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https://www.readbyqxmd.com/read/28640862/a-biosystems-approach-to-identify-the-molecular-signaling-mechanisms-of-tmem30a-during-tumor-migration
#1
Jiao Wang, Qian Wang, Dongfang Lu, Fangfang Zhou, Dong Wang, Ruili Feng, Kai Wang, Robert Molday, Jiang Xie, Tieqiao Wen
Understanding the molecular mechanisms underlying cell migration, which plays an important role in tumor growth and progression, is critical for the development of novel tumor therapeutics. Overexpression of transmembrane protein 30A (TMEM30A) has been shown to initiate tumor cell migration, however, the molecular mechanisms through which this takes place have not yet been reported. Thus, we propose the integration of computational and experimental approaches by first predicting potential signaling networks regulated by TMEM30A using a) computational biology methods, b) our previous mass spectrometry results of the TMEM30A complex in mouse tissue, and c) a number of migration-related genes manually collected from the literature, and subsequently performing molecular biology experiments including the in vitro scratch assay and real-time quantitative polymerase chain reaction (qPCR) to validate the reliability of the predicted network...
2017: PloS One
https://www.readbyqxmd.com/read/28640584/spectroscopic-evidence-for-a-h-bond-network-at-y356-located-at-the-subunit-interface-of-active-e-coli-ribonucleotide-reductase
#2
Thomas U Nick, Kanchana R Ravichandran, JoAnne Stubbe, Müge Kasanmascheff, Marina Bennati
The reaction catalyzed by E. coli ribonucleotide reductase (RNR) composed of α and β subunits that form an active α2β2 complex is a paradigm for proton-coupled electron transfer (PCET) processes in biological transformations. β2 contains the diferric tyrosyl radical (Y122•) cofactor that initiates a radical transfer (RT) over 35 Å via a specific pathway of amino acids (Y122• ↔ [W48] ↔ Y356 in β2 to Y731 ↔Y730↔ C439 in α2). Experimental evidence exists for co-linear and orthogonal PCET in α2 and β2 respectively...
June 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28628855/progress-in-programming-spatiotemporal-patterns-and-machine-assembly-in-cell-free-protein-expression-systems
#3
REVIEW
Alexandra M Tayar, Shirley S Daube, Roy H Bar-Ziv
Building biological systems outside the cell is an emerging interdisciplinary research field aimed to study design principles, and to emulate biological functions for technology. Reconstructing programmable cellular functions, from assembly of protein/nucleic-acid machines to spatially distributed systems, requires implementing minimal systems of molecular interactions encoded in genes, source-sink protein expression dynamics, and materials platforms for reaction-diffusion scenarios. Here, we first review how molecular turnover mechanisms, combined with nonlinear interactions and feedback in cell-free gene networks enable programmable dynamic expression patterns in various compartments...
June 16, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28623901/biomarker-correlation-network-in-colorectal-carcinoma-by-tumor-anatomic-location
#4
Reiko Nishihara, Kimberly Glass, Kosuke Mima, Tsuyoshi Hamada, Jonathan A Nowak, Zhi Rong Qian, Peter Kraft, Edward L Giovannucci, Charles S Fuchs, Andrew T Chan, John Quackenbush, Shuji Ogino, Jukka-Pekka Onnela
BACKGROUND: Colorectal carcinoma evolves through a multitude of molecular events including somatic mutations, epigenetic alterations, and aberrant protein expression, influenced by host immune reactions. One way to interrogate the complex carcinogenic process and interactions between aberrant events is to model a biomarker correlation network. Such a network analysis integrates multidimensional tumor biomarker data to identify key molecular events and pathways that are central to an underlying biological process...
