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https://www.readbyqxmd.com/read/29150615/balancing-a-genetic-toggle-switch-by-real-time-feedback-control-and-periodic-forcing
#1
Jean-Baptiste Lugagne, Sebastián Sosa Carrillo, Melanie Kirch, Agnes Köhler, Gregory Batt, Pascal Hersen
Cybergenetics is a novel field of research aiming at remotely pilot cellular processes in real-time with to leverage the biotechnological potential of synthetic biology. Yet, the control of only a small number of genetic circuits has been tested so far. Here we investigate the control of multistable gene regulatory networks, which are ubiquitously found in nature and play critical roles in cell differentiation and decision-making. Using an in silico feedback control loop, we demonstrate that a bistable genetic toggle switch can be dynamically maintained near its unstable equilibrium position for extended periods of time...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29125127/design-of-dynamic-genetic-memory
#2
Yu-Jia Hu, Chun-Liang Lin, Wei-Xian Li
In electronic systems, dynamic random access memory (DRAM) is one of the core modules in the modern silicon computer. As for a bio-computer, one would need a mechanism for storage of bio-information named 'data', which, in binary logic, has two levels, logical high and logical low, or in the normalised form, '1' and '0'. This study proposes a possible genetic DRAM based on the modified electronic configuration, which uses the biological reaction to fulfil an equivalent RC circuit constituting a memory cell...
December 2017: IET Systems Biology
https://www.readbyqxmd.com/read/29105095/minimally-invasive-technique-for-coxofemoral-luxation-stabilisation-using-transarticular-toggle-system-a-cadaveric-study
#3
U Segal, J Shani, R Joseph
OBJECTIVE: To present a novel, semi-closed, surgical technique for coxofemoral luxation stabilisation using a transarticular toggle rod. STUDY DESIGN: Cadaveric study. MATERIALS AND METHODS: Craniodorsal luxation was generated by transecting the ligamentum teres in 12 coxofemoral joints and was then reduced using a closed technique. Anteversion and inclination angles were measured using fluoroscopic projections. An arthroscope was inserted through a bone tunnel drilled from the third trochanter through the femoral neck...
November 3, 2017: Journal of Small Animal Practice
https://www.readbyqxmd.com/read/28947816/an-integrative-circuit-host-modelling-framework-for-predicting-synthetic-gene-network-behaviours
#4
Chen Liao, Andrew E Blanchard, Ting Lu
One fundamental challenge in synthetic biology is the lack of quantitative tools that accurately describe and predict the behaviours of engineered gene circuits. This challenge arises from multiple factors, among which the complex interdependence of circuits and their host is a leading cause. Here we present a gene circuit modelling framework that explicitly integrates circuit behaviours with host physiology through bidirectional circuit-host coupling. The framework consists of a coarse-grained but mechanistic description of host physiology that involves dynamic resource partitioning, multilayered circuit-host coupling including both generic and system-specific interactions, and a detailed kinetic module of exogenous circuits...
September 25, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28928941/computational-design-of-molecular-motors-as-nanocircuits-in-leishmaniasis
#5
Dipali Kosey, Shailza Singh
Cutaneous leishmaniasis is the most common form of lesihmaniasis, caused by Leishmania major and is spread by the bite of a sandfly .This species infects the macrophages and dendritic cells Due to multi-drug resistance, there is a need for a new therapeutic technique. Recently, a novel molecular motor of Leishmania, Myosin XXI, was classified and characterized. In addition, the drug resistance in this organism has been linked with the overexpression of ABC transporters. Systems biology aims to study the simulation and modeling of natural biological systems whereas synthetic biology deals with building novel and artificial biological parts and devices  Together they have contributed enormously to drug discovery, vaccine design and development, infectious disease detection and diagnostics...
2017: F1000Research
https://www.readbyqxmd.com/read/28775277/environmental-influence-on-pristionchus-pacificus-mouth-form-through-different-culture-methods
#6
Michael S Werner, Bogdan Sieriebriennikov, Tobias Loschko, Suryesh Namdeo, Masa Lenuzzi, Mohannad Dardiry, Tess Renahan, Devansh Raj Sharma, Ralf J Sommer
Environmental cues can impact development to elicit distinct phenotypes in the adult. The consequences of phenotypic plasticity can have profound effects on morphology, life cycle, and behavior to increase the fitness of the organism. The molecular mechanisms governing these interactions are beginning to be elucidated in a few cases, such as social insects. Nevertheless, there is a paucity of systems that are amenable to rigorous experimentation, preventing both detailed mechanistic insight and the establishment of a generalizable conceptual framework...
August 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28763188/a-tug-of-war-mechanism-for-pattern-formation-in-a-genetic-network
#7
Marcella M Gomez, Murat Arcak
Synthesizing spatial patterns with genetic networks is an ongoing challenge in synthetic biology. A successful demonstration of pattern formation would imply a better understanding of systems in the natural world and advance applications in synthetic biology. In developmental systems, transient patterning may suffice in order to imprint instructions for long-term development. In this paper we show that transient but persistent patterns can emerge from a realizable synthetic gene network based on a toggle switch...
