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Biological reaction network

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https://www.readbyqxmd.com/read/28328240/insights-on-cryopreserved-sheep-fibroblasts-by-cryomicroscopy-and-gene-expression-analysis
#1
Antonella Idda, Daniela Bebbere, Giuseppina Corona, Laura Masala, Elisa Casula, Alberto Cincotti, Sergio Ledda
Cryopreservation includes a set of techniques aimed at storing biological samples and preserving their biochemical and functional features without any significant alterations. This study set out to investigate the effects induced by cryopreservation on cultured sheepskin fibroblasts (CSSF) through cryomicroscopy and gene expression analysis after subsequent in vitro culture. CSSF cells were cryopreserved in a cryomicroscope (CM) or in a straw programmable freezer (SPF) using a similar thermal profile (cooling rate -5°C/min to -120°C, then -150°C/min to -196°C)...
March 22, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28316886/identification-of-dysregulated-genes-in-rheumatoid-arthritis-based-on-bioinformatics-analysis
#2
Ruihu Hao, Haiwei Du, Lin Guo, Fengde Tian, Ning An, Tiejun Yang, Changcheng Wang, Bo Wang, Zihao Zhou
BACKGROUND: Rheumatoid arthritis (RA) is a chronic auto-inflammatory disorder of joints. The present study aimed to identify the key genes in RA for better understanding the underlying mechanisms of RA. METHODS: The integrated analysis of expression profiling was conducted to identify differentially expressed genes (DEGs) in RA. Moreover, functional annotation, protein-protein interaction (PPI) network and transcription factor (TF) regulatory network construction were applied for exploring the potential biological roles of DEGs in RA...
2017: PeerJ
https://www.readbyqxmd.com/read/28299727/metal-fluorides-tools-for-structural-and-computational-analysis-of-phosphoryl-transfer-enzymes
#3
REVIEW
Yi Jin, Robert W Molt, G Michael Blackburn
The phosphoryl group, PO3(-), is the dynamic structural unit in the biological chemistry of phosphorus. Its transfer from a donor to an acceptor atom, with oxygen much more prevalent than nitrogen, carbon, or sulfur, is at the core of a great majority of enzyme-catalyzed reactions involving phosphate esters, anhydrides, amidates, and phosphorothioates. The serendipitous discovery that the phosphoryl group could be labeled by "nuclear mutation," by substitution of PO3(-) by MgF3(-) or AlF4(-), has underpinned the application of metal fluoride (MF x ) complexes to mimic transition states for enzymatic phosphoryl transfer reactions, with sufficient stability for experimental analysis...
April 2017: Topics in Current Chemistry (Journal)
https://www.readbyqxmd.com/read/28297929/flexible-dynamics-of-two-quorum-sensing-coupled-repressilators
#4
Edward H Hellen, Evgeny Volkov
Genetic oscillators play important roles in cell life regulation. The regulatory efficiency usually depends strongly on the emergence of stable collective dynamic modes, which requires designing the interactions between genetic networks. We investigate the dynamics of two identical synthetic genetic repressilators coupled by an additional plasmid which implements quorum sensing (QS) in each network thereby supporting global coupling. In a basic genetic ring oscillator network in which three genes inhibit each other in unidirectional manner, QS stimulates the transcriptional activity of chosen genes providing for competition between inhibitory and stimulatory activities localized in those genes...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28297095/adverse-reactions-to-orthodontic-materials
#5
I Sifakakis, T Eliades
Adverse effects can arise from the clinical use of orthodontic materials, due to the release of constituent substances (ions from alloys and monomers, degradation by-products, and additives from polymers). Moreover, intraoral aging affects the biologic properties of materials. The aim of this review is to present the currently identified major adverse effects of the metallic and polymeric components found in orthodontic appliances and materials. Corrosion in metallic orthodontic attachments releases metal ions, mainly iron, chromium, and nickel...
March 2017: Australian Dental Journal
https://www.readbyqxmd.com/read/28274840/systemic-qsar-and-phenotypic-virtual-screening-chasing-butterflies-in-drug-discovery
#6
REVIEW
Maykel Cruz-Monteagudo, Stephan Schürer, Eduardo Tejera, Yunierkis Pérez-Castillo, José L Medina-Franco, Aminael Sánchez-Rodríguez, Fernanda Borges
Current advances in systems biology suggest a new change of paradigm reinforcing the holistic nature of the drug discovery process. According to the principles of systems biology, a simple drug perturbing a network of targets can trigger complex reactions. Therefore, it is possible to connect initial events with final outcomes and consequently prioritize those events, leading to a desired effect. Here, we introduce a new concept, 'Systemic Chemogenomics/Quantitative Structure-Activity Relationship (QSAR)'. To elaborate on the concept, relevant information surrounding it is addressed...
