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Biological noise

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https://www.readbyqxmd.com/read/28441042/aberrantly-expressed-long-noncoding-rnas-in-recurrent-implantation-failure-a-microarray-related-study
#1
Li-Juan Fan, Hong-Jing Han, Jing Guan, Xiao-Wei Zhang, Qing-Hua Cui, Huan Shen, Cheng Shi
Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs longer than 200 nucleotides. They were long regarded as transcription noise for their low expression and non-protein coding features. Recent published reports indicate that lncRNAs are involved in virtually every aspect of human biology. We aimed to profile the endometrial lncRNA expression pattern in women with recurrent implantation failure (RIF) and predict the function of the genes of the dysregulated lncRNA transcripts. Endometrial samples (24) were collected during window of implantation (14 RIF women and 10 women who conceived after embryo transfer)...
April 25, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28434879/sonoluminescence-and-acoustic-emission-spectra-at-different-stages-of-cavitation-zone-development
#2
N V Dezhkunov, A Francescutto, L Serpe, R Canaparo, G Cravotto
The way in which a cavitation zone develops in a focused pulsed ultrasound field is studied in this work. Sonoluminescence (SL), total hydrophone output and cavitation noise spectra have been recorded across a gradual, smooth increase in applied voltage. It is shown that the cavitation zone passes through a number of stages of evolution, according to increasing ultrasound intensity, decreasing pulse period and increasing ultrasound pulse duration. Sonoluminescence is absent in the first phase and the hydrophone output spectra consists of a main line with two or three harmonics whose intensity is much lower than that of the main (fundamental) line...
April 6, 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28433588/how-environmental-noise-can-contract-and-destroy-a-persistence-zone-in-population-models-with-allee-effect
#3
Irina Bashkirtseva, Lev Ryashko
A problem of the analysis of the noise-induced extinction in population models with Allee effect is considered. To clarify mechanisms of the extinction, we suggest a new technique combining an analysis of the geometry of attractors and their stochastic sensitivity. For the conceptual one-dimensional discrete Ricker-type model, on the base of the bifurcation analysis, deterministic persistence zones are constructed in the space of initial states and biological parameters. It is shown that the random environmental noise can contract, and even destroy these persistence zones...
April 19, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28432993/chemical-biological-and-dna-markers-for-tracing-slaughterhouse-effluent
#4
P J Harvey, M P Taylor, H K Handley, S Foster, M R Gillings, A J Asher
Agricultural practices, if not managed correctly, can have a negative impact on receiving environments via waste disposal and discharge. In this study, a chicken slaughter facility on the rural outskirts of Sydney, Australia, has been identified as a possible source of persistent effluent discharge into a peri-urban catchment. Questions surrounding the facility's environmental management practices go back more than four decades. Despite there having never been a definitive determination of the facility's impact on local stream water quality, the New South Wales Environment Protection Authority (NSW EPA) has implemented numerous pollution reduction requirements to manage noise and water pollution at the slaughter facility...
April 19, 2017: Environmental Research
https://www.readbyqxmd.com/read/28431025/1h-magnetic-resonance-spectroscopy-of-live-human-sperm
#5
S Reynolds, S J Calvert, M N Paley, A A Pacey
STUDY QUESTION: Can 1H Magnetic Resonance Spectroscopy (MRS) be used to obtain information about the molecules and metabolites in live human spermatozoa? SUMMARY ANSWER: Percoll-based density gradient centrifugation (DGC) followed by a further two washing steps, yielded enough sperm with minimal contamination (<0.01%) from seminal fluid to permit effective MRS which detected significant differences (p < 0.05) in the choline/glycerophosphocholine, lipid and lactate regions of the 1H MRS spectrum between sperm in the pellet and those from the 40/80% interface...
April 18, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28428974/perspective-a-toolbox-for-protein-structure-determination-in-physiological-environment-through-oriented-2d-ordered-site-specific-immobilization
#6
M Altissimo, M Kiskinova, R Mincigrucci, L Vaccari, C Guarnaccia, C Masciovecchio
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28420043/-alcohol-consumption-prevalence-in-civil-servants
#7
Josep Maria Molina Aragonés, Cristina Abadia Castelló
Temporomandibular dysfunction syndrome (TMDS) includes a number of clinical conditions involving the temporomandibular joint (TMJ), the muscles involved in mastication, or both. The symptoms of TMDS include decreased mobility, masticatory muscle pain, TMJ pain, functional alteration accompanied by articular noises, myofascial pain or deviation of the mouth opening. Work with visual display terminals (VDTs) has become widespread in the past several years and the conditions associated with this type of work have been associated with the appearance of certain musculoskeletal pathologies...
April 2017: Archivos de Prevención de Riesgos Laborales
https://www.readbyqxmd.com/read/28419796/-third-working-conditions-and-health-survey-in-navarre-spain-main-findings
#8
Vega García
OBJECTIVE: To describe health problems and working conditions perceived by workers of Navarra, Spain. METHODS: Conduct of the Third Survey of Working Conditions and Health in Navarre. We administered the Seventh Spanish National Survey of Working Conditions questionnaire by personal interviews conducted in the workers' homes between October 2014 and December 2014, and using a three-stage stratified sampling approach, by economic activity, work establishment size and gender...
