcriptional regulated flux balance analysis (TRFBA) algorithm that integrates transcriptional regulatory and metabolic models using a set of expression data for various perturbations. RESULTS: TRFBA considers the expression levels of genes as a new continuous variable and introduces two new linear constraints...
January 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28065750/physicochemical-properties-and-biological-activities-of-novel-blend-films-using-oxidized-pectin-chitosan
#7
Asma Chetouani, Nadège Follain, Stéphane Marais, Christophe Rihouey, Meriem Elkolli, Mahmoud Bounekhel, Djafer Benachour, Didier Le Cerf
Pectin has been widely used in a variety of biomedical applications. In this study, it was modified with sodium periodate as an oxidant and characterized by physicochemical methods Periodate oxidation increased the contents of dialdehyde units and carboxyl groups in pectin, and a decrease in pectin viscosity was measured. The oxidization reaction led to a significant decrease in all values of molecular weight and size (Mn, Mw, [η] and Rh) as determined by size exclusion chromatography (SEC), which allowed the selection of the oxidized pectin to be added to chitosan...
January 5, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28051268/immunoregulatory-effect-of-neuronal-like-cells-in-inducting-differentiation-of-bone-marrow-mesenchymal-stem-cells
#8
J Xu, H Lu, Z-N Miao, W-J Wu, Y -Z Jiang, F Ge, W-F Fang, A-H Zhu, G Chen, J-H Zhou, Y-Z Lu, Z-F Tang, Y Wang
OBJECTIVE: To evaluate the immune activity of bone marrow mesenchymal stem cells (BMSCs), and explore the biological characteristics and capabilities of BMSCs and the potential to be differentiated into neuronal cells in vitro. MATERIALS AND METHODS: The BMSCs were isolated and proliferated in vitro to generate the xenogeneic mixed lymphocyte reaction. Moreover, peripheral BMSCs (pBMSCs) were added according to different ratios, which methods were stated as follows: 1: Dulbecco's Modified Eagle Medium (DMEM) + 10% Fetal Bovine Serum (FBS) + 1 μmol/L all-trans-retinoic acid (ATRA) + 20 μg/L basic fibroblast growth factor (bFGF) + 20 μg/L epidermal growth factor (EGF); 2: DMEM + 2% dimethyl sulfoxide (DMSO) + 100 μmol/L butylated hydroxyanisole (BHA)...
December 2016: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28049424/a-mixed-integer-linear-programming-approach-to-the-reduction-of-genome-scale-metabolic-networks
#9
Annika Röhl, Alexander Bockmayr
BACKGROUND: Constraint-based analysis has become a widely used method to study metabolic networks. While some of the associated algorithms can be applied to genome-scale network reconstructions with several thousands of reactions, others are limited to small or medium-sized models. In 2015, Erdrich et al. introduced a method called NetworkReducer, which reduces large metabolic networks to smaller subnetworks, while preserving a set of biological requirements that can be specified by the user...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28041911/disinhibition-of-the-intergeniculate-leaflet-network-in-the-wag-rij-rat-model-of-absence-epilepsy
#10
Lukasz Chrobok, Katarzyna Palus, Jagoda Stanislawa Jeczmien-Lazur, Anna Chrzanowska, Mariusz Kepczynski, Marian Henryk Lewandowski
The intergeniculate leaflet (IGL) of the thalamus is a retinorecipient structure implicated in orchestrating circadian rhythmicity. The IGL network is highly GABAergic and consists mainly of neuropeptide Y-synthesising and enkephalinergic neurons. A high density of GFAP-immunoreactive astrocytes has been observed in the IGL, with a probable function in guarding neuronal inhibition. Interestingly, putatively enkephalinergic IGL neurons generate action potentials with an infra-slow oscillatory (ISO) pattern in vivo in urethane anesthetised Wistar rats, under light-on conditions only...
December 30, 2016: Experimental Neurology
https://www.readbyqxmd.com/read/28039779/reaction-times-in-visual-search-can-be-explained-by-a-simple-model-of-neural-synchronization
#11
Yakov Kazanovich, Roman Borisyuk
We present an oscillatory neural network model that can account for reaction times in visual search experiments. The model consists of a central oscillator that represents the central executive of the attention system and a number of peripheral oscillators that represent objects in the display. The oscillators are described as generalized Kuramoto type oscillators with adapted parameters. An object is considered as being included in the focus of attention if the oscillator associated with this object is in-phase with the central oscillator...
December 10, 2016: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28033256/identified-molecular-mechanism-of-interaction-between-environmental-risk-factors-and-differential-expression-genes-in-cartilage-of-kashin-beck-disease
#12
Fang-Fang Yu, Yan-Xiang Zhang, Lian-He Zhang, Wen-Rong Li, Xiong Guo, Mikko J Lammi
As environmental risk factors (ERFs) play an important role in the pathogenesis of Kashin-Beck disease (KBD), it is important to identify the interaction between ERFs and differentially expression genes (DEGs) in KBD. The environmental response genes (ERGs) were analyzed in cartilage of KBD in comparison to normal controls.We searched 5 English and 3 Chinese databases from inception to September 2015, to identify case-control studies that examined ERFs for KBD using integrative meta-analysis and systematic review...
December 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28029779/hydrogel-droplet-microfluidics-for-high-throughput-single-molecule-cell-analysis
#13
Zhi Zhu, Chaoyong James Yang
Heterogeneity among individual molecules and cells has posed significant challenges to traditional bulk assays, due to the assumption of average behavior, which would lose important biological information in heterogeneity and result in a misleading interpretation. Single molecule/cell analysis has become an important and emerging field in biological and biomedical research for insights into heterogeneity between large populations at high resolution. Compared with the ensemble bulk method, single molecule/cell analysis explores the information on time trajectories, conformational states, and interactions of individual molecules/cells, all key factors in the study of chemical and biological reaction pathways...
