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https://www.readbyqxmd.com/read/28529578/long-non-coding-rna-expression-profiles-in-gallbladder-carcinoma-identified-using-microarray-analysis
#1
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
https://www.readbyqxmd.com/read/28521733/nfpscanner-a-webtool-for-knowledge-based-deciphering-of-biomedical-networks
#2
Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hao Hong, Xiaochen Bo, Fei Li
BACKGROUND: Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are using a wide range of omics data to elaborately construct various context-specific differential molecular networks. However, they cannot easily gain insight into unfamiliar gene networks with the tools that are currently available for pathways resource and network analysis...
May 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28511181/1-cmdb-a-curated-database-of-genomic-variations-of-the-one-carbon-metabolism-pathway
#3
Manoj K Bhat, Veerendra P Gadekar, Aditya Jain, Bobby Paul, Padmalatha S Rai, Kapaettu Satyamoorthy
BACKGROUND: The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded...
May 17, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28510536/effect-of-nanostructures-orientation-on-electroosmotic-flow-in-a-microfluidic-channel
#4
An Eng Lim, Chun Yee Lim, Yee Cheong Lam, Rafael Taboryski, Shu Rui Wang
Electroosmotic flow (EOF) is an electric-field-induced fluid flow that has numerous micro-/nanofluidic applications, ranging from pumping to chemical and biomedical analyses. Nanoscale networks/structures are often integrated in microchannels for a broad range of applications, such as electrophoretic separation of biomolecules, high reaction efficiency catalytic microreactors, and enhancement of heat transfer and sensing. Their introduction has been known to reduce EOF. Hitherto, a proper study on the effect of nanostructures orientation on EOF in a microfluidic channel is yet to be carried out...
May 16, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28505786/nonequilibrium-nature-of-adaptation-in-bacterial-chemotaxis-a-fluctuation-dissipation-theorem-approach
#5
Chen Jia
Adaptation is a crucial biological function possessed by many sensory systems. In this paper, we show that the fluctuation-dissipation theorem (FDT) serves as an ideal mathematical tool to study adaptation. With the aid of the nonequilibrium FDT developed by Seifert and Speck [Europhys. Lett. 89, 10007 (2010)EULEEJ0295-507510.1209/0295-5075/89/10007], we demonstrate the nonequilibrium nature of adaptation in bacterial chemotaxis. We further show that nonequilibrium is a necessary condition for adaptation even beyond the linear response regime using the spectral theory of generator matrices...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28505258/modelling-and-mathematical-analysis-of-the-m-_-2-receptor-dependent-joint-signalling-and-secondary-messenger-network-in-cho-cells
#6
Benjamin Engelhardt, Janine Holze, Christina Elliott, George S Baillie, Maik Kschischo, Holger Fröhlich
The muscarinic M$_{2}$ receptor is a prominent member of the GPCR family and strongly involved in heart diseases. Recently published experimental work explored the cellular response to iperoxo-induced M$_{2}$ receptor stimulation in Chinese hamster ovary (CHO) cells. To better understand these responses, we modelled and analysed the muscarinic M$_{2}$ receptor-dependent signalling pathway combined with relevant secondary messenger molecules using mass action. In our literature-based joint signalling and secondary messenger model, all binding and phosphorylation events are explicitly taken into account in order to enable subsequent stoichiometric matrix analysis...
May 15, 2017: Mathematical Medicine and Biology: a Journal of the IMA
https://www.readbyqxmd.com/read/28502000/reverse-phase-protein-microarrays
#7
Elisa Baldelli, Valerie Calvert, Alex Hodge, Amy VanMeter, Emanuel F Petricoin, Mariaelena Pierobon
While genes and RNA encode information about cellular status, proteins are considered the engine of the cellular machine, as they are the effective elements that drive all cellular functions including proliferation, migration, differentiation, and apoptosis. Consequently, investigations of the cellular protein network are considered a fundamental tool for understanding cellular functions.Alteration of the cellular homeostasis driven by elaborate intra- and extracellular interactions has become one of the most studied fields in the era of personalized medicine and targeted therapy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28493880/identifying-stochastic-oscillations-in-single-cell-live-imaging-time-series-using-gaussian-processes
#8
Nick E Phillips, Cerys Manning, Nancy Papalopulu, Magnus Rattray
Multiple biological processes are driven by oscillatory gene expression at different time scales. Pulsatile dynamics are thought to be widespread, and single-cell live imaging of gene expression has lead to a surge of dynamic, possibly oscillatory, data for different gene networks. However, the regulation of gene expression at the level of an individual cell involves reactions between finite numbers of molecules, and this can result in inherent randomness in expression dynamics, which blurs the boundaries between aperiodic fluctuations and noisy oscillators...