June 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28618495/robustness-of-synthetic-oscillators-in-growing-and-dividing-cells
#5
Joris Paijmans, David K Lubensky, Pieter Rein Ten Wolde
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. Elowitz and Leibler [Nature (London) 403, 335 (2000)NATUAS0028-083610.1038/35002125] showed that by rational design of the reaction network, and using existing biological components, they could create a network that exhibits periodic gene expression, dubbed the repressilator. More recently, Stricker et al. [Nature (London) 456, 516 (2008)NATUAS0028-083610.1038/nature07389] presented another synthetic oscillator, called the dual-feedback oscillator, which is more stable...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28605562/microorganisms-associated-with-pneumonia-in-children-5-years-of-age-in-developing-and-emerging-countries-the-gabriel-pneumonia-multicenter-prospective-case-control-study
#6
Thomas Bénet, Valentina Sánchez Picot, Mélina Messaoudi, Monidarin Chou, Tekchheng Eap, Jianwei Wang, Kunling Shen, Jean-William Pape, Vanessa Rouzier, Shally Awasthi, Nitin Pandey, Ashish Bavdekar, Sonali Sanghavi, Annick Robinson, Mala Rakoto-Andrianarivelo, Maryam Sylla, Souleymane Diallo, Pagbajabyn Nymadawa, Nymadawaagiin Naranbat, Graciela Russomando, Wilma Basualdo, Florence Komurian-Pradel, Hubert Endtz, Philippe Vanhems, Gláucia Paranhos-Baccalà
Background.: Pneumonia, the leading infectious cause of child mortality globally, mainly afflicts developing countries. This prospective observational study aimed to assess the microorganisms associated with pneumonia in children aged <5 years in developing and emerging countries. Methods.: A multicenter, case-control study by the GABRIEL (Global Approach to Biological Research, Infectious diseases and Epidemics in Low-income countries) network was conducted between 2010 and 2014 in Cambodia, China, Haiti, India (2 sites), Madagascar, Mali, Mongolia, and Paraguay...
June 12, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28600136/an-all-encompassing-global-convergence-result-for-processive-multisite-phosphorylation-systems
#7
Mitchell Eithun, Anne Shiu
Phosphorylation, the enzyme-mediated addition of a phosphate group to a molecule, is a ubiquitous chemical mechanism in biology. Multisite phosphorylation, the addition of phosphate groups to multiple sites of a single molecule, may be distributive or processive. Distributive systems, which require an enzyme and substrate to bind several times in order to add multiple phosphate groups, can be bistable. Processive systems, in contrast, require only one binding to add all phosphate groups, and were recently shown to be globally stable...
June 6, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28594845/temperature-amplitude-coupling-for-stable-biological-rhythms-at-different-temperatures
#8
Gen Kurosawa, Atsuko Fujioka, Satoshi Koinuma, Atsushi Mochizuki, Yasufumi Shigeyoshi
Most biological processes accelerate with temperature, for example cell division. In contrast, the circadian rhythm period is robust to temperature fluctuation, termed temperature compensation. Temperature compensation is peculiar because a system-level property (i.e., the circadian period) is stable under varying temperature while individual components of the system (i.e., biochemical reactions) are usually temperature-sensitive. To understand the mechanism for period stability, we measured the time series of circadian clock transcripts in cultured C6 glioma cells...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28587453/tetranuclear-manganese-models-of-the-oec-displaying-hydrogen-bonding-interactions-application-to-electrocatalytic-water-oxidation-to-hydrogen-peroxide
#9
Zhiji Han, Kyle T Horak, Heui Beom Lee, Theodor Agapie
Toward the development of structural and functional models of the oxygen evolving complex (OEC) of photosystem II (PSII), we report the synthesis of site-differentiated tetranuclear manganese complexes featuring three six-coordinate and one five-coordinate Mn centers. To incorporate biologically relevant second coordination sphere interactions, substituents capable of hydrogen bonding are included as pyrazolates with phenylamino groups. Complexes with terminal anionic ligands, OH- or Cl-, bound to the lower coordinate metal center are supported through the hydrogen-bonding network in a fashion reminiscent to the enzymatic active site...