April 2017: Archivos de Prevención de Riesgos Laborales
https://www.readbyqxmd.com/read/28415353/noise-induced-symmetry-breaking-far-from-equilibrium-and-the-emergence-of-biological-homochirality
#9
Farshid Jafarpour, Tommaso Biancalani, Nigel Goldenfeld
The origin of homochirality, the observed single-handedness of biological amino acids and sugars, has long been attributed to autocatalysis, a frequently assumed precursor for early life self-replication. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross-inhibition of the two chiral states, an unlikely scenario for early life self-replicators. Here we present a theory for a stochastic individual-level model of autocatalytic prebiotic self-replicators that are maintained out of thermal equilibrium...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28414750/effect-of-transcription-factor-resource-sharing-on-gene-expression-noise
#10
Dipjyoti Das, Supravat Dey, Robert C Brewster, Sandeep Choubey
Gene expression is intrinsically a stochastic (noisy) process with important implications for cellular functions. Deciphering the underlying mechanisms of gene expression noise remains one of the key challenges of regulatory biology. Theoretical models of transcription often incorporate the kinetics of how transcription factors (TFs) interact with a single promoter to impact gene expression noise. However, inside single cells multiple identical gene copies as well as additional binding sites can compete for a limiting pool of TFs...
April 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28409952/nonsymmetric-interactions-trigger-collective-swings-in-globally-ordered-systems
#11
Andrea Cavagna, Irene Giardina, Asja Jelic, Stefania Melillo, Leonardo Parisi, Edmondo Silvestri, Massimiliano Viale
Many systems in nature, from ferromagnets to flocks of birds, exhibit ordering phenomena on the large scale. In condensed matter systems, order is statistically robust for large enough dimensions, with relative fluctuations due to noise vanishing with system size. Several biological systems, however, are less stable and spontaneously change their global state on relatively short time scales. Here we show that there are two crucial ingredients in these systems that enhance the effect of noise, leading to collective changes of state on finite time scales and off-equilibrium behavior: the nonsymmetric nature of interactions between individuals, and the presence of local heterogeneities in the topology of the network...
March 31, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28402621/specific-imaging-of-intracellular-lipid-droplets-using-a-benzothiadiazole-derivative-with-solvatochromic-properties
#12
Hanna Appelqvist, Kati Stranius, Karl Börjesson, K Peter R Nilsson, Christine Dyrager
Altered lipid metabolism and extensive lipid storage in cells have been associated with various medical disorders, including cancer. The development of fluorescent probes that specifically accumulate in lipid deposits is therefore of great interest in order to study pathological processes that are linked to dysregulated lipogenesis. In the present study, we present a small fluorescent benzothiadiazole dye that specifically stains lipid droplets in living and fixated cells. The photophysical characterization of the probe revealed strong solvatochromic behavior, large Stokes shifts, and high fluorescent quantum yields in hydrophobic solvents...
April 26, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28397688/engineering-of-a-synthetic-quadrastable-gene-network-to-approach-waddington-landscape-and-cell-fate-determination
#13
Fuqing Wu, Ri-Qi Su, Ying-Cheng Lai, Xiao Wang
The process of cell fate determination has been depicted intuitively as cells travelling and resting on a rugged landscape, which has been probed by various theoretical studies. However, few studies have experimentally demonstrated how underlying gene regulatory networks shape the landscape and hence orchestrate cellular decision-making in the presence of both signal and noise. Here we tested different topologies and verified a synthetic gene circuit with mutual inhibition and auto-activations to be quadrastable, which enables direct study of quadruple cell fate determination on an engineered landscape...
April 11, 2017: ELife
https://www.readbyqxmd.com/read/28393373/a-population-based-approach-to-analyzing-pulses-in-time-series-of-hormone-data
#14
K W Horton, N E Carlson, G K Grunwald, M J Mulvahill, A J Polotsky
Studies of reproductive physiology involve rapid sampling protocols that result in time series of hormone concentrations. The signature pattern in these times series is pulses of hormone release. Various statistical models for quantifying the pulsatile release features exist. Currently these models are fitted separately to each individual and the resulting estimates averaged to arrive at post hoc population-level estimates. When the signal-to-noise ratio is small or the time of observation is short (e.g., 6 h), this two-stage estimation approach can fail...
April 9, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28393138/new-method-to-study-the-vibrational-modes-of-biomolecules-in-the-terahertz-range-based-on-a-single-stage-raman-spectrometer
#15
Basanth S Kalanoor, Maria Ronen, Ziv Oren, Doron Gerber, Yaakov R Tischler
The low-frequency vibrational (LFV) modes of biomolecules reflect specific intramolecular and intermolecular thermally induced fluctuations that are driven by external perturbations, such as ligand binding, protein interaction, electron transfer, and enzymatic activity. Large efforts have been invested over the years to develop methods to access the LFV modes due to their importance in the studies of the mechanisms and biological functions of biomolecules. Here, we present a method to measure the LFV modes of biomolecules based on Raman spectroscopy that combines volume holographic filters with a single-stage spectrometer, to obtain high signal-to-noise-ratio spectra in short acquisition times...
March 31, 2017: ACS Omega
https://www.readbyqxmd.com/read/28392451/electron-tomography-simulator-with-realistic-3d-phantom-for-evaluation-of-acquisition-alignment-and-reconstruction-methods
#16
Xiaohua Wan, Tsvi Katchalski, Christopher Churas, Sreya Ghosh, Sebastien