November 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28747731/dynamical-sensitivity-control-of-a-single-spin-quantum-sensor
#8
Andrii Lazariev, Silvia Arroyo-Camejo, Ganesh Rahane, Vinaya Kumar Kavatamane, Gopalakrishnan Balasubramanian
The Nitrogen-Vacancy (NV) defect in diamond is a unique quantum system that offers precision sensing of nanoscale physical quantities at room temperature beyond the current state-of-the-art. The benchmark parameters for nanoscale magnetometry applications are sensitivity, spectral resolution, and dynamic range. Under realistic conditions the NV sensors controlled by conventional sensing schemes suffer from limitations of these parameters. Here we experimentally show a new method called dynamical sensitivity control (DYSCO) that boost the benchmark parameters and thus extends the practical applicability of the NV spin for nanoscale sensing...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724287/active-solvent-modulation-a-valve-based-approach-to-improve-separation-compatibility-in-two-dimensional-liquid-chromatography
#9
Dwight R Stoll, Konstantin Shoykhet, Patrik Petersson, Stephan Buckenmaier
Two-dimensional liquid chromatography (2D-LC) is increasingly being viewed as a viable tool for solving difficult separation problems, ranging from targeted separations of structurally similar molecules to untargeted separations of highly complex mixtures. In spite of this performance potential, though, many users find method development challenging and most frequently cite the "incompatibility" between the solvent systems used in the first and second dimensions as a major obstacle. This solvent strength related incompatibility can lead to severe peak distortion and loss of resolution and sensitivity in the second dimension...
September 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28585107/a-technique-to-define-extrahepatic-biliary-anatomy-using-robotic-near-infrared-fluorescent-cholangiography
#10
Ajay V Maker, Nicholas Kunda
BACKGROUND: Bile duct injury is a rare but serious complication of minimally invasive cholecystectomy. Traditionally, intraoperative cholangiogram has been used in difficult cases to help delineate anatomical structures, however, new imaging modalities are currently available to aid in the identification of extrahepatic biliary anatomy, including near-infrared fluorescent cholangiography (NIFC) using indocyanine green (ICG).1-5 The objective of the study was to evaluate if this technique may aid in safe dissection to obtain the critical view...
November 2017: Journal of Gastrointestinal Surgery: Official Journal of the Society for Surgery of the Alimentary Tract
https://www.readbyqxmd.com/read/28578162/rapid-convergence-of-optimal-control-in-nmr-using-numerically-constructed-toggling-frames
#11
Paul Coote, Clemens Anklin, Walter Massefski, Gerhard Wagner, Haribabu Arthanari
We present a numerical method for rapidly solving the Bloch equation for an arbitrary time-varying spin-1/2 Hamiltonian. The method relies on fast, vectorized computations such as summation and quaternion multiplication, rather than slow computations such as matrix exponentiation. A toggling frame is constructed in which the Hamiltonian is time-invariant, and therefore has a simple analytical solution. The key insight is that constructing this frame is faster than solving the system dynamics in the original frame...
August 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28488874/an-optically-modulated-self-assembled-resonance-energy-transfer-pass-gate
#12
Craig D LaBoda, Alvin R Lebeck, Chris L Dwyer
We demonstrate an optically controlled molecular-scale pass gate that uses the photoinduced dark states of fluorescent molecules to modulate the flow of excitons. The device consists of four fluorophores spatially arranged on a self-assembled DNA nanostructure. Together, they form a resonance energy transfer (RET) network resembling a standard transistor with a source, channel, drain, and gate. When the gate fluorophore is directly excited, the device is toggled on. Excitons flow freely from the source to the drain, producing strong output fluorescence...
June 14, 2017: Nano Letters
https://www.readbyqxmd.com/read/28470816/patient-specific-methods-for-room-mounted-x-ray-imagers-for-monoscopic-stereoscopic-prostate-motion-monitoring
#13
M Tynan R Stevens, Dave D Parsons, James L Robar
PURPOSE: To investigate the improvement of combined monoscopic/stereoscopic prostate motion monitoring with room-mounted dual x-ray systems by adopting patient specific methods. METHODS: The linac couch was used as a motion stage to simulate 40 highly dynamic real patient prostate trajectories. For each trajectory, 40 s pretreatment and 120 s treatment periods were extracted to represent a typical treatment fraction. Motion was monitored via continuous stereoscopic x-ray imaging of a single gold fiducial and images were retrospectively divided into periods of stereoscopic and monoscopic imaging to simulate periodic blocking of the room-mounted system by the gantry during arc-based therapy...
May 4, 2017: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28465380/the-angiopoietin-tie2-signaling-axis-in-systemic-inflammation
#14
REVIEW
Samir M Parikh
Systemic inflammation is a hallmark of commonly encountered diseases ranging from bacterial sepsis to sterile syndromes such as major trauma. Derangements in the host vasculature contribute to the cardinal manifestations of sepsis in profound ways. Recent studies of control pathways regulating the vascular endothelium have illuminated how this single cell layer toggles between quiescence and activation to affect the development of shock and multiorgan dysfunction. This article focuses on one such control pathway, the Tie2 receptor and its ligands the angiopoietins, to describe a growing body of genetic, biochemical, mechanistic, and human studies that implicate Tie2 as a critical switch...
July 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28418225/an-iterative-module-in-the-azalomycin%C3%A2-f-polyketide-synthase-contains-a-switchable-enoylreductase-domain
#15
Wei Xu, Guifa Zhai, Yuanzhen Liu, Yuan Li, Yanrong Shi, Kui Hong, Hui Hong, Peter F Leadlay, Zixin Deng, Yuhui Sun
Detailed analysis of the modular Type I polyketide synthase (PKS) involved in the biosynthesis of the marginolactone azalomycin F in mangrove Streptomyces sp. 211726 has shown that only nineteen extension modules are required to accomplish twenty cycles of polyketide chain elongation. Analysis of the products of a PKS mutant specifically inactivated in the dehydratase domain of extension-module 1 showed that this module catalyzes two successive elongations with different outcomes. Strikingly, the enoylreductase domain of this module can apparently be "toggled" off and on : it functions in only the second of these two cycles...
May 8, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28415246/synchronization-dynamics-on-the-picosecond-time-scale-in-coupled-josephson-junction-neurons
#16
K Segall, M LeGro, S Kaplan, O Svitelskiy, S Khadka, P Crotty, D Schult
Conventional digital computation is rapidly approaching physical limits for speed and energy dissipation. Here we fabricate and test a simple neuromorphic circuit that models neuronal somas, axons, and synapses with superconducting Josephson junctions. The circuit models two mutually coupled excitatory neurons. In some regions of parameter space the neurons are desynchronized. In others, the Josephson neurons synchronize in one of two states, in-phase or antiphase. An experimental alteration of the delay and strength of the connecting synapses can toggle the system back and forth in a phase-flip bifurcation...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28374330/timing-of-pmma-cement-application-for-pedicle-screw-augmentation-affects-screw-anchorage
#17
Werner Schmoelz, Christian Heinz Heinrichs, Sven Schmidt, Angel R Piñera, Felix Tome-Bermejo, Javier M Duart, Marlies Bauer, Luis Álvarez Galovich
INTRODUCTION: Cement augmentation is an established method to increase the pedicle screw (PS) anchorage in osteoporotic vertebral bodies. The ideal timing for augmentation when a reposition maneuver is necessary is controversial. While augmentation of the PS before reposition maneuver may increase the force applied it on the vertebrae, it bears the risk to impair PS anchorage, whereas augmenting the PS after the maneuver may restore this anchorage and prevent early screw loosening. The purpose of the present study was to evaluate the effect of cement application timing on PS anchorage in the osteoporotic vertebral body...
November 2017: European Spine Journal
https://www.readbyqxmd.com/read/28362798/interrogating-the-topological-robustness-of-gene-regulatory-circuits-by-randomization
#18
Bin Huang, Mingyang Lu, Dongya Jia, Eshel Ben-Jacob, Herbert Levine, Jose N Onuchic
One of the most important roles of cells is performing their cellular tasks properly for survival. Cells usually achieve robust functionality, for example, cell-fate decision-making and signal transduction, through multiple layers of regulation involving many genes. Despite the combinatorial complexity of gene regulation, its quantitative behavior has been typically studied on the basis of experimentally verified core gene regulatory circuitry, composed of a small set of important elements. It is still unclear how such a core circuit operates in the presence of many other regulatory molecules and in a crowded and noisy cellular environment...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28274123/a-glucose-sensing-toggle-switch-for-autonomous-high-productivity-genetic-control
#19
William Bothfeld, Grace Kapov, Keith E J Tyo
Many biosynthetic strategies are coupled to growth, which is inherently limiting, as (1) excess feedstock (e.g., sugar) may be converted to biomass, instead of product, (2) essential genes must be maintained, and (3) growth toxicity must be managed. A decoupled growth and production phase strategy could avoid these issues. We have developed a toggle switch that uses glucose sensing to enable this two-phase strategy. Temporary glucose starvation precisely and autonomously activates product pathway expression in rich or minimal media, obviating the requirement for expensive inducers...
March 30, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28219948/genomic-integration-of-wnt-%C3%AE-catenin-and-bmp-smad1-signaling-coordinates-foregut-and-hindgut-transcriptional-programs
#20
Mariana L Stevens, Praneet Chaturvedi, Scott A Rankin, Melissa Macdonald, Sajjeev Jagannathan, Masashi Yukawa, Artem Barski, Aaron M Zorn
Digestive system development is orchestrated by combinatorial signaling interactions between endoderm and mesoderm, but how these signals are interpreted in the genome is poorly understood. Here we identified the transcriptomes of Xenopus foregut and hindgut progenitors, which are conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/β-catenin acts as a genome-wide toggle between foregut and hindgut programs...
April 1, 2017: Development
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