March 6, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28268606/mechanisms-of-stochastic-focusing-and-defocusing-in-biological-reaction-networks-insight-from-accurate-chemical-master-equation-acme-solutions
#7
Gamze Gursoy, Anna Terebus, Youfang Cao, Jie Liang
Stochasticity plays important roles in regulation of biochemical reaction networks when the copy numbers of molecular species are small. Studies based on Stochastic Simulation Algorithm (SSA) has shown that a basic reaction system can display stochastic focusing (SF) by increasing the sensitivity of the network as a result of the signal noise. Although SSA has been widely used to study stochastic networks, it is ineffective in examining rare events and this becomes a significant issue when the tails of probability distributions are relevant as is the case of SF...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28268600/biologically-inspired-design-of-feedback-control-systems-implemented-using-dna-strand-displacement-reactions
#8
Mathias Foo, Rucha Sawlekar, Vishwesh V Kulkarni, Declan G Bates
The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28263984/managing-uncertainty-in-metabolic-network-structure-and-improving-predictions-using-ensemblefba
#9
Matthew B Biggs, Jason A Papin
Genome-scale metabolic network reconstructions (GENREs) are repositories of knowledge about the metabolic processes that occur in an organism. GENREs have been used to discover and interpret metabolic functions, and to engineer novel network structures. A major barrier preventing more widespread use of GENREs, particularly to study non-model organisms, is the extensive time required to produce a high-quality GENRE. Many automated approaches have been developed which reduce this time requirement, but automatically-reconstructed draft GENREs still require curation before useful predictions can be made...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28259128/directed-regulation-of-multienzyme-complexes-of-2-oxo-acid-dehydrogenases-using-phosphonate-and-phosphinate-analogs-of-2-oxo-acids
#10
REVIEW
A V Artiukhov, A V Graf, V I Bunik
2-Oxo acid dehydrogenase complexes are important metabolic checkpoints functioning at the intercept of sugar and amino acid degradation. This review presents a short summary of architectural, catalytic, and regulatory principles of the complexes structure and function, based on recent advances in studies of well-characterized family members. Special attention is given to use of synthetic phosphonate and phosphinate analogs of 2-oxo acids as selective and efficient inhibitors of the cognate complexes in biological systems of bacterial, plant, and animal origin...
December 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28251479/changes-in-lncrnas-and-related-genes-in-%C3%AE-thalassemia-minor-and-%C3%AE-thalassemia-major
#11
Jing Ma, Fei Liu, Xin Du, Duan Ma, Likuan Xiong
β-thalassemia is caused by β-globin gene mutations. However, heterogeneous phenotypes were found in individuals with same genotype, and still undescribed mechanism underlies such variation. We collected blood samples from 30 β-thalassemia major, 30 β-thalassemia minor patients, and 30 matched normal controls. Human lncRNA Array v2.0 (8 × 60 K, Arraystar) was used to detect changes in long non-coding RNAs (lncRNAs) and mRNAs in three samples each from β-thalassemia major, β-thalassemia minor, and control groups...
March 2, 2017: Frontiers of Medicine
https://www.readbyqxmd.com/read/28249418/efficient-stochastic-simulation-of-biochemical-reactions-with-noise-and-delays
#12
Vo Hong Thanh, Roberto Zunino, Corrado Priami
The stochastic simulation algorithm has been used to generate exact trajectories of biochemical reaction networks. For each simulation step, the simulation selects a reaction and its firing time according to a probability that is proportional to the reaction propensity. We investigate in this paper new efficient formulations of the stochastic simulation algorithm to improve its computational efficiency. We examine the selection of the next reaction firing and reduce its computational cost by reusing the computation in the previous step...
February 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28247842/leukemia-inhibitory-factor-promotes-aggressiveness-of-chordoma
#13
Sukru Gulluoglu, Mesut Sahin, Emre Can Tuysuz, Cumhur Kaan Yaltirik, Aysegul Kuskucu, Ferda Ozkan, Fikrettin Sahin, Ugur Ture, Omer Faruk Bayrak
Chordomas are rare tumors of the spine and skull base that are locally destructive and resistant to chemo- and radiation therapy, with a poor prognosis and limited therapeutic options. Chordoma patients have a long life expectancy with high mortality from the disease. Cancer stem cells, which are known to exist in chordomas, have extensive proliferative and self-renewal potential, and are responsible for maintaining tumor heterogeneity along with chemotherapy and radiotherapy resistance. The leukemia inhibitory factor has multiple functions in stem-cell biology, the immune response, and cancer, and is potentially a key molecule that allows cancer stem cells to self-renew...
