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Integrative Biology: Quantitative Biosciences From Nano to Macro

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https://www.readbyqxmd.com/read/29138780/biological-network-border-detection
#1
Paulo E P Burke, Cesar H Comin, Filipi N Silva, Luciano da F Costa
Complex networks have been widely used to model biological systems. The concept of accessibility has been proposed recently as a means to organize the nodes of complex networks as belonging to its border or center. Such an approach paves the way to investigating how the functional and structural properties of nodes vary with their respective position in the networks. In this work, we approach such a problem in a biological context applying border detection to Protein-Protein Interaction networks from four organisms of the Mycoplasma genus...
November 15, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29120470/modulation-of-cellular-polarization-and-migration-by-ephrin-eph-signal-mediated-boundary-formation
#2
Sahar Javaherian, Elisa D'Arcangelo, Benjamin Slater, Camila Londono, Bin Xu, Alison P McGuigan
Compartment boundaries are essential for ensuring proper cell organization during embryo development and in adult tissues, yet the mechanisms underlying boundary establishment are not completely understood. A number of mechanisms, including (i) differential adhesion, (ii) differential tension, and (iii) cell signaling-mediated cell repulsion, are known to contribute and likely a context-dependent balance of each of these dictates boundary implementation. The ephrin/Eph signaling pathway is known to impact boundary formation in higher animals...
November 9, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29114690/effect-of-amino-acid-mutations-on-intra-dimer-tubulin-tubulin-binding-strength-of-microtubules
#3
Ning Liu, Ramana Pidaparti, Xianqiao Wang
Energetic interactions inside αβ-tubulin dimers of a microtubule (MT) with atomic resolutions are of importance in determining the mechanical properties and structural stability of the MT as well as designing self-assembled functional structures from it. Here, we carry out several comprehensive atomistic simulations to investigate the interaction properties within αβ-tubulin dimers and effect of residue mutations on the intra-dimer tubulin-tubulin (IDTT) binding strength. Results indicate that the force-displacement responses of the dimer could be roughly divided into three stages involving increasing, decreasing, and fluctuating forces...
November 8, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29109999/enhanced-directional-cell-migration-induced-by-vaccinia-virus-on-a-microfluidic-based-multi-shear-cell-migration-assay-platform
#4
Cheng Wang, Na Xu, Yu-Jun Yang, Qiu-Mei Wu, Dai-Wen Pang, Zhi-Ling Zhang
Virus-induced cell migration plays important roles in the direct and rapid spread of virus particles. As cell migration is also regulated by shear stress, it is necessary to explore the cell migration behavior influenced by multiple factors including a virus and shear stress. In this report, a three-layer microfluidic chip with symmetric channels was designed and fabricated to investigate vaccinia virus-induced cell migration in different shear stress environments. Regular "exclusion zones" without cell damage were formed by microvalves...
November 7, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29098230/rna-mediated-tilda-for-improved-cell-capacity-and-enhanced-detection-of-multiply-spliced-hiv-rna
#5
Hannah M Pezzi, Scott M Berry, David J Beebe, Rob Striker
Quantification of the HIV viral reservoir is critical to understanding HIV latency, advancing patient care and ultimately achieving a cure. To quantify the reservoir, a new metric was recently introduced, which quantified cells carrying multiply spliced HIV RNA. The developed assay, Tat/rev Induced Limiting Dilution Assay (TILDA), enables quantification of cells containing multiply-spliced HIV RNA events as an indicator of reservoir size. Due to TILDA's reliance on a limiting dilution format paired with the rarity of target events, numerous individual reactions are required to obtain a single endpoint...
November 13, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29098213/single-cell-analysis-of-early-antiviral-gene-expression-reveals-a-determinant-of-stochastic-ifnb1-expression
#6
Sultan Doğanay, Maurice Youzong Lee, Alina Baum, Jessie Peh, Sun-Young Hwang, Joo-Yeon Yoo, Paul J Hergenrother, Adolfo García-Sastre, Sua Myong, Taekjip Ha
RIG-I-like receptors (RLRs) are cytoplasmic sensors of viral RNA that trigger the signaling cascade that leads to type I interferon (IFN) production. Transcriptional induction of RLRs by IFN is believed to play the role of positive feedback to further amplify viral sensing. We found that RLRs and several other IFN-stimulated genes (ISGs) are induced early in viral infection independent of IFN. Expression of these early ISGs requires IRF3/IRF7 and is highly correlated amongst them. Simultaneous detection of mRNA of IFNB1, viral replicase, and ISGs revealed distinct populations of IFNB1 expressing and non-expressing cells which are highly correlated with the levels of early ISGs but are uncorrelated with IFN-dependent ISGs and viral gene expression...
November 13, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29091092/three-dimensional-morphometry-of-collagen-fibrils-in-membranous-bone
#7
Mana Hashimoto, Noriyuki Nagaoka, Kaori Tabata, Tomoyo Tanaka, Ryuta Osumi, Naoya Odagaki, Toru Hara, Hiroshi Kamioka
The collagen network acts as a scaffold for calcification and its three-dimensional structure influences bone strength. It is therefore important to observe the collagen network in detail and three-dimensionally. In this study, we observed the collagen network of chick embryonic calvariae in membranous bone three-dimensionally using orthogonally arranged FIB-SEM. A 25 × 25 μm area of chick embryonic calvaria was observed at a high resolution (25 nm per pixel). The inside of the bone (i.e. the primary calcified tissue), the bone cells (i...
