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Biological noise

Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe, Karen M Page
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules-morphogens-guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms...
October 2016: PLoS Computational Biology
Alessandro Borri, Pasquale Palumbo, Abhyudai Singh
Synthetic biology combines different branches of biology and engineering aimed at designing synthetic biological circuits able to replicate emergent properties useful for the biotechnology industry, human health and environment. The role of negative feedback in noise propagation for a basic enzymatic reaction scheme is investigated. Two feedback control schemes on enzyme expression are considered: one from the final product of the pathway activity, the other from the enzyme accumulation. Both schemes are designed to provide the same steady-state average values of the involved players, in order to evaluate the feedback performances according to the same working mode...
October 2016: IET Systems Biology
Do Young Noh, Chan Kim, Yoonhee Kim, Changyong Song
Achieving a resolution near 1 nm is a critical issue in coherent x-ray diffraction imaging (CDI) for applications in materials and biology. Albeit with various advantages of CDI based on synchrotrons and newly developed x-ray free electron lasers, its applications would be limited without improving resolution well below 10 nm. Here, we review the issues and efforts in improving CDI resolution including various methods for resolution determination. Enhancing diffraction signal at large diffraction angles, with the aid of interference between neighboring strong scatterers or templates, is reviewed and discussed in terms of increasing signal-to-noise ratio...
October 18, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Sitah F Alanazi, Khalid S Alzimami, Magdy M Ghannam, Ibrahim J Aljammaz, Faisal Alrumayan, Salem A Sassi
PURPOSE: Interest in PET imaging using zirconium-89 (Zr) (t1/2=78.41 h)-labeled tracers for the tracking and quantification of monoclonal antibodies (mAbs) is growing, mainly because of its well-matched physical half-life with the biological half-life of intact mAbs. This study aims to evaluate the imaging characteristics of Zr-PET in comparison with those obtained using fluorine-18 fluorodeoxyglucose (F-FDG) PET (gold standard tracer in PET imaging) using a Time-Of-Flight (TOF) PET/computed tomography (CT) scanner...
October 4, 2016: Nuclear Medicine Communications
Jose Negrete, Alain Pumir, Hsin-Fang Hsu, Christian Westendorf, Marco Tarantola, Carsten Beta, Eberhard Bodenschatz
Biological systems with their complex biochemical networks are known to be intrinsically noisy. Here we investigate the dynamics of actin polymerization of amoeboid cells, which are close to the onset of oscillations. We show that the large phenotypic variability in the polymerization dynamics can be accurately captured by a generic nonlinear oscillator model in the presence of noise. We determine the relative role of the noise with a single dimensionless, experimentally accessible parameter, thus providing a quantitative description of the variability in a population of cells...
September 30, 2016: Physical Review Letters
Jakub Jędrak, Anna Ochab-Marcinek
We study a stochastic model of gene expression, in which protein production has a form of random bursts whose size distribution is arbitrary, whereas protein decay is a first-order reaction. We find exact analytical expressions for the time evolution of the cumulant-generating function for the most general case when both the burst size probability distribution and the model parameters depend on time in an arbitrary (e.g., oscillatory) manner, and for arbitrary initial conditions. We show that in the case of periodic external activation and constant protein degradation rate, the response of the gene is analogous to the resistor-capacitor low-pass filter, where slow oscillations of the external driving have a greater effect on gene expression than the fast ones...
September 2016: Physical Review. E
Kevin R Pilkiewicz, Michael L Mayo
The internal biochemical state of a cell is regulated by a vast transcriptional network that kinetically correlates the concentrations of numerous proteins. Fluctuations in protein concentration that encode crucial information about this changing state must compete with fluctuations caused by the noisy cellular environment in order to successfully transmit information across the network. Oftentimes, one protein must regulate another through a sequence of intermediaries, and conventional wisdom, derived from the data processing inequality of information theory, leads us to expect that longer sequences should lose more information to noise...