February 28, 2017: Oncology Research
https://www.readbyqxmd.com/read/28239705/chemical-communication-and-dynamics-of-droplet-emulsions-in-networks-of-belousov-zhabotinsky-micro-oscillators-produced-by-microfluidics
#14
Kristian Torbensen, Federico Rossi, Sandra Ristori, Ali Abou-Hassan
Chemical communication leading to synchronization and collective behaviour of dynamic elements, such as cell colonies, is a widespread phenomenon with biological, physical and chemical importance. Such synchronization between elements proceeds via chemical communication by emmision, interdiffusion and reception of specific messenger molecules. On a lab scale, these phenomena can be modeled by encapsulating an oscillating chemical reaction, which serves as a signal (information) sender/receiver element, inside microcompartments such as droplet emulsions, liposomes and polymersomes...
February 27, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28226785/mechanisms-of-stochastic-focusing-and-defocusing-in-biological-reaction-networks-insight-from-accurate-chemical-master-equation-acme-solutions
#15
Gamze Giirsoy, Anna Terebus, Youfang Cao, Jie Liang, Gamze Gursoy, Anna Terebus, Youfang Cao, Jie Liang, Gamze Gursoy, Youfang Cao, Anna Terebus, Jie Liang
Stochasticity plays important roles in regulation of biochemical reaction networks when the copy numbers of molecular species are small. Studies based on Stochastic Simulation Algorithm (SSA) has shown that a basic reaction system can display stochastic focusing (SF) by increasing the sensitivity of the network as a result of the signal noise. Although SSA has been widely used to study stochastic networks, it is ineffective in examining rare events and this becomes a significant issue when the tails of probability distributions are relevant as is the case of SF...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226779/biologically-inspired-design-of-feedback-control-systems-implemented-using-dna-strand-displacement-reactions
#16
Mathias Foo, Rucha Sawlekar, Vishwesh V Kulkarni, Declan G Bates, Mathias Foo, Rucha Sawlekar, Vishwesh V Kulkarni, Declan G Bates, Vishwesh V Kulkarni, Rucha Sawlekar, Declan G Bates, Mathias Foo
The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28214907/a-pilot-study-of-bacterial-regrowth-in-water-pipelines
#17
Laura Mancini, Stefania Marcheggiani, Cinzia Grasso, Cristina Romanelli, Antonio Mistretta, Marina Marranzano
Bacterial regrowth in water distribution systems results in deterioration of bacteriological quality of drinking water, as well as accelerated corrosion of the pipelines. The aim of the present study was to analyze the phenomena of colonization and bacterial regrowth in source water and in the water distribution systems of three distribution networks in the province of Catania (Sicily, Italy). The BART™ (Biological Activity Reaction Test) method was used, which is also capable of determining the potential aggressiveness of microbial species in water...
November 2016: Igiene e Sanità Pubblica
https://www.readbyqxmd.com/read/28212624/understanding-the-response-to-endurance-exercise-using-a-systems-biology-approach-combining-blood-metabolomics-transcriptomics-and-mirnomics-in-horses
#18
Núria Mach, Yuliaxis Ramayo-Caldas, Allison Clark, Marco Moroldo, Céline Robert, Eric Barrey, Jesús Maria López, Laurence Le Moyec
BACKGROUND: Endurance exercise in horses requires adaptive processes involving physiological, biochemical, and cognitive-behavioral responses in an attempt to regain homeostasis. We hypothesized that the identification of the relationships between blood metabolome, transcriptome, and miRNome during endurance exercise in horses could provide significant insights into the molecular response to endurance exercise. For this reason, the serum metabolome and whole-blood transcriptome and miRNome data were obtained from ten horses before and after a 160 km endurance competition...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212602/happi-2-a-comprehensive-and-high-quality-map-of-human-annotated-and-predicted-protein-interactions
#19
Jake Y Chen, Ragini Pandey, Thanh M Nguyen
BACKGROUND: Human protein-protein interaction (PPI) data is essential to network and systems biology studies. PPI data can help biochemists hypothesize how proteins form complexes by binding to each other, how extracellular signals propagate through post-translational modification of de-activated signaling molecules, and how chemical reactions are coupled by enzymes involved in a complex biological process. Our capability to develop good public database resources for human PPI data has a direct impact on the quality of future research on genome biology and medicine...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28203405/weighted-gene-co-expression-network-analysis-in-identification-of-metastasis-related-genes-of-lung-squamous-cell-carcinoma-based-on-the-cancer-genome-atlas-database
#20
Feng Tian, Jinlong Zhao, Xinlei Fan, Zhenxing Kang
BACKGROUND: Lung squamous cell carcinoma (lung SCC) is a common type of malignancy. Its pathogenesis mechanism of tumor development is unclear. The aim of this study was to identify key genes for diagnosis biomarkers in lung SCC metastasis. METHODS: We searched and downloaded mRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database to identify differences in mRNA expression of primary tumor tissues from lung SCC with and without metastasis...
January 2017: Journal of Thoracic Disease
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