June 6, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28584880/sulfate-radicals-enable-a-non-enzymatic-krebs-cycle-precursor
#10
Markus A Keller, Domen Kampjut, Stuart A Harrison, Markus Ralser
The evolutionary origins of the tricarboxylic acid cycle (TCA), or Krebs cycle, are so far unclear. Despite a few years ago, the existence of a simple non-enzymatic Krebs-cycle catalyst has been dismissed 'as an appeal to magic', citrate and other intermediates have meanwhile been discovered on a carbonaceous meteorite and do interconvert non-enzymatically. To identify the non-enzymatic Krebs cycle catalyst, we used combinatorial, quantitative high-throughput metabolomics to systematically screen iron and sulfate reaction milieus that orient on Archean sediment constituents...
March 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28582616/molecular-engineering-of-robustness-and-resilience-in-enzymatic-reaction-networks
#11
Albert S Y Wong, Aleksandr A Pogodaev, Ilia N Vialshin, Britta Helwig, Wilhelm T S Huck
Living systems rely on complex networks of chemical reactions to control the concentrations 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. One of the greatest challenges in chemistry is the creation of such functionality from chemical reactions. A key limitation is our lack of understanding of how molecular structure impacts on the dynamics of chemical reaction networks, preventing the design of networks that are robust (i...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28577119/gene-networks-for-total-number-born-in-pigs-across-divergent-environments
#12
Lucas L Verardo, Marcos S Lopes, Pramod Mathur, Ole Madsen, Fabyano F Silva, Martien A M Groenen, Egbert F Knol, Paulo S Lopes, Simone E F Guimarães
For reproductive traits such as total number born (TNB), variance due to different environments is highly relevant in animal breeding. In this study, we aimed to perform a gene-network analysis for TNB in pigs across different environments using genomic reaction norm models. Thus, based on relevant single-nucleotide polymorphisms and linkage disequilibrium blocks across environments obtained from GWAS, different sets of candidate genes having biological roles linked to TNB were identified. Network analysis across environment levels resulted in gene interactions consistent with known mammal's fertility biology, captured relevant transcription factors for TNB biology and pointing out different sets of candidate genes for TNB in different environments...
June 2, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28576040/engineered-3d-scaffolds-of-photocrosslinked-chitosan-gelatin-hydrogel-hybrids-for-chronic-wound-dressings-and-regeneration
#13
Isadora C Carvalho, Herman S Mansur
Wound repair is one of the most complex biological processes in human life. To date, no ideal biomaterial solution has been identified, which that encompasses all functions and properties of real skin tissue. Thus, this study focused on the synthesis of new biocompatible hybrid hydrogel scaffolds based on methacrylate-functionalized high molecular mass chitosan with gelatin-A photocrosslinked with UV radiation to tailor matrix network properties. These hybrid hydrogels were produced via freeze-drying and were extensively characterized by swelling and degradation measurements, Fourier transform infrared spectroscopy (FTIR), UV-visible spectroscopy (UV-Vis), scanning electron microscopy (SEM-EDS), and micro-computed tomography (micro-CT)...
September 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28575754/mapping-modeling-and-characterization-of-protein-protein-interactions-on-a-proteomic-scale
#14
REVIEW
T M Cafarelli, A Desbuleux, Y Wang, S G Choi, D De Ridder, M Vidal
Proteins effect a number of biological functions, from cellular signaling, organization, mobility, and transport to catalyzing biochemical reactions and coordinating an immune response. These varied functions are often dependent upon macromolecular interactions, particularly with other proteins. Small-scale studies in the scientific literature report protein-protein interactions (PPIs), but slowly and with bias towards well-studied proteins. In an era where genomic sequence is readily available, deducing genotype-phenotype relationships requires an understanding of protein connectivity at proteome-scale...
May 30, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28573780/mathematical-approach-to-nonlocal-interactions-using-a-reaction-diffusion-system
#15
REVIEW
Yoshitaro Tanaka, Hiroko Yamamoto, Hirokazu Ninomiya
In recent years, spatial long range interactions during developmental processes have been introduced as a result of the integration of microscopic information, such as molecular events and signaling networks. They are often called nonlocal interactions. If the profile of a nonlocal interaction is determined by experiments, we can easily investigate how patterns generate by numerical simulations without detailed microscopic events. Thus, nonlocal interactions are useful tools to understand complex biosystems...