December 28, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28028826/identification-of-the-potential-biomarkers-for-the-metastasis-of-rectal-adenocarcinoma
#14
Yang Hua, Xiukun Ma, Xianglong Liu, Xiangfei Yuan, Hai Qin, Xipeng Zhang
Rectal cancer is a common malignant tumor of the digestive tract, with a high incidence and high mortality. This study aimed to identify the potential biomarkers and therapeutic targets for rectal adenocarcinoma (RAC) metastasis. The expression profiling of RAC patients with metastasis and RAC patients without metastasis was downloaded from The Cancer Genome Atlas (TCGA) database. The datasets were used to identify the genes associated with RAC metastasis. Fifty up-regulated genes and seventeen down-regulated genes were identified in the primary tumor loci of RAC metastasis compared with non-metastasis...
December 28, 2016: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://www.readbyqxmd.com/read/28019687/improving-with-practice-a-neural-model-of-mathematical-development
#15
Sean Aubin, Aaron R Voelker, Chris Eliasmith
The ability to improve in speed and accuracy as a result of repeating some task is an important hallmark of intelligent biological systems. Although gradual behavioral improvements from practice have been modeled in spiking neural networks, few such models have attempted to explain cognitive development of a task as complex as addition. In this work, we model the progression from a counting-based strategy for addition to a recall-based strategy. The model consists of two networks working in parallel: a slower basal ganglia loop and a faster cortical network...
December 26, 2016: Topics in Cognitive Science
https://www.readbyqxmd.com/read/28011642/structure-and-polymannuronate-specificity-of-a-eukaryotic-member-of-the-polysaccharide-lyase-family-14
#16
Hui-Min Qin, Takuya Miyakawa, Akira Inoue, Ryuji Nishiyama, Akira Nakamura, Atsuko Asano, Yoriko Sawano, Takao Ojima, Masaru Tanokura
Alginate is an abundant algal polysaccharide, composed of β-D-mannuronate and its C5 epimer α-L-guluronate, that is a useful biomaterial in cell biology and tissue engineering, with applications in cancer and aging research. The alginate lyase (EC 4.2.2.3) from Aplysia kurodai, AkAly30, is a eukaryotic member of the polysaccharide lyase 14 (PL-14) family and degrades alginate by cleaving the glycosidic bond through a β-elimination reaction. Here, we present the structural basis for the substrate specificity, with a preference for polymannuronate, of AkAly30...
December 23, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28009235/expression-profile-of-long-noncoding-rnas-in-human-cerebral-aneurysms-a-microarray-analysis
#17
Hao Li, Haiyan Yue, Yajing Hao, Haowen Li, Shuo Wang, Lanbing Yu, Dong Zhang, Yong Cao, Jizong Zhao
OBJECTIVE The pathogenesis of cerebral aneurysms (CAs) remains largely unknown. Long noncoding RNAs (lncRNAs) were reported recently to play crucial roles in many physiological and biological processes. Here, the authors compared the gene-expression profiles of CAs and their control arteries to investigate the potential functions of lncRNAs in the formation of CAs. METHODS A prospective case-control study was designed to identify the changes in expression of lncRNAs and mRNAs between 12 saccular CA samples (case group) and 12 paired superficial temporal artery samples (control group)...
December 23, 2016: Journal of Neurosurgery
https://www.readbyqxmd.com/read/27996025/in-vitro-synthesis-of-a-major-facilitator-transporter-for-specific-active-transport-across-droplet-interface-bilayers
#18
Heather E Findlay, Nicola J Harris, Paula J Booth
Nature encapsulates reactions within membrane-bound compartments, affording sequential and spatial control over biochemical reactions. Droplet Interface Bilayers are evolving into a valuable platform to mimic this key biological feature in artificial systems. A major issue is manipulating flow across synthetic bilayers. Droplet Interface Bilayers must be functionalised, with seminal work using membrane-inserting toxins, ion channels and pumps illustrating the potential. Specific transport of biomolecules, and notably transport against a concentration gradient, across these bilayers has yet to be demonstrated...
December 20, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27994612/barley-brassinosteroid-mutants-provide-an-insight-into-phytohormonal-homeostasis-in-plant-reaction-to-drought-stress
#19
Damian Gruszka, Anna Janeczko, Michal Dziurka, Ewa Pociecha, Jana Oklestkova, Iwona Szarejko
Brassinosteroids (BRs) are a class of steroid phytohormones, which regulate various processes of morphogenesis and physiology-from seed development to regulation of flowering and senescence. An accumulating body of evidence indicates that BRs take part in regulation of physiological reactions to various stress conditions, including drought. Many of the physiological functions of BRs are regulated by a complicated, and not fully elucidated network of interactions with metabolic pathways of other phytohormones...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27993002/recycling-in-asymmetric-catalysis
#20
Christina Moberg
Cyclic reaction networks consisting of an enantioselective product-forming step and a reverse reaction of the undesired enantiomer back to starting reactant are important for the generation of compounds with high enantiomeric purity. In order to avoid an equilibrium racemic state, a unidirectional cyclic process where product formation and regeneration of starting reactant proceed through different mechanistic pathways is required. Such processes must necessarily include a thermodynamically unfavorable step, since the product of the forward reaction is the reactant of the reverse reaction and vice versa...
December 20, 2016: Accounts of Chemical Research
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