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Journal articles on the topic 'Biomolecular oscillators'
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Agrawal, Deepak K., Elisa Franco, and Rebecca Schulman. "A self-regulating biomolecular comparator for processing oscillatory signals." Journal of The Royal Society Interface 12, no. 111 (October 2015): 20150586. http://dx.doi.org/10.1098/rsif.2015.0586.
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While many cellular processes are driven by biomolecular oscillators, precise control of a downstream on/off process by a biochemical oscillator signal can be difficult: over an oscillator's period, its output signal varies continuously between its amplitude limits and spends a significant fraction of the time at intermediate values between these limits. Further, the oscillator's output is often noisy, with particularly large variations in the amplitude. In electronic systems, an oscillating signal is generally processed by a downstream device such as a comparator that converts a potentially noisy oscillatory input into a square wave output that is predominantly in one of two well-defined on and off states. The comparator's output then controls downstream processes. We describe a method for constructing a synthetic biochemical device that likewise produces a square-wave-type biomolecular output for a variety of oscillatory inputs. The method relies on a separation of time scales between the slow rate of production of an oscillatory signal molecule and the fast rates of intermolecular binding and conformational changes. We show how to control the characteristics of the output by varying the concentrations of the species and the reaction rates. We then use this control to show how our approach could be applied to process different in vitro and in vivo biomolecular oscillators, including the p53-Mdm2 transcriptional oscillator and two types of in vitro transcriptional oscillators. These results demonstrate how modular biomolecular circuits could, in principle, be combined to build complex dynamical systems. The simplicity of our approach also suggests that natural molecular circuits may process some biomolecular oscillator outputs before they are applied downstream.
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Bokka, Venkat, Abhishek Dey, and Shaunak Sen. "Period–amplitude co-variation in biomolecular oscillators." IET Systems Biology 12, no. 4 (August 1, 2018): 190–98. http://dx.doi.org/10.1049/iet-syb.2018.0015.
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Banerjee, Soumyadip, Venkat Bokka, and Shaunak Sen. "Attenuation of Pulse Disturbances in Biomolecular Oscillators." IFAC-PapersOnLine 51, no. 1 (2018): 301–6. http://dx.doi.org/10.1016/j.ifacol.2018.05.031.
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Koeppl, H., M. Hafner, A. Ganguly, and A. Mehrotra. "Deterministic characterization of phase noise in biomolecular oscillators." Physical Biology 8, no. 5 (August 10, 2011): 055008. http://dx.doi.org/10.1088/1478-3975/8/5/055008.
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Zhou, Peipei, Shuiming Cai, Zengrong Liu, Luonan Chen, and Ruiqi Wang. "Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems." Chaos, Solitons & Fractals 50 (May 2013): 115–26. http://dx.doi.org/10.1016/j.chaos.2012.11.011.
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Tassinari, Riccardo, Claudia Cavallini, Elena Olivi, Federica Facchin, Valentina Taglioli, Chiara Zannini, Martina Marcuzzi, and Carlo Ventura. "Cell Responsiveness to Physical Energies: Paving the Way to Decipher a Morphogenetic Code." International Journal of Molecular Sciences 23, no. 6 (March 15, 2022): 3157. http://dx.doi.org/10.3390/ijms23063157.
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We discuss emerging views on the complexity of signals controlling the onset of biological shapes and functions, from the nanoarchitectonics arising from supramolecular interactions, to the cellular/multicellular tissue level, and up to the unfolding of complex anatomy. We highlight the fundamental role of physical forces in cellular decisions, stressing the intriguing similarities in early morphogenesis, tissue regeneration, and oncogenic drift. Compelling evidence is presented, showing that biological patterns are strongly embedded in the vibrational nature of the physical energies that permeate the entire universe. We describe biological dynamics as informational processes at which physics and chemistry converge, with nanomechanical motions, and electromagnetic waves, including light, forming an ensemble of vibrations, acting as a sort of control software for molecular patterning. Biomolecular recognition is approached within the establishment of coherent synchronizations among signaling players, whose physical nature can be equated to oscillators tending to the coherent synchronization of their vibrational modes. Cytoskeletal elements are now emerging as senders and receivers of physical signals, “shaping” biological identity from the cellular to the tissue/organ levels. We finally discuss the perspective of exploiting the diffusive features of physical energies to afford in situ stem/somatic cell reprogramming, and tissue regeneration, without stem cell transplantation.
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Iacobelli, Peter. "Circadian dysregulation and Alzheimer’s disease: A comprehensive review." Brain Science Advances 8, no. 4 (November 30, 2022): 221–57. http://dx.doi.org/10.26599/bsa.2022.9050021.
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Alzheimer’s disease (AD), the foremost variant of dementia, has been associated with a menagerie of risk factors, many of which are considered to be modifiable. Among these modifiable risk factors is circadian rhythm, the chronobiological system that regulates sleep‐wake cycles, food consumption timing, hydration timing, and immune responses amongst many other necessary physiological processes. Circadian rhythm at the level of the suprachiasmatic nucleus (SCN), is tightly regulated in the human body by a host of biomolecular substances, principally the hormones melatonin, cortisol, and serotonin. In addition, photic information projected along afferent pathways to the SCN and peripheral oscillators regulates the synthesis of these hormones and mediates the manner in which they act on the SCN and its substructures. Dysregulation of this cycle, whether induced by environmental changes involving irregular exposure to light, or through endogenous pathology, will have a negative impact on immune system optimization and will heighten the deposition of Aβ and the hyperphosphorylation of the tau protein. Given these correlations, it appears that there is a physiologic association between circadian rhythm dysregulation and AD. This review will explore the physiology of circadian dysregulation in the AD brain, and will propose a basic model for its role in AD‐typical pathology, derived from the literature compiled and referenced throughout.
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Takinoue, Masahiro, Daisuke Kiga, Koh-ichiroh Shohda, and Akira Suyama. "RNA Oscillator: Limit Cycle Oscillations based on Artificial Biomolecular Reactions." New Generation Computing 27, no. 2 (February 2009): 107–27. http://dx.doi.org/10.1007/s00354-008-0057-5.
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Banerjee, Soumyadip, and Shaunak Sen. "Robustness of a biomolecular oscillator to pulse perturbations." IET Systems Biology 14, no. 3 (June 1, 2020): 127–32. http://dx.doi.org/10.1049/iet-syb.2019.0029.
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Poznanski, Roman, Eda Alemdar, Cacha Lleuvelyn, Valeriy Sbitnev, and Erkki Brandas. "Journal of Multiscale Neuroscience." Journal of Multiscale Neuroscience 1, no. 2 (October 28, 2022): 109–33. http://dx.doi.org/10.56280/1546792195.
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information based on an inter-cerebral superfast, spontaneous information pathway involving protein-protein interactions. Protons are convenient quantum objects for transferring bit units in a complex water medium like the brain. The phonon-polariton interaction in such a medium adds informational complexity involving complex protein interactions that are essential for the superfluid-like highway to enable the consciousness process to penetrate brain regions due to different regulated gene sets as opposed to single region-specific genes. Protein pathways in the cerebral cortices are connected in a single network of thousands of proteins. To understand the role of inter-cerebral communication, we postulate protonic currents in interfacial water crystal lattices result from phonon-polariton vibrations, which can lead in the presence of an electromagnetic field, to ultra-rapid communication where thermo-qubits, physical feelings, and protons that are convenient quantum objects for transferring bit units in a complex water medium. The relative equality between the frequencies of thermal oscillations due to the energy of the quasi-protonic movement about a closed loop and the frequencies of electromagnetic oscillations confirms the existence of quasi-polaritons. Phonon-polaritons are electromagnetic waves coupled to lattice vibrational modes. Still, when generated specifically by protons, they are referred to as phonon-coupled quasi-particles, i.e., providing a coupling with vibrational motions. We start from quasiparticles and move up the scale to biomolecular communication in subcellular, cellular and neuronal structures, leading to the negentropic entanglement of multiscale ‘bits’ of information. Espousing quantum potential chemistry, the interdependence of intrinsic information on the negative gain in the steady-state represents the mesoscopic aggregate of the microscopic random quantum-thermal fluctuations expressed through a negentropically derived, temperature-dependent, dissipative quantum potential energy. The latter depends on the time derivative of the spread function and temperature, which fundamentally explains the holonomic brain theory.
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Panda, Swati. "Biomolecular Piezoelectric Materials for Biosensors." Prabha Materials Science Letters 1, no. 1 (September 1, 2022): 37–49. http://dx.doi.org/10.33889/pmsl.2022.1.1.006.
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Piezoelectric biosensors are a type of analytical equipment that works based on recording affinity interactions. A piezoelectric platform, also known as a piezoelectric crystal, is a sensor component that works on the premise of oscillations changing according to the presence of a mass on the piezoelectric crystal surface. Owing to their high piezoelectricity, biocompatibility, as well as different electrical properties, biomolecular piezoelectric materials are thought to be promising candidates for future piezoelectric biosensors. When biological components in the human body are stressed, they are estimated to produce electric fields that promote cell growth and repair. As a by-product, piezoelectricity research in biological tissues and their elements has drawn much attention recently. This article specifies the principle of the advancement in piezoelectricity research of representative biomolecular materials, which are nucleic acids such as amino acids (DNA, RNA), peptides, proteins, and viruses. We also explored the origins and processes of piezoelectricity in biomolecular materials for biosensor application. Various advantages of using piezoelectric biomolecular materials for biosensor applications are elaborated. Lastly, a comprehensive idea of future challenges and discussion are provided.
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Psarellis, Yorgos M., Michail Kavousanakis, Michael A. Henson, and Ioannis G. Kevrekidis. "Limits of entrainment of circadian neuronal networks." Chaos: An Interdisciplinary Journal of Nonlinear Science 33, no. 1 (January 2023): 013137. http://dx.doi.org/10.1063/5.0122744.
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Circadian rhythmicity lies at the center of various important physiological and behavioral processes in mammals, such as sleep, metabolism, homeostasis, mood changes, and more. Misalignment of intrinsic neuronal oscillations with the external day–night cycle can disrupt such processes and lead to numerous disorders. In this work, we computationally determine the limits of circadian synchronization to external light signals of different frequency, duty cycle, and simulated amplitude. Instead of modeling circadian dynamics with generic oscillator models (e.g., Kuramoto-type), we use a detailed computational neuroscience model, which integrates biomolecular dynamics, neuronal electrophysiology, and network effects. This allows us to investigate the effect of small drug molecules, such as Longdaysin, and connect our results with experimental findings. To combat the high dimensionality of such a detailed model, we employ a matrix-free approach, while our entire algorithmic pipeline enables numerical continuation and construction of bifurcation diagrams using only direct simulation. We, thus, computationally explore the effect of heterogeneity in the circadian neuronal network, as well as the effect of the corrective therapeutic intervention of Longdaysin. Last, we employ unsupervised learning to construct a data-driven embedding space for representing neuronal heterogeneity.
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Gu, Yuangang, Allan Widom, and Paul M. Champion. "Spectral line shapes of damped quantum oscillators: Applications to biomolecules." Journal of Chemical Physics 100, no. 4 (February 15, 1994): 2547–60. http://dx.doi.org/10.1063/1.467232.
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Cuba Samaniego, Christian, Giulia Giordano, Franco Blanchini, and Elisa Franco. "Stability analysis of an artificial biomolecular oscillator with non-cooperative regulatory interactions." Journal of Biological Dynamics 11, no. 1 (November 10, 2016): 102–20. http://dx.doi.org/10.1080/17513758.2016.1245790.
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Tanaka, Shigenori. "Modulation of excitation energy transfer by conformational oscillations in biomolecular systems." Chemical Physics Letters 508, no. 1-3 (May 2011): 139–43. http://dx.doi.org/10.1016/j.cplett.2011.04.037.
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Olsman, Noah, and Fulvio Forni. "Antithetic integral feedback for the robust control of monostable and oscillatory biomolecular circuits." IFAC-PapersOnLine 53, no. 2 (2020): 16826–33. http://dx.doi.org/10.1016/j.ifacol.2020.12.1176.
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Duan, Hong-Guang, Valentyn I. Prokhorenko, Richard J. Cogdell, Khuram Ashraf, Amy L. Stevens, Michael Thorwart, and R. J. Dwayne Miller. "Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer." Proceedings of the National Academy of Sciences 114, no. 32 (July 25, 2017): 8493–98. http://dx.doi.org/10.1073/pnas.1702261114.
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During the first steps of photosynthesis, the energy of impinging solar photons is transformed into electronic excitation energy of the light-harvesting biomolecular complexes. The subsequent energy transfer to the reaction center is commonly rationalized in terms of excitons moving on a grid of biomolecular chromophores on typical timescales <100 fs. Today’s understanding of the energy transfer includes the fact that the excitons are delocalized over a few neighboring sites, but the role of quantum coherence is considered as irrelevant for the transfer dynamics because it typically decays within a few tens of femtoseconds. This orthodox picture of incoherent energy transfer between clusters of a few pigments sharing delocalized excitons has been challenged by ultrafast optical spectroscopy experiments with the Fenna–Matthews–Olson protein, in which interference oscillatory signals up to 1.5 ps were reported and interpreted as direct evidence of exceptionally long-lived electronic quantum coherence. Here, we show that the optical 2D photon echo spectra of this complex at ambient temperature in aqueous solution do not provide evidence of any long-lived electronic quantum coherence, but confirm the orthodox view of rapidly decaying electronic quantum coherence on a timescale of 60 fs. Our results can be considered as generic and give no hint that electronic quantum coherence plays any biofunctional role in real photoactive biomolecular complexes. Because in this structurally well-defined protein the distances between bacteriochlorophylls are comparable to those of other light-harvesting complexes, we anticipate that this finding is general and directly applies to even larger photoactive biomolecular complexes.
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Inoue, Masaki, Hikaru Ikuta, Shuichi Adachi, Jun-Ichi Imura, and Kazuyuki Aihara. "A Computational Method for Robust Bifurcation Analysis and Its Application to Biomolecular Systems." International Journal of Bifurcation and Chaos 25, no. 07 (June 30, 2015): 1540012. http://dx.doi.org/10.1142/s021812741540012x.
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We consider a general uncertain nonlinear dynamical system defined in a certain model set, and reformulate a problem of robustness bifurcation analysis (RBA), which has been originally formulated in our previous work. As such, we develop an efficient computational method for the RBA, which can be used for quantitative evaluation of bifurcation robustness in uncertain dynamical systems. Specifically, we first linearize the uncertain system properly and then apply a feedback transformation technique to reduce the RBA problem to a linear robustness analysis one, which can be solved using μ-analysis, a common analysis technique in robust control theory. Finally, we provide robustness analysis of a gene regulatory network model where oscillatory behavior appears according to Hopf bifurcation. We give quantitative evaluation of the bifurcation robustness using the RBA method proposed here.
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Dey, Supravat, and Abhyudai Singh. "Diverse role of decoys on emergence and precision of oscillations in a biomolecular clock." Biophysical Journal 120, no. 24 (December 2021): 5564–74. http://dx.doi.org/10.1016/j.bpj.2021.11.013.
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Ghosh, Ashmita, Saumyakanti Khanra, Gopinath Haldar, Tridib Kumar Bhowmick, and Kalyan Gayen. "Diverse Cyanobacteria Resource from North East Region of India for Valuable Biomolecules: Phycobiliprotein, Carotenoid, Carbohydrate and Lipid." Current Biochemical Engineering 5, no. 1 (September 27, 2019): 21–33. http://dx.doi.org/10.2174/2212711905666180817105828.
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Background: :North east region of India is well known as biodiversity hotspot with endemic flora and fauna. Organisms belonging to the cyanobacterial species are commonly known as blue green algae and are found in diverse categories in the environment of north-east India. Potentials of these cyanobacterial species are mostly unexplored. Present study aimed to isolate, identify and evaluate the potential cyanobacterial strains for the sustainable producers of biomolecules with agricultural, therapeutic and industrial significance.Methods::Growth and biochemical characterization were performed with the isolated cyanobacterial species to investigate the growth kinetics, cellular pigments (carotenoid, phycobiliprotein and chlorophyll), protein, carbohydrate and lipid content.Results::Three Phormidium sp., one Oscillatoria sp., and one Microcoleus sp. were isolated from the Tripura state (North-east region of India). Results revealed that isolated Oscillatoria sp. has high lipid (~20%), protein (~40%), and carbohydrate (~30%) yield. Further, two isolated Phormidium sp., produced significant amount of carotenoids (~23 mg/gm dry biomass), phycobiliprotein (~20-25%) and high protein (~55%). Microcoleus sp. produced 62% carbohydrate and 20% phycobiliprotein with significant amount of carotenoids (~17 mg/gm dry biomass).Conclusion::Isolated Oscillatoria sp. is the promising resource for lipid and nutritional supplement due to high accumulated primary metabolites. Two Phormidium sp., can be used as animal and human nutritional food supplement and also can be further investigated for pigment production at industrial scale. Isolated Microcoleus sp. is the potential resource of carbohydrate and pigment. Isolated cyanobacterial strains are identified as viable candidates for the industrial production of biomass as well as other value added biomolecules.
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Snyder, Patrick, Amitabh Joshi, and Juan D. Serna. "Modeling a Nanocantilever-Based Biosensor Using a Stochastically Perturbed Harmonic Oscillator." International Journal of Nanoscience 13, no. 02 (April 2014): 1450011. http://dx.doi.org/10.1142/s0219581x14500112.
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Nanoscale biosensors are devices designed to detect analytes by combining biological components and physicochemical detectors. A well-known design of these sensors involves the implementation of nanocantilevers. These microscopic diving boards are coated with binding probes that have an affinity for a particular amino acid, enzyme or protein in living organisms. When these probes attract target particles, such as biomolecules, the binding of these particles changes the vibrating frequency of the cantilever. This process is random in nature and produces fluctuations in the frequency and damping of the cantilever. In this paper, we studied the effect of these fluctuations using a stochastically perturbed, classical harmonic oscillator.
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Cloutier, Mathieu, and Peter Wellstead. "The control systems structures of energy metabolism." Journal of The Royal Society Interface 7, no. 45 (October 14, 2009): 651–65. http://dx.doi.org/10.1098/rsif.2009.0371.
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The biochemical regulation of energy metabolism (EM) allows cells to modulate their energetic output depending on available substrates and requirements. To this end, numerous biomolecular mechanisms exist that allow the sensing of the energetic state and corresponding adjustment of enzymatic reaction rates. This regulation is known to induce dynamic systems properties such as oscillations or perfect adaptation. Although the various mechanisms of energy regulation have been studied in detail from many angles at the experimental and theoretical levels, no framework is available for the systematic analysis of EM from a control systems perspective. In this study, we have used principles well known in control to clarify the basic system features that govern EM. The major result is a subdivision of the biomolecular mechanisms of energy regulation in terms of widely used engineering control mechanisms: proportional, integral, derivative control, and structures: feedback, cascade and feed-forward control. Evidence for each mechanism and structure is demonstrated and the implications for systems properties are shown through simulations. As the equivalence between biological systems and control components presented here is generic, it is also hypothesized that our work could eventually have an applicability that is much wider than the focus of the current study.
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Daly, Steven, Frédéric Rosu, and Valérie Gabelica. "Mass-resolved electronic circular dichroism ion spectroscopy." Science 368, no. 6498 (June 25, 2020): 1465–68. http://dx.doi.org/10.1126/science.abb1822.
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DNA and proteins are chiral: Their three-dimensional structures cannot be superimposed with their mirror images. Circular dichroism spectroscopy is widely used to characterize chiral compounds, but data interpretation is difficult in the case of mixtures. We recorded the electronic circular dichroism spectra of DNA helices separated in a mass spectrometer. We studied guanine-rich strands having various secondary structures, electrosprayed them as negative ions, irradiated them with an ultraviolet nanosecond optical parametric oscillator laser, and measured the difference in electron photodetachment efficiency between left and right circularly polarized light. The reconstructed circular dichroism ion spectra resembled those of their solution-phase counterparts, thereby allowing us to assign the DNA helical topology. The ability to measure circular dichroism directly on biomolecular ions expands the capabilities of mass spectrometry for structural analysis.
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Diamond, Spencer, Darae Jun, Benjamin E. Rubin, and Susan S. Golden. "The circadian oscillator inSynechococcus elongatuscontrols metabolite partitioning during diurnal growth." Proceedings of the National Academy of Sciences 112, no. 15 (March 30, 2015): E1916—E1925. http://dx.doi.org/10.1073/pnas.1504576112.
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Synechococcus elongatusPCC 7942 is a genetically tractable model cyanobacterium that has been engineered to produce industrially relevant biomolecules and is the best-studied model for a prokaryotic circadian clock. However, the organism is commonly grown in continuous light in the laboratory, and data on metabolic processes under diurnal conditions are lacking. Moreover, the influence of the circadian clock on diurnal metabolism has been investigated only briefly. Here, we demonstrate that the circadian oscillator influences rhythms of metabolism during diurnal growth, even though light–dark cycles can drive metabolic rhythms independently. Moreover, the phenotype associated with loss of the core oscillator protein, KaiC, is distinct from that caused by absence of the circadian output transcriptional regulator, RpaA (regulator of phycobilisome-associated A). Although RpaA activity is important for carbon degradation at night, KaiC is dispensable for those processes. Untargeted metabolomics analysis and glycogen kinetics suggest that functional KaiC is important for metabolite partitioning in the morning. Additionally, output from the oscillator functions to inhibit RpaA activity in the morning, andkaiC-null strains expressing a mutant KaiC phosphomimetic, KaiC-pST, in which the oscillator is locked in the most active output state, phenocopies aΔrpaAstrain. Inhibition of RpaA by the oscillator in the morning suppresses metabolic processes that normally are active at night, andkaiC-null strains show indications of oxidative pentose phosphate pathway activation as well as increased abundance of primary metabolites. Inhibitory clock output may serve to allow secondary metabolite biosynthesis in the morning, and some metabolites resulting from these processes may feed back to reinforce clock timing.
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Ozeki, Tomomitsu, Mizuki Morita, Hiroshi Yoshimine, Hiroyuki Furusawa, and Yoshio Okahata. "Hydration and Energy Dissipation Measurements of Biomolecules on a Piezoelectric Quartz Oscillator by Admittance Analyses." Analytical Chemistry 79, no. 1 (January 2007): 79–88. http://dx.doi.org/10.1021/ac060873x.
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Vyas, Hitarthi, Aliasgar Vohra, Kapil Upadhyay, Menaka Thounaojam, Ravirajsinh Jadeja, Nilay Dalvi, Manuela Bartoli, and Ranjitsinh Devkar. "miR34a-5p impedes CLOCK expression in chronodisruptive C57BL/6J mice and potentiates pro-atherogenic manifestations." PLOS ONE 18, no. 8 (August 10, 2023): e0283591. http://dx.doi.org/10.1371/journal.pone.0283591.
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Introduction Altered circadian rhythms underlie manifestation of several cardiovascular disorders, however a little is known about the mediating biomolecules. Multiple transcriptional-translational feedback loops control circadian-clockwork wherein; micro RNAs (miRNAs) are known to manifest post transcriptional regulation. This study assesses miR34a-5p as a mediating biomolecule. Method 8–10-week-old male C57BL/6J mice (n = 6/group) were subjected to photoperiodic manipulation induced chronodisruption and thoracic aortae were examined for miRNA, gene (qPCR) and protein (Immunoblot) expression studies. Histomorphological changes were assessed for pro-atherogenic manifestations (fibrillar arrangement, collagen/elastin ratio, intima-media thickening). Computational studies for miRNA-mRNA target prediction were done using TargetScan and miRDB. Correlative in vitro studies were done in serum synchronized HUVEC cells. Time point based studies were done at five time points (ZT 0, 6, 12, 18, 24) in 24h. Results Chronodisruption induced hypomethylation in the promoter region of miR34a-5p, in the thoracic aortae, culminating in elevated miRNA titers. In a software-based detection of circadian-clock-associated targets of miR34a-5p, Clock and Sirt1 genes were identified. Moreover, miR34a-5p exhibited antagonist circadian oscillations to that of its target genes CLOCK and SIRT1 in endothelial cells. Luciferase reporter gene assay further showed that miR34a-5p interacts with the 3’UTR of the Clock gene to lower its expression, disturbing the operation of positive arm of circadian clock system. Elevated miR34a-5p and impeded SIRT1 expression in a chronodisruptive aortae exhibited pro-atherogenic changes observed in form of gene expression, increased collagen/elastin ratio, fibrillar derangement and intimal-media thickening. Conclusion The study reports for the first time chronodisruption mediated miR34a-5p elevation, its circadian expression and interaction with the 3’UTR of Clock gene to impede its expression. Moreover, elevated miR34a-5p and lowered SIRT1 expression in the chronodisruptive aortae lead off cause-consequence relationship of chronodisruption mediated proatherogenic changes.
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Greetham, Gregory M., Ian P. Clark, Benjamin Young, Robby Fritsch, Lucy Minnes, Neil T. Hunt, and Mike Towrie. "Time-Resolved Temperature-Jump Infrared Spectroscopy at a High Repetition Rate." Applied Spectroscopy 74, no. 6 (March 30, 2020): 720–27. http://dx.doi.org/10.1177/0003702820913636.
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Time-resolved temperature-jump infrared absorption spectroscopy at a 0.5 to 1 kHz repetition rate is presented. A 1 kHz neodymium-doped yttrium aluminum garnet (Nd:YAG) laser pumping an optical parametric oscillator provided >70 µJ, 3.75 µm pump pulses, which delivered a temperature jump via excitation of the O–D stretch of a D2O solution. A 10 kHz train of mid-infrared probe pulses was used to monitor spectral changes following the temperature jump. Calibration with trifluoroacetic acid solution showed that a temperature jump of 10 K lasting for tens of microseconds was achieved, sufficient to observe fast processes in functionally relevant biomolecular mechanisms. Modeling of heating profiles across ≤10 µm path length cells and subsequent cooling dynamics are used to describe the initial <100 ns cooling at the window surface and subsequent, >10 µs cooling dynamics of the bulk solution.
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HORING, NORMAN J. MORGENSTERN, and H. L. CUI. "SURFACE-PLASMON-RESONANCE BASED OPTICAL SENSING." International Journal of High Speed Electronics and Systems 18, no. 01 (March 2008): 71–78. http://dx.doi.org/10.1142/s012915640800514x.
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Over the past twenty years, surface plasmon resonance has been developed as an effective technique for use in real-time biotechnological measurements of the kinetics of label-free biomolecular interactions with high sensitivity.1-16 On a fundamental level, it is the dielectric-imaging involvement of the adsorbed biomolecular layer (DNA for example) in shifting the surface plasmon resonance (SPR) frequency by means of electrostatic coupling at the interface with the metal film substrate that facilitates SPR-based optical sensing. Of course, there are various factors that can influence surface plasmon resonance, including plasma nonlocality, phonons, multiplicity of layers, all of which should be carefully examined. Moreover, tunable SPR phenomenology based on the role of a magnetic field (both classically and quantum mechanically) merits consideration in regard to the field's effects on both the substrate17 and the adsorbed layer(s).18 This paper is focused on the establishment of the basic equations governing surface plasmon resonance, incorporating all the features cited above. In it, we present the formulation and closed-form analytical solution for the dynamic, nonlocal screening function of a thick substrate material with a thin external adsorbed layer, which can be extended to multiple layers. The result involves solution of the random phase approximation (RPA) integral equation for the spatially inhomogeneous system of the substrate and adsorbed layer,19-25 given the individual polarizabilities of the thick substrate and the layer. (This is tantamount to the space-time matrix inversion of the inhomogeneous joint dielectric function of the system.) The frequency poles of the resulting screening function determine the shifted surface (and bulk) plasmon resonances and the associated residues at the resonance frequencies provide their relative excitation amplitudes. The latter represent the response strengths of the surface plasmon resonances (oscillator strengths), and will be of interest in optimizing the materials to be employed.
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Krylov, Viacheslav V., and Elena A. Osipova. "Molecular Biological Effects of Weak Low-Frequency Magnetic Fields: Frequency–Amplitude Efficiency Windows and Possible Mechanisms." International Journal of Molecular Sciences 24, no. 13 (July 1, 2023): 10989. http://dx.doi.org/10.3390/ijms241310989.
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This review covers the phenomenon of resonance-like responses of biological systems to low-frequency magnetic fields (LFMF). The historical development of this branch of magnetobiology, including the most notable biophysical models that explain the resonance-like responses of biological systems to LFMF with a specific frequency and amplitude, is given. Two groups can be distinguished among these models: one considers ion-cofactors of proteins as the primary targets for the LFMF influence, and the other regards the magnetic moments of particles in biomolecules. Attention is paid to the dependence of resonance-like LFMF effects on the cell type. A radical-pair mechanism of the magnetic field’s influence on biochemical processes is described with the example of cryptochrome. Conditions for this mechanism’s applicability to explain the biological effects of LFMF are given. A model of the influence of LFMF on radical pairs in biochemical oscillators, which can explain the frequency–amplitude efficiency windows of LFMF, is proposed.
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Unarta, Ilona Christy, Siqin Cao, Shintaroh Kubo, Wei Wang, Peter Pak-Hang Cheung, Xin Gao, Shoji Takada, and Xuhui Huang. "Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model." Proceedings of the National Academy of Sciences 118, no. 17 (April 21, 2021): e2024324118. http://dx.doi.org/10.1073/pnas.2024324118.
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To initiate transcription, the holoenzyme (RNA polymerase [RNAP] in complex with σ factor) loads the promoter DNA via the flexible loading gate created by the clamp and β-lobe, yet their roles in DNA loading have not been characterized. We used a quasi-Markov State Model (qMSM) built from extensive molecular dynamics simulations to elucidate the dynamics of Thermus aquaticus holoenzyme’s gate opening. We showed that during gate opening, β-lobe oscillates four orders of magnitude faster than the clamp, whose opening depends on the Switch 2’s structure. Myxopyronin, an antibiotic that binds to Switch 2, was shown to undergo a conformational selection mechanism to inhibit clamp opening. Importantly, we reveal a critical but undiscovered role of β-lobe, whose opening is sufficient for DNA loading even when the clamp is partially closed. These findings open the opportunity for the development of antibiotics targeting β-lobe of RNAP. Finally, we have shown that our qMSMs, which encode non-Markovian dynamics based on the generalized master equation formalism, hold great potential to be widely applied to study biomolecular dynamics.
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Fawole, Olutosin, Subhashish Dolai, Hsuan-Yu Leu, Jules Magda, and Massood Tabib-Azar. "Remote Microwave and Field-Effect Sensing Techniques for Monitoring Hydrogel Sensor Response." Micromachines 9, no. 10 (October 17, 2018): 526. http://dx.doi.org/10.3390/mi9100526.
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This paper presents two novel techniques for monitoring the response of smart hydrogels composed of synthetic organic materials that can be engineered to respond (swell or shrink, change conductivity and optical properties) to specific chemicals, biomolecules or external stimuli. The first technique uses microwaves both in contact and remote monitoring of the hydrogel as it responds to chemicals. This method is of great interest because it can be used to non-invasively monitor the response of subcutaneously implanted hydrogels to blood chemicals such as oxygen and glucose. The second technique uses a metal-oxide-hydrogel field-effect transistor (MOHFET) and its associated current-voltage characteristics to monitor the hydrogel’s response to different chemicals. MOHFET can be easily integrated with on-board telemetry electronics for applications in implantable biosensors or it can be used as a transistor in an oscillator circuit where the oscillation frequency of the circuit depends on the analyte concentration.
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Hamlin, Preston, W. John Thrasher, Walid Keyrouz, and Michael Mascagni. "Geometry entrapment in Walk-on-Subdomains." Monte Carlo Methods and Applications 25, no. 4 (December 1, 2019): 329–40. http://dx.doi.org/10.1515/mcma-2019-2052.
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Abstract One method of computing the electrostatic energy of a biomolecule in a solution uses a continuum representation of the solution via the Poisson–Boltzmann equation. This can be solved in many ways, and we consider a Monte Carlo method of our design that combines the Walk-on-Spheres and Walk-on-Subdomains algorithms. In the course of examining the Monte Carlo implementation of this method, an issue was discovered in the Walk-on-Subdomains portion of the algorithm which caused the algorithm to sometimes take an abnormally long time to complete. As the problem occurs when a walker repeatedly oscillates between two subdomains, it is something that could cause a large increase in runtime for any method that used a similar algorithm. This issue is described in detail and a potential solution is examined.
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Penkov, Nikita V. "Relationships between Molecular Structure of Carbohydrates and Their Dynamic Hydration Shells Revealed by Terahertz Time-Domain Spectroscopy." International Journal of Molecular Sciences 22, no. 21 (November 4, 2021): 11969. http://dx.doi.org/10.3390/ijms222111969.
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Despite more than a century of research on the hydration of biomolecules, the hydration of carbohydrates is insufficiently studied. An approach to studying dynamic hydration shells of carbohydrates in aqueous solutions based on terahertz time-domain spectroscopy assay is developed in the current work. Monosaccharides (glucose, galactose, galacturonic acid) and polysaccharides (dextran, amylopectin, polygalacturonic acid) solutions were studied. The contribution of the dissolved carbohydrates was subtracted from the measured dielectric permittivities of aqueous solutions based on the corresponding effective medium models. The obtained dielectric permittivities of the water phase were used to calculate the parameters describing intermolecular relaxation and oscillatory processes in water. It is established that all of the analyzed carbohydrates lead to the increase of the binding degree of water. Hydration shells of monosaccharides are characterized by elevated numbers of hydrogen bonds and their mean energies compared to undisturbed water, as well as by elevated numbers and the lifetime of free water molecules. The axial orientation of the OH(4) group of sugar facilitates a wider distribution of hydrogen bond energies in hydration shells compared to equatorial orientation. The presence of the carboxylic group affects water structure significantly. The hydration of polysaccharides is less apparent than that of monosaccharides, and it depends on the type of glycosidic bonds.
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Li, Peng-Fei, Hua Yuan, Zi-Dong Cheng, Li-Bing Qian, Zhong-Lin Liu, Bo Jin, Shuai Ha, et al. "Stable transmission of low energy electrons in glass tube with outer surface grounded conductively shielding." Acta Physica Sinica 71, no. 7 (2022): 074101. http://dx.doi.org/10.7498/aps.71.20212036.
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<sec>The electron microbeam is useful for modifying certain fragments of biomolecule. It is successful to apply the guiding effect to making the microbeam of positively charged particles by using single glass capillary. However, the mechanism for the electron transport through insulating capillaries is unclear. Meanwhile, previous researches show that there are oscillations of the transmission intensity of electrons with time in the glass capillaries with outer serface having no grounded conductive shielding, So, the application of glass capillary to making the microbeam of electrons is limited.</sec><sec>In this paper, the transmission of 1.5 and 0.9 keV electrons through the glass capillary without/with the grounded conductive-coated outer surface are investigated, respectively. This study aims to understand the mechanism for low energy electron transport in the glass capillaries, and find the conditions for the steady transport of the electrons. Two-dimensional angular distribution of the transported electrons and its time evolution are measured. It is found that the intensity of the transported electrons with the incident energy through the glass capillaries for the glass capillaries without and with the grounded conductive-coated outer surface show the typical geometrical transmission characteristics. The time evolution of the 1.5- keV electron transport presents an extremely complex variation for the glass capillary without the grounded conductive-coated outer surface. The intensity first falls, then rises and finally oscillates around a certain mean value. Correspondingly, the angular distribution center experiences moving towards positive-negative-settlement. In comparison, the charge-up process of the 0.9 keV electron transport through the glass capillary with the grounded conductive-coated outer surface shows a relatively simple behavior. At first, the intensity declines rapidly with time. Then, it slowly rises till a certain value and stays steady subsequently. The angular distribution of transported electrons follows the intensity distribution in general, but with some delay. It quickly moves to negative direction then comes back to positive direction. Finally, it regresses extremely slowly and ends up around the tilt angle. To better understand the physics behind the observed phenomena, the simulation for the interaction of the electrons with SiO<sub>2</sub> material is performed to obtain the possible deposited charge distribution by the CASINO code. Based on the analysis of the experimental results and the simulated charge deposition, the conditions for stabilizing the electron transport through glass capillary arepresented.</sec>
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Kim, Ji Hyun, Seong Jun Park, Jin-Woo Han, and Jae-Hyuk Ahn. "Surface Potential-Controlled Oscillation in FET-Based Biosensors." Sensors 21, no. 6 (March 10, 2021): 1939. http://dx.doi.org/10.3390/s21061939.
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Field-effect transistor (FET)-based biosensors have garnered significant attention for their label-free electrical detection of charged biomolecules. Whereas conventional output parameters such as threshold voltage and channel current have been widely used for the detection and quantitation of analytes of interest, they require bulky instruments and specialized readout circuits, which often limit point-of-care testing applications. In this study, we demonstrate a simple conversion method that transforms the surface potential into an oscillating signal as an output of the FET-based biosensor. The oscillation frequency is proposed as a parameter for FET-based biosensors owing to its intrinsic advantages of simple and compact implementation of readout circuits as well as high compatibility with neuromorphic applications. An extended-gate biosensor comprising an Al2O3-deposited sensing electrode and a readout transistor is connected to a ring oscillator that generates surface potential-controlled oscillation for pH sensing. Electrical measurement of the oscillation frequency as a function of pH reveals that the oscillation frequency can be used as a sensitive and reliable output parameter in FET-based biosensors for the detection of chemical and biological species. We confirmed that the oscillation frequency is directly correlated with the threshold voltage. For signal amplification, the effects of circuit parameters on pH sensitivity are investigated using different methods, including electrical measurements, analytical calculations, and circuit simulations. An Arduino board to measure the oscillation frequency is integrated with the proposed sensor to enable portable and real-time pH measurement for point-of-care testing applications.
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Qi, Miao, Nancy Meng Ying Zhang, Kaiwei Li, Swee Chuan Tjin, and Lei Wei. "Hybrid Plasmonic Fiber-Optic Sensors." Sensors 20, no. 11 (June 8, 2020): 3266. http://dx.doi.org/10.3390/s20113266.
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With the increasing demand of achieving comprehensive perception in every aspect of life, optical fibers have shown great potential in various applications due to their highly-sensitive, highly-integrated, flexible and real-time sensing capabilities. Among various sensing mechanisms, plasmonics based fiber-optic sensors provide remarkable sensitivity benefiting from their outstanding plasmon–matter interaction. Therefore, surface plasmon resonance (SPR) and localized SPR (LSPR)-based hybrid fiber-optic sensors have captured intensive research attention. Conventionally, SPR- or LSPR-based hybrid fiber-optic sensors rely on the resonant electron oscillations of thin metallic films or metallic nanoparticles functionalized on fiber surfaces. Coupled with the new advances in functional nanomaterials as well as fiber structure design and fabrication in recent years, new solutions continue to emerge to further improve the fiber-optic plasmonic sensors’ performances in terms of sensitivity, specificity and biocompatibility. For instance, 2D materials like graphene can enhance the surface plasmon intensity at the metallic film surface due to the plasmon–matter interaction. Two-dimensional (2D) morphology of transition metal oxides can be doped with abundant free electrons to facilitate intrinsic plasmonics in visible or near-infrared frequencies, realizing exceptional field confinement and high sensitivity detection of analyte molecules. Gold nanoparticles capped with macrocyclic supramolecules show excellent selectivity to target biomolecules and ultralow limits of detection. Moreover, specially designed microstructured optical fibers are able to achieve high birefringence that can suppress the output inaccuracy induced by polarization crosstalk and meanwhile deliver promising sensitivity. This review aims to reveal and explore the frontiers of such hybrid plasmonic fiber-optic platforms in various sensing applications.
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Bertaux, François, Samuel Marguerat, and Vahid Shahrezaei. "Division rate, cell size and proteome allocation: impact on gene expression noise and implications for the dynamics of genetic circuits." Royal Society Open Science 5, no. 3 (March 2018): 172234. http://dx.doi.org/10.1098/rsos.172234.
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The cell division rate, size and gene expression programmes change in response to external conditions. These global changes impact on average concentrations of biomolecule and their variability or noise. Gene expression is inherently stochastic, and noise levels of individual proteins depend on synthesis and degradation rates as well as on cell-cycle dynamics. We have modelled stochastic gene expression inside growing and dividing cells to study the effect of division rates on noise in mRNA and protein expression. We use assumptions and parameters relevant to Escherichia coli , for which abundant quantitative data are available. We find that coupling of transcription, but not translation rates to the rate of cell division can result in protein concentration and noise homeostasis across conditions. Interestingly, we find that the increased cell size at fast division rates, observed in E. coli and other unicellular organisms, buffers noise levels even for proteins with decreased expression at faster growth. We then investigate the functional importance of these regulations using gene regulatory networks that exhibit bi-stability and oscillations. We find that network topology affects robustness to changes in division rate in complex and unexpected ways. In particular, a simple model of persistence, based on global physiological feedback, predicts increased proportion of persister cells at slow division rates. Altogether, our study reveals how cell size regulation in response to cell division rate could help controlling gene expression noise. It also highlights that understanding circuits' robustness across growth conditions is key for the effective design of synthetic biological systems.
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Delgadillo, Roberto F., Katie A. Carnes, Nestor Valles-Villarreal, Omar Olmos, Kathia Zaleta-Rivera, and Lawrence J. Parkhurst. "Dual-Channel Stopped-Flow Apparatus for Simultaneous Fluorescence, Anisotropy, and FRET Kinetic Data Acquisition for Binary and Ternary Biological Complexes." Biosensors 10, no. 11 (November 19, 2020): 180. http://dx.doi.org/10.3390/bios10110180.
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The Stopped-Flow apparatus (SF) tracks molecular events by mixing the reactants in sub-millisecond regimes. The reaction of intrinsically or extrinsically labeled biomolecules can be monitored by recording the fluorescence, F(t), anisotropy, r(t), polarization, p(t), or FRET, F(t)FRET, traces at nanomolar concentrations. These kinetic measurements are critical to elucidate reaction mechanisms, structural information, and even thermodynamics. In a single detector SF, or L-configuration, the r(t), p(t), and F(t) traces are acquired by switching the orientation of the emission polarizer to collect the IVV and IVH signals however it requires two-shot experiments. In a two-detector SF, or T-configuration, these traces are collected in a single-shot experiment, but it increases the apparatus’ complexity and price. Herein, we present a single-detector dual-channel SF to obtain the F(t) and r(t) traces simultaneously, in which a photo-elastic modulator oscillates by 90° the excitation light plane at a 50 kHz frequency, and the emission signal is processed by a set of electronic filters that split it into the r(t) and F(t) analog signals that are digitized and stored into separated spreadsheets by a custom-tailored instrument control software. We evaluated the association kinetics of binary and ternary biological complexes acquired with our dual-channel SF and the traditional methods; such as a single polarizer at the magic angle to acquire F(t), a set of polarizers to track F(t), and r(t), and by energy transfer quenching, F(t)FRET. Our dual-channel SF economized labeled material and yielded rate constants in excellent agreement with the traditional methods.
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Nisha, Ananthan, Pandaram Maheswari, Santhanakumar Subanya, Ponnusamy Munusamy Anbarasan, Karuppaiya Balasundaram Rajesh, and Zbigniew Jaroszewicz. "Ag-Ni bimetallic film on CaF2 prism for high sensitive surface plasmon resonance sensor." Photonics Letters of Poland 13, no. 3 (September 30, 2021): 58. http://dx.doi.org/10.4302/plp.v13i3.1114.
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We present a surface plasmon resonance (SPR) structure based on Kretschmann configuration incorporating bimetallic layers of noble (Ag) and magnetic materials (Ni) over CaF2 prism. Extensive numerical analysis based on transfer matrix theory has been performed to characterize the sensor response considering sensitivity, full width at half maxima, and minimum reflection. Notably, the proposed structure, upon suitably optimizing the thickness of bimetallic layer provides consistent enhancement of sensitivity over other competitive SPR structures. Hence we believe that this proposed SPR sensor could find the new platform for the medical diagnosis, chemical examination and biological detection. Full Text: PDF ReferencesJ. Homola, S.S. Yee, G. Gauglitz, "Surface plasmon resonance sensor based on planar light pipe: theoretical optimization analysis", Sens. Actuators B Chem. 54, 3 (1999). CrossRef X.D. Hoa, A.G. Kirk, M. Tabrizian, "Towards integrated and sensitive surface plasmon resonance biosensors: A review of recent progress", Bioelectron, 23, 151 (2007). CrossRef Z. Lin, L. Jiang, L. Wu, J. Guo, X. Dai, Y. Xiang, D. Fan, "Tuning and Sensitivity Enhancement of Surface Plasmon Resonance Biosensor With Graphene Covered Au-MoS 2-Au Films", IEEE Photonics J. 8(6), 4803308 (2016). CrossRef T. Srivastava, R. Jha, R. Das, "High-Performance Bimetallic SPR Sensor Based on Periodic-Multilayer-Waveguides", IEEE Photonics Technol. Lett. 23(20), 1448 (2011). CrossRef P.K. Maharana, R. Jha, "Chalcogenide prism and graphene multilayer based surface plasmon resonance affinity biosensor for high performance", Sens. Actuators B Chem. 169, 161 (2012). CrossRef R. Verma, B.D. Gupta, R. Jha, "Sensitivity enhancement of a surface plasmon resonance based biomolecules sensor using graphene and silicon layers", Sens. Actuators B Chem. 160, 623 (2011). CrossRef I. 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Sajal, "Theoretical Study of Surface Plasmon Resonance-based Fiber Optic Sensor Utilizing Cobalt and Nickel Films", Braz. J. Phys. 46, 288 (2016). CrossRef K. Shah, N.K. Sharma, AIP Conf. Proc. 2009, 020040 (2018). [23] G. AlaguVibisha, Jeeban Kumar Nayak, P. Maheswari, N. Priyadharsini, A. Nisha, Z. Jaroszewicz, K.B. Rajesh, "Sensitivity enhancement of surface plasmon resonance sensor using hybrid configuration of 2D materials over bimetallic layer of Cu–Ni", Opt. Commun. 463, 125337 (2020). CrossRef A. Nisha, P. Maheswari, P.M. Anbarasan, K.B. Rajesh, Z. Jaroszewicz, "Sensitivity enhancement of surface plasmon resonance sensor with 2D material covered noble and magnetic material (Ni)", Opt. Quantum Electron. 51, 19 (2019). CrossRef M.H.H. Hasib, J.N. Nur, C. Rizal, K.N. Shushama, "Improved Transition Metal Dichalcogenides-Based Surface Plasmon Resonance Biosensors", Condens.Matter 4, 49, (2019). CrossRef S. Herminjard, L. Sirigu, H. P. Herzig, E. Studemann, A. Crottini, J.P. 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Sarkar, Tanmoy, Katharina Lieberth, Aristea Pavlou, Thomas Frank, Volker Mailaender, Iain McCulloch, Paul W. M. Blom, Fabrizio Torriccelli, and Paschalis Gkoupidenis. "An organic artificial spiking neuron for in situ neuromorphic sensing and biointerfacing." Nature Electronics, November 7, 2022. http://dx.doi.org/10.1038/s41928-022-00859-y.
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AbstractThe effective mimicry of neurons is key to the development of neuromorphic electronics. However, artificial neurons are not typically capable of operating in biological environments, which limits their ability to interface with biological components and to offer realistic neuronal emulation. Organic artificial neurons based on conventional circuit oscillators have been created, but they require many elements for their implementation. Here we report an organic artificial neuron that is based on a compact nonlinear electrochemical element. The artificial neuron can operate in a liquid and is sensitive to the concentration of biological species (such as dopamine or ions) in its surroundings. The system offers in situ operation and spiking behaviour in biologically relevant environments—including typical physiological and pathological concentration ranges (5–150 mM)—and with ion specificity. Small-amplitude (1–150 mV) electrochemical oscillations and noise in the electrolytic medium shape the neuronal dynamics, whereas changes in ionic (≥2% over the physiological baseline) and biomolecular (≥ 0.1 mM dopamine) concentrations modulate the neuronal excitability. We also create biohybrid interfaces in which an artificial neuron functions synergistically and in real time with epithelial cell biological membranes.
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Bardozzo, Francesco, Pietro Lió, and Roberto Tagliaferri. "Signal metrics analysis of oscillatory patterns in bacterial multi-omic networks." Bioinformatics, November 13, 2020. http://dx.doi.org/10.1093/bioinformatics/btaa966.
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Abstract Motivation One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and protein regulatory networks towards the design of oscillatory networks for producing useful compounds. Therefore, at different levels of application and for different purposes, the study of biomolecular oscillations can lead to different clues about the mechanisms underlying living cells. It is known that network-level interactions involve more than one type of biomolecule as well as biological processes operating at multiple omic levels. Combining network/pathway-level information with genetic information it is possible to describe well-understood or unknown bacterial mechanisms and organism-specific dynamics. Results Following the methodologies used in signal processing and communication engineering, a methodology is introduced to identify and quantify the extent of multi-omic oscillations. These are due to the process of multi-omic integration and depend on the gene positions on the chromosome. Ad hoc signal metrics are designed to allow further biotechnological explanations and provide important clues about the oscillatory nature of the pathways and their regulatory circuits. Our algorithms designed for the analysis of multi-omic signals are tested and validated on 11 different bacteria for thousands of multi-omic signals perturbed at the network level by different experimental conditions. Information on the order of genes, codon usage, gene expression and protein molecular weight is integrated at three different functional levels. Oscillations show interesting evidence that network-level multi-omic signals present a synchronized response to perturbations and evolutionary relations along taxa. Availability and implementation The algorithms, the code (in language R), the tool, the pipeline and the whole dataset of multi-omic signal metrics are available at: https://github.com/lodeguns/Multi-omicSignals. Supplementary information Supplementary data are available at Bioinformatics online.
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Bartholomai, Bradley M., Amy S. Gladfelter, Jennifer J. Loros, and Jay C. Dunlap. "PRD-2 mediates clock-regulated perinuclear localization of clock gene RNAs within the circadian cycle of Neurospora." Proceedings of the National Academy of Sciences 119, no. 31 (July 26, 2022). http://dx.doi.org/10.1073/pnas.2203078119.
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The transcription–translation negative feedback loops underlying animal and fungal circadian clocks are remarkably similar in their molecular regulatory architecture and, although much is understood about their central mechanism, little is known about the spatiotemporal dynamics of the gene products involved. A common feature of these circadian oscillators is a significant temporal delay between rhythmic accumulation of clock messenger RNAs (mRNAs) encoding negative arm proteins, for example, frq in Neurospora and Per1-3 in mammals, and the appearance of the clock protein complexes assembled from the proteins they encode. Here, we report use of single-molecule RNA fluorescence in situ hybridization (smFISH) to show that the fraction of nuclei actively transcribing the clock gene frq changes in a circadian manner, and that these mRNAs cycle in abundance with fewer than five transcripts per nucleus at any time. Spatial point patterning statistics reveal that frq is spatially clustered near nuclei in a time of day–dependent manner and that clustering requires an RNA-binding protein, PRD-2 (PERIOD-2), recently shown also to bind to mRNA encoding another core clock component, casein kinase 1. An intrinsically disordered protein, PRD-2 displays behavior in vivo and in vitro consistent with participation in biomolecular condensates. These data are consistent with a role for phase-separating RNA-binding proteins in spatiotemporally organizing clock mRNAs to facilitate local translation and assembly of clock protein complexes.
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Arbel-Goren, Rinat, Valentina Buonfiglio, Francesca Di Patti, Sergio Camargo, Anna Zhitnitsky, Ana Valladares, Enrique Flores, Antonia Herrero, Duccio Fanelli, and Joel Stavans. "Robust, coherent, and synchronized circadian clock-controlled oscillations along Anabaena filaments." eLife 10 (March 22, 2021). http://dx.doi.org/10.7554/elife.64348.
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Circadian clocks display remarkable reliability despite significant stochasticity in biomolecular reactions. We study the dynamics of a circadian clock-controlled gene at the individual cell level in Anabaena sp. PCC 7120, a multicellular filamentous cyanobacterium. We found significant synchronization and spatial coherence along filaments, clock coupling due to cell-cell communication, and gating of the cell cycle. Furthermore, we observed low-amplitude circadian oscillatory transcription of kai genes encoding the post-transcriptional core oscillatory circuit and high-amplitude oscillations of rpaA coding for the master regulator transducing the core clock output. Transcriptional oscillations of rpaA suggest an additional level of regulation. A stochastic one-dimensional toy model of coupled clock cores and their phosphorylation states shows that demographic noise can seed stochastic oscillations outside the region where deterministic limit cycles with circadian periods occur. The model reproduces the observed spatio-temporal coherence along filaments and provides a robust description of coupled circadian clocks in a multicellular organism.
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Gutierrez, Brenda C., Marcelo R. Pita Almenar, Luciano J. Martínez, Manuel Siñeriz Louis, Virginia H. Albarracín, María del Rocío Cantero, and Horacio F. Cantiello. "Honeybee Brain Oscillations Are Generated by Microtubules. The Concept of a Brain Central Oscillator." Frontiers in Molecular Neuroscience 14 (September 29, 2021). http://dx.doi.org/10.3389/fnmol.2021.727025.
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Microtubules (MTs) are important structures of the cytoskeleton in neurons. Mammalian brain MTs act as biomolecular transistors that generate highly synchronous electrical oscillations. However, their role in brain function is largely unknown. To gain insight into the MT electrical oscillatory activity of the brain, we turned to the honeybee (Apis mellifera) as a useful model to isolate brains and MTs. The patch clamp technique was applied to MT sheets of purified honeybee brain MTs. High resistance seal patches showed electrical oscillations that linearly depended on the holding potential between ± 200 mV and had an average conductance in the order of ~9 nS. To place these oscillations in the context of the brain, we also explored local field potential (LFP) recordings from the Triton X-permeabilized whole honeybee brain unmasking spontaneous oscillations after but not before tissue permeabilization. Frequency domain spectral analysis of time records indicated at least two major peaks at approximately ~38 Hz and ~93 Hz in both preparations. The present data provide evidence that MT electrical oscillations are a novel signaling mechanism implicated in brain wave activity observed in the insect brain.
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O’ Neill, John S., Nathaniel P. Hoyle, J. Brian Robertson, Rachel S. Edgar, Andrew D. Beale, Sew Y. Peak-Chew, Jason Day, Ana S. H. Costa, Christian Frezza, and Helen C. Causton. "Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis." Nature Communications 11, no. 1 (September 17, 2020). http://dx.doi.org/10.1038/s41467-020-18330-x.
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Abstract Yeast physiology is temporally regulated, this becomes apparent under nutrient-limited conditions and results in respiratory oscillations (YROs). YROs share features with circadian rhythms and interact with, but are independent of, the cell division cycle. Here, we show that YROs minimise energy expenditure by restricting protein synthesis until sufficient resources are stored, while maintaining osmotic homeostasis and protein quality control. Although nutrient supply is constant, cells sequester and store metabolic resources via increased transport, autophagy and biomolecular condensation. Replete stores trigger increased H+ export which stimulates TORC1 and liberates proteasomes, ribosomes, chaperones and metabolic enzymes from non-membrane bound compartments. This facilitates translational bursting, liquidation of storage carbohydrates, increased ATP turnover, and the export of osmolytes. We propose that dynamic regulation of ion transport and metabolic plasticity are required to maintain osmotic and protein homeostasis during remodelling of eukaryotic proteomes, and that bioenergetic constraints selected for temporal organisation that promotes oscillatory behaviour.
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Quo, Chang F., and May D. Wang. "Quantitative analysis of numerical solvers for oscillatory biomolecular system models." BMC Bioinformatics 9, S6 (May 2008). http://dx.doi.org/10.1186/1471-2105-9-s6-s17.
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Hancock, Edward J., and Diego A. Oyarzún. "Stabilization of antithetic control via molecular buffering." Journal of The Royal Society Interface 19, no. 188 (March 2022). http://dx.doi.org/10.1098/rsif.2021.0762.
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A key goal in synthetic biology is the construction of molecular circuits that robustly adapt to perturbations. Although many natural systems display perfect adaptation, whereby stationary molecular concentrations are insensitive to perturbations, its de novo engineering has proven elusive. The discovery of the antithetic control motif was a significant step towards a universal mechanism for engineering perfect adaptation. Antithetic control provides perfect adaptation in a wide range of systems, but it can lead to oscillatory dynamics due to loss of stability; moreover, it can lose perfect adaptation in fast growing cultures. Here, we introduce an extended antithetic control motif that resolves these limitations. We show that molecular buffering, a widely conserved mechanism for homeostatic control in Nature, stabilizes oscillations and allows for near-perfect adaptation during rapid growth. We study multiple buffering topologies and compare their performance in terms of their stability and adaptation properties. We illustrate the benefits of our proposed strategy in exemplar models for biofuel production and growth rate control in bacterial cultures. Our results provide an improved circuit for robust control of biomolecular systems.
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Prados, A., A. Carpio, and L. L. Bonilla. "Spin-oscillator model for the unzipping of biomolecules by mechanical force." Physical Review E 86, no. 2 (August 21, 2012). http://dx.doi.org/10.1103/physreve.86.021919.
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Ozcan, Burak, Ece Bayrak, and Cevat Erisken. "Characterization of Human Dental Pulp Tissue Under Oscillatory Shear and Compression." Journal of Biomechanical Engineering 138, no. 6 (May 2, 2016). http://dx.doi.org/10.1115/1.4033437.
Full textAbstract:
Availability of material as well as biological properties of native tissues is critical for biomaterial design and synthesis for regenerative engineering. Until recently, selection of biomaterials and biomolecule carriers for dental pulp regeneration has been done randomly or based on experience mainly due to the absence of benchmark data for dental pulp tissue. This study, for the first time, characterizes the linear viscoelastic material functions and compressive properties of human dental pulp tissue harvested from wisdom teeth, under oscillatory shear and compression. The results revealed a gel-like behavior of the pulp tissue over the frequency range of 0.1–100 rps. Uniaxial compression tests generated peak normal stress and compressive modulus values of 39.1±20.4 kPa and 5.5±2.8 kPa, respectively. Taken collectively, the linear viscoelastic and uniaxial compressive properties of the human dental pulp tissue reported here should enable the better tailoring of biomaterials or biomolecule carriers to be employed in dental pulp regeneration.
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Maestri, Stefano, Emanuela Merelli, and Marco Pettini. "Agent-based models for detecting the driving forces of biomolecular interactions." Scientific Reports 12, no. 1 (February 3, 2022). http://dx.doi.org/10.1038/s41598-021-04205-8.
Full textAbstract:
AbstractAgent-based modelling and simulation have been effectively applied to the study of complex biological systems, especially when composed of many interacting entities. Representing biomolecules as autonomous agents allows this approach to bring out the global behaviour of biochemical processes as resulting from local molecular interactions. In this paper, we leverage the capabilities of the agent paradigm to construct an in silico replica of the glycolytic pathway; the aim is to detect the role that long-range electrodynamic forces might have on the rate of glucose oxidation. Experimental evidences have shown that random encounters and short-range potentials might not be sufficient to explain the high efficiency of biochemical reactions in living cells. However, while the latest in vitro studies are limited by present-day technology, agent-based simulations provide an in silico support to the outcomes hitherto obtained and shed light on behaviours not yet well understood. Our results grasp properties hard to uncover through other computational methods, such as the effect of electromagnetic potentials on glycolytic oscillations.