June 2, 2017: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/28560425/investigating-critical-genes-and-gene-interaction-networks-that-mediate-cyclophosphamide-sensitivity-in-chronic-myelogenous-leukemia
#16
Xiao He, Yuying Deng, Wei Yue
Drug resistance is an obstacle in the treatment of chronic myelogenous leukemia (CML), and is a common reason for treatment failure or disease progression. However, the underlying mechanisms of cyclophosphamide resistance remain poorly defined. In the present study, microarray data concerning cyclophosphamide‑sensitive and ‑resistant chronic myelogenous leukemia cell lines were analyzed. A total of 258 differentially‑expressed genes (DEGs) were identified between these two groups, from which 139 DEGs were upregulated and 119 were downregulated...
July 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28558369/long-non-coding-rna-expression-profiling-in-obesity-mice-with-folic-acid-supplement
#17
Feifei Ma, Wei Li, Renqiao Tang, Zhuo Liu, Shengrong Ouyang, Dingding Cao, Yuanyuan Li, Jianxin Wu
BACKGROUND/AIMS: Obesity is a major contributor to the growing prevalence of metabolic and cardiovascular diseases. This study was designed to investigate the effect of folic acid (FA) on obese mice by detecting the genome-wide expression profile of lncRNAs and mRNAs in the heart. METHODS: Heart samples were collected from mice fed with standard diet (SD), high-fat diet (HFD) and high-fat diet with FA intake (HFDF). LncRNAs and mRNAs between HFD and HFDF group were analyzed by lncRNA microarray...
2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28539121/network-mirroring-for-drug-repositioning
#18
Sunghong Park, Dong-Gi Lee, Hyunjung Shin
BACKGROUND: Although drug discoveries can provide meaningful insights and significant enhancements in pharmaceutical field, the longevity and cost that it takes can be extensive where the success rate is low. In order to circumvent the problem, there has been increased interest in 'Drug Repositioning' where one searches for already approved drugs that have high potential of efficacy when applied to other diseases. To increase the success rate for drug repositioning, one considers stepwise screening and experiments based on biological reactions...
May 18, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28536831/abnormal-expression-of-long-non-coding-rnas-in-myocardial-infarction
#19
Tao Wu, Huan-Dong Wu, Zao-Xian Xu, Fei Han, Bi-Qi Zhang, Jian Sun, Shen-Jiang Hu
Myocardial infarction (MI) is the leading cause of fatality worldwide. Our study aimed to investigate the dysregulated long non-coding RNA (lncRNA) in MI and elucidate the mechanism of it in MI. The lncRNA and mRNA expression profiling of the whole left ventricular tissue of MI mice model (8 mice) and Sham group (8 mice) was obtained based on microarray analysis. Differentially expressed lnRNAs/mRNA (DELs/DEMs) were identified in MI. DELs/DEMs co-expression network construction, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were conducted to predict the biological functions of DEMs...
May 23, 2017: Heart and Vessels
https://www.readbyqxmd.com/read/28529578/long-non-coding-rna-expression-profiles-in-gallbladder-carcinoma-identified-using-microarray-analysis
#20
Jiwen Wang, Han Liu, Xiaokun Shen, Yueqi Wang, Dexiang Zhang, Sheng Shen, Tao Suo, Hongtao Pan, Yue Ming, Kan Ding, Houbao Liu
Gallbladder carcinoma (GBC) is the most common biliary tract cancer and exhibits poor patient prognosis. Previous studies have identified that long non-coding RNAs (lncRNAs) serve important regulatory roles in cancer biology. Alterations in lncRNAs are associated with several types of cancer. However, the contribution of lncRNAs to GBC remains unclear. To investigate the lncRNAs that are potentially involved in GBC, lncRNA profiles were identified in three pairs of human GBC and corresponding peri-carcinomatous tissue samples using microarray analysis...
May 2017: Oncology Letters
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