May 11, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28490602/processes-on-the-emergent-landscapes-of-biochemical-reaction-networks-and-heterogeneous-cell-population-dynamics-differentiation-in-living-matters
#9
REVIEW
Sui Huang, Fangting Li, Joseph X Zhou, Hong Qian
The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat...
May 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28489346/metal-organic-frameworks-at-the-biointerface-synthetic-strategies-and-applications
#10
Christian Doonan, Raffaele Riccò, Kang Liang, Darren Bradshaw, Paolo Falcaro
Many living organisms are capable of producing inorganic materials of precisely controlled structure and morphology. This ubiquitous process is termed biomineralization and is observed in nature from the macroscale (e.g., formation of exoskeletons) down to the nanoscale (e.g., mineral storage and transportation in proteins). Extensive research efforts have pursued replicating this chemistry with the overarching aims of synthesizing new materials of unprecedented physical properties and understanding the complex mechanisms that occur at the biological-inorganic interface...
May 10, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28484081/identification-of-aberrantly-expressed-long-non-coding-rnas-in-stomach-adenocarcinoma
#11
Jianbin Gu, Yong Li, Liqiao Fan, Qun Zhao, Bibo Tan, Kelei Hua, Guobin Wu
AIM: Stomach adenocarcinoma (STAD) is a common malignancy worldwide. This study aimed to identify the aberrantly expressed long non-coding RNAs (lncRNAs) in STAD. RESULTS: Total of 74 DElncRNAs and 449 DEmRNAs were identified in STAD compared with paired non-tumor tissues. The DElncRNA/DEmRNA co-expression network was constructed, which covered 519 nodes and 2993 edges. The qRT-PCR validation results of DElncRNAs were consistent with our bioinformatics analysis based on RNA-sequencing...
April 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28479069/automated-pathway-and-reaction-prediction-facilitates-in-silico-identification-of-unknown-metabolites-in-human-cohort-studies
#12
Jan D Quell, Werner Römisch-Margl, Marco Colombo, Jan Krumsiek, Anne M Evans, Robert Mohney, Veikko Salomaa, Ulf de Faire, Leif C Groop, Felix Agakov, Helen C Looker, Paul McKeigue, Helen M Colhoun, Gabi Kastenmüller
Identification of metabolites in non-targeted metabolomics continues to be a bottleneck in metabolomics studies in large human cohorts. Unidentified metabolites frequently emerge in the results of association studies linking metabolite levels to, for example, clinical phenotypes. For further analyses these unknown metabolites must be identified. Current approaches utilize chemical information, such as spectral details and fragmentation characteristics to determine components of unknown metabolites. Here, we propose a systems biology model exploiting the internal correlation structure of metabolite levels in combination with existing biochemical and genetic information to characterize properties of unknown molecules...
April 4, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28464073/breeding-and-genetics-symposium-breeding-for-resilience-to-heat-stress-effects-in-dairy-ruminants-a-comprehensive-review
#13
M J Carabaño, M Ramón, C Díaz, A Molina, M D Pérez-Guzmán, J M Serradilla
Selection for heat tolerant (HT) animals in dairy production has been so far linked to estimation of declines in production using milk recording and meteorological information on the day of control using reaction norms. Results from these models show that there is a reasonable amount of genetic variability in the individual response to high heat loads, which makes feasible selection of HT animals at low costs. However, the antagonistic relationship between level of production and response to heat stress (HS) implies that selection for HT animals under this approach must be done with caution so that productivity is not damaged...
April 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28447912/targeting-ret-in-patients-with-ret-rearranged-lung-cancers-results-from-the-global-multicenter-ret-registry
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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 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
#20
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
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