November 13, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29043354/lipidomic-profiles-of-drosophila-melanogaster-and-cactophilic-fly-species-models-of-human-metabolic-diseases
#8
Daniel Cázarez-García, Mariana Ramírez Loustalot-Laclette, Therese Ann Markow, Robert Winkler
The metabolic syndrome (MetS) is associated with serious diseases and represents an important threat for global public health. The common fruit fly (Drosophila melanogaster) has served as a model organism to study physiological processes of the MetS, because central metabolic pathways are conserved among species, and because the flies are easy to cultivate in a laboratory. In nature, D. melanogaster is a fruit generalist, feeding on diets rich in simple carbohydrates. Other Drosophilids, however, have specialized on distinct resources...
November 13, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29022985/correction-a-bioenergetic-mechanism-for-amoeboid-like-cell-motility-profiles-tested-in-a-microfluidic-electrotaxis-assay
#9
Hagit Peretz-Soroka, Reuven Tirosh, Jolly Hipolito, Erwin Huebner, Murray Alexander, Jason Fiege, Francis Lin
Correction for 'A bioenergetic mechanism for amoeboid-like cell motility profiles tested in a microfluidic electrotaxis assay' by Hagit Peretz-Soroka et al., Integr. Biol., 2017, DOI: .
November 13, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28960219/a-bioenergetic-mechanism-for-amoeboid-like-cell-motility-profiles-tested-in-a-microfluidic-electrotaxis-assay
#10
Hagit Peretz-Soroka, Reuven Tirosh, Jolly Hipolito, Erwin Huebner, Murray Alexander, Jason Fiege, Francis Lin
The amoeboid-like cell motility is known to be driven by the acidic enzymatic hydrolysis of ATP in the actin-myosin system. However, the electro-mechano-chemical coupling, whereby the free energy of ATP hydrolysis is transformed into the power of electrically polarized cell movement, is poorly understood. Previous experimental studies showed that actin filaments motion, cytoplasmic streaming, and muscle contraction can be reconstituted under actin-activated ATP hydrolysis by soluble non-filamentous myosin fragments...
November 13, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28914311/comparing-caenorhabditis-elegans-gentle-and-harsh-touch-response-behavior-using-a-multiplexed-hydraulic-microfluidic-device
#11
Patrick D McClanahan, Joyce H Xu, Christopher Fang-Yen
The roundworm Caenorhabditis elegans is an important model system for understanding the genetics and physiology of touch. Classical assays for C. elegans touch, which involve manually touching the animal with a probe and observing its response, are limited by their low throughput and qualitative nature. We developed a microfluidic device in which several dozen animals are subject to spatially localized mechanical stimuli with variable amplitude. The device contains 64 sinusoidal channels through which worms crawl, and hydraulic valves that deliver touch stimuli to the worms...
October 16, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28884171/model-guided-identification-of-novel-gene-amplification-targets-for-improving-succinate-production-in-escherichia-coli-nzn111
#12
Xingxing Jian, Ningchuan Li, Qian Chen, Qiang Hua
Reconstruction and application of genome-scale metabolic models (GEMs) have facilitated metabolic engineering by providing a platform on which systematic computational analysis of metabolic networks can be performed. In this study, a GEM of Escherichia coli NZN111 was employed by the analysis of production and growth coupling (APGC) algorithm to identify genetic strategies for the overproduction of succinate. Through in silico simulation and reaction expression analysis, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), triosephosphate isomerase (TPI), and phosphoenolpyruvate carboxylase (PPC), encoded by gapA, pgk, tpiA, and ppc, respectively, were selected for experimental overexpression...
October 16, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28862705/membrane-and-genomic-dna-dual-targeting-of-citrus-flavonoid-naringenin-against-staphylococcus-aureus
#13
Lang-Hong Wang, Man-Sheng Wang, Xin-An Zeng, Xi-Ming Xu, Charles S Brennan
The antimicrobial mechanism of naringenin, one of the citrus antibacterial flavonoids against food-borne Staphylococcus aureus ATCC 6538, was investigated in this study. Analysis of gas chromatography-mass spectrometry (GC-MS) and fluorescence showed that relatively low concentrations of naringenin caused perturbations in the membrane fatty acid composition and the conformation of membrane proteins through changing the microenvironment of phenylalanine, tyrosine, and tryptophan residues. Exposure of naringenin at higher levels significantly increased membrane permeability and changed the morphology of S...
October 16, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28853753/a-multiscale-study-of-the-role-of-dynamin-in-the-regulation-of-glucose-uptake
#14
Raphaël Trouillon, M Cristina Letizia, Keir J Menzies, Laurent Mouchiroud, Johan Auwerx, Kristina Schoonjans, Martin A M Gijs
Glucose uptake in muscle cells in response to insulin is a fundamental mechanism for metabolism. The inability of cells to mobilize the specific glucose transporter GLUT4 is believed to be at least partially accountable for diseases, like diabetes, where cells do not respond to an insulin stimulus. In this work, a microchip is used to detect electrochemically glucose uptake from C2C12 myoblasts cultured on a patch of paper upon exposure to insulin. More importantly, the data suggest a new role for dynamin, a molecular motor which would be involved in GLUT4 translocation by facilitating exocytosis...
October 16, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28840922/a-microfluidic-oxygen-gradient-demonstrates-differential-activation-of-the-hypoxia-regulated-transcription-factors-hif-1%C3%AE-and-hif-2%C3%AE
#15
Megan L Rexius-Hall, Jalees Rehman, David T Eddington
Gas-perfused microchannels generated a linear oxygen gradient via diffusion across a 100 μm polydimethylsiloxane (PDMS) membrane. The device enabled exposure of a single monolayer of cells sharing culture media to a heterogeneous oxygen landscape, thus reflecting the oxygen gradients found at the microscale in the physiological setting and allowing for the real-time exchange of paracrine factors and metabolites between cells exposed to varying oxygen levels. By tuning the distance between two gas supply channels, the slope of the oxygen gradient was controlled...
September 18, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28831492/quantitative-profiling-of-innate-immune-activation-by-viral-infection-in-single-cells
#16
Andrea C Timm, Jay W Warrick, John Yin
Cells infected by viruses can exhibit diverse patterns of viral and cellular gene expression. The patterns arise in part from the stochastic or noisy reaction kinetics associated with the small number of genomes, enzymes, and other molecules that typically initiate virus replication and activate cellular anti-viral defenses. It is not known what features, if any, of the early viral or cellular gene expression correlate with later processes of viral replication or cell survival. Here we used two fluorescent reporters to visualize innate immune activation of human prostate cancer (PC3) cells against infection by vesicular stomatitis virus...
September 18, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28795726/a-hollow-fiber-system-for-simple-generation-of-human-brain-organoids
#17
Yujuan Zhu, Li Wang, Fangchao Yin, Yue Yu, Yaqing Wang, Hui Liu, Hui Wang, Ning Sun, Haitao Liu, Jianhua Qin
3D organoids exhibit near-physiological morphogenesis and histology relying on the self-organization of human pluripotent stem cells (hPSCs), representing a new class of in vitro model for studying developmental biology and diseases. An engineered approach is highly desirable to generate sufficient organoids in a simple and efficient manner. Herein, we present a new strategy for the simple formation of massive human brain organoids from hiPSCs within a hollow fiber reactor system by combining fiber materials with the developmental biology principle...
September 18, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28752870/endothelium-induced-three-dimensional-invasion-of-heterogeneous-glioma-initiating-cells-in-a-microfluidic-coculture-platform
#18
Yuta Chonan, Sotaro Taki, Oltea Sampetrean, Hideyuki Saya, Ryo Sudo
Glioblastoma (GBM) is a highly invasive primary brain tumor that displays cellular heterogeneity, which is composed of glioma initiating cells (GICs) and their differentiated progeny. GICs play an important role in driving aggressive invasion. In particular, the interaction between GICs and blood vessels is critical because blood vessels are known to serve as routes for the invasion of GICs. However, the effect of endothelial cells on the three-dimensional (3D) invasion process of GICs as well as the spatial relationship between GICs and their differentiated progeny remains unclear...
September 18, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28726920/pheomelanin-molecular-vibration-is-associated-with-mitochondrial-ros-production-in-melanocytes-and-systemic-oxidative-stress-and-damage
#19
Ismael Galván, Alberto Jorge, María García-Gil
Vibrations in covalent bonds affect electron delocalization within molecules, as reported in polymers. If synthesized by living cells, the electron delocalization of polymers affects the stabilization of cellular free radicals, but biomolecular vibration has never been considered a potential source of cytotoxicity. Here we show that the vibrational characteristics of natural pheomelanin and eumelanin contribute to feather color expression in four poultry breeds with different melanin-based pigmentation patterns, but only the vibrational characteristics of pheomelanin are related to the production of reactive oxygen species (ROS) in the mitochondria of melanocytes and to systemic levels of cellular oxidative stress and damage...
September 18, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28726917/engineering-micromyocardium-to-delineate-cellular-and-extracellular-regulation-of-myocardial-tissue-contractility
#20
Nethika R Ariyasinghe, Caitlin H Reck, Alyssa A Viscio, Andrew P Petersen, Davi M Lyra-Leite, Nathan Cho, Megan L McCain
Cardiovascular diseases are a leading cause of death, in part due to limitations of existing models of the myocardium. Myocardium consists of aligned, contractile cardiac myocytes interspersed with fibroblasts that synthesize extracellular matrix (ECM). The cellular demographics and biochemical and mechanical properties of the ECM remodel in many different cardiac diseases. However, the impact of diverse cellular and extracellular remodeling on the contractile output of the myocardium are poorly understood...
September 18, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
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