September 2016: Physical Review. E
Anatoly Yambartsev, Michael A Perlin, Yevgeniy Kovchegov, Natalia Shulzhenko, Karina L Mine, Xiaoxi Dong, Andrey Morgun
BACKGROUND: Gene covariation networks are commonly used to study biological processes. The inference of gene covariation networks from observational data can be challenging, especially considering the large number of players involved and the small number of biological replicates available for analysis. RESULTS: We propose a new statistical method for estimating the number of erroneous edges in reconstructed networks that strongly enhances commonly used inference approaches...
October 13, 2016: Biology Direct
Ji-Yong An, Zhu-Hong You, Xing Chen, De-Shuang Huang, Zheng-Wei Li, Gang Liu, Yin Wang
Self-interacting Proteins (SIPs) play an essential role in a wide range of biological processes, such as gene expression regulation, signal transduction, enzyme activation and immune response. Because of the limitations for experimental self-interaction proteins identification, developing an effective computational method based on protein sequence to detect SIPs is much important. In the study, we proposed a novel computational approach called RVMBIGP that combines the Relevance Vector Machine (RVM) model and Bi-gram probability (BIGP) to predict SIPs based on protein sequence...
October 8, 2016: Oncotarget
Laurent Potvin-Trottier, Nathan D Lord, Glenn Vinnicombe, Johan Paulsson
Synthetically engineered genetic circuits can perform a wide variety of tasks but are generally less accurate than natural systems. Here we revisit the first synthetic genetic oscillator, the repressilator, and modify it using principles from stochastic chemistry in single cells. Specifically, we sought to reduce error propagation and information losses, not by adding control loops, but by simply removing existing features. We show that this modification created highly regular and robust oscillations. Furthermore, some streamlined circuits kept 14 generation periods over a range of growth conditions and kept phase for hundreds of generations in single cells, allowing cells in flasks and colonies to oscillate synchronously without any coupling between them...
October 12, 2016: Nature
M B Morrissey
Meta-analysis is increasingly used to synthesize major patterns in the large literatures within ecology and evolution. Meta-analytic methods that do not account for the process of observing data, which we may refer to as 'informal meta-analyses', may have undesirable properties. In some cases, informal meta-analyses may produce results that are unbiased, but do not necessarily make the best possible use of available data. In other cases, unbiased statistical noise in individual reports in the literature can potentially be converted into severe systematic biases in informal meta-analyses...
October 2016: Journal of Evolutionary Biology
Chelsea Blankenship, Fawen Zhang, Robert Keith
BACKGROUND: Although most cochlear implant (CI) users achieve improvements in speech perception, there is still a wide variability in speech perception outcomes. There is a growing body of literature that supports the relationship between individual differences in temporal processing and speech perception performance in CI users. Previous psychophysical studies have emphasized the importance of temporal acuity for overall speech perception performance. Measurement of gap detection thresholds (GDTs) is the most common measure currently used to assess temporal resolution...
October 2016: Journal of the American Academy of Audiology
Jacob P Keller, Loren L Looger
Transmembrane transporter proteins allow the passage of essentially all biologically important molecules across the lipid membranes of cells and organelles and are therefore of central importance to all forms of life. Current methods of transporter measurement, however, are lacking in several dimensions. Herein, a method is presented in which oscillating stimuli are presented to transporter-expressing cells, and activity is measured through imaging the corresponding oscillating responses of intracellular fluorescent sensors...
October 6, 2016: Molecular Cell
Pablo Villegas, José Ruiz-Franco, Jorge Hidalgo, Miguel A Muñoz
Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline between their ordered and disordered phases. Critical networks have been argued to lead to a number of functional advantages such as maximal dynamical range, maximal sensitivity to environmental changes, as well as to an excellent tradeoff between stability and flexibility...
October 7, 2016: Scientific Reports
Paulo R F Rocha, Paul Schlett, Ulrike Kintzel, Volker Mailänder, Lode K J Vandamme, Gunther Zeck, Henrique L Gomes, Fabio Biscarini, Dago M de Leeuw
Microelectrode arrays (MEA) record extracellular local field potentials of cells adhered to the electrodes. A disadvantage is the limited signal-to-noise ratio. The state-of-the-art background noise level is about 10 μVpp. Furthermore, in MEAs low frequency events are filtered out. Here, we quantitatively analyze Au electrode/electrolyte interfaces with impedance spectroscopy and noise measurements. The equivalent circuit is the charge transfer resistance in parallel with a constant phase element that describes the double layer capacitance, in series with a spreading resistance...
October 6, 2016: Scientific Reports
Nick E Phillips, Cerys S Manning, Tom Pettini, Veronica Biga, Elli Marinopoulou, Peter Stanley, James Boyd, James Bagnall, Pawel Paszek, David G Spiller, Michael Rh White, Marc Goodfellow, Tobias Galla, Magnus Rattray, Nancy Papalopulu
Recent studies suggest that cells make stochastic choices with respect to differentiation or division. However, the molecular mechanism underlying such stochasticity is unknown. We previously proposed that the timing of vertebrate neuronal differentiation is regulated by molecular oscillations of a transcriptional repressor, HES1, tuned by a post-transcriptional repressor, miR-9. Here, we computationally model the effects of intrinsic noise on the Hes1/miR-9 oscillator as a consequence of low molecular numbers of interacting species, determined experimentally...
October 4, 2016: ELife
Michiko Nishiyama, Masako Sonobe, Kazuhiro Watanabe
In this paper, we present a pulse pressure waveform sensor that does not constrain a wearer's daily activity; the sensor uses hetero-core fiber optics. Hetero-core fiber sensors have been found to be sensitive to moderate bending. To detect minute pulse pressure changes from the radial artery at the wrist, we devised a fiber sensor arrangement using three-point bending supports. We analyzed and evaluated the measurement validity using wavelet transformation, which is well-suited for biological signal processing...
September 1, 2016: Biomedical Optics Express
Masahiro Yamanari, Satoru Tsuda, Taiki Kokubun, Yukihiro Shiga, Kazuko Omodaka, Naoko Aizawa, Yu Yokoyama, Noriko Himori, Shiho Kunimatsu-Sanuki, Kazuichi Maruyama, Hiroshi Kunikata, Toru Nakazawa
Estimation of polarimetric parameters has been a fundamental issue to assess biological tissues that have form birefringence or polarization scrambling in polarization-sensitive optical coherence tomography (PS-OCT). We present a mathematical framework to provide a maximum likelihood estimation of the target covariance matrix and its incoherent target decomposition to estimate a Jones matrix of a dominant scattering mechanism, called Cloude-Pottier decomposition, thereby deriving the phase retardation and the optic axis of the sample...
September 1, 2016: Biomedical Optics Express
Susana Posada-Cespedes, David Seifert, Niko Beerenwinkel
Rapidly evolving RNA viruses prevail within a host as a collection of closely related variants, referred to as viral quasispecies. Advances in high-throughput sequencing (HTS) technologies have facilitated the assessment of the genetic diversity of such virus populations at an unprecedented level of detail. However, analysis of HTS data from virus populations is challenging due to short, error-prone reads. In order to account for uncertainties originating from these limitations, several computational and statistical methods have been developed for studying the genetic heterogeneity of virus population...
September 28, 2016: Virus Research
Jiachang Li, Xingjun Zhu, Meng Xue, Wei Feng, Rongliang Ma, Fuyou Li
Lanthanide upconversion nanophosphors (Ln-UCNPs) have attracted great attention in a variety of fields, benefiting from low background fluorescence interference and a high signal-to-noise ratio of upconversion luminescence. However, the establishment of Ln-UCNPs with dual near-infrared (NIR) emission channels still remains challenging. Herein, we report the design and synthesis of Nd(3+)-sensitized NaYbF4:Tm@NaYF4:Yb@NaNdF4:Yb hierarchical-structured nanoparticles that emit NIR luminescence at 696 and 980 nm under excitation at 808 nm...
October 17, 2016: Inorganic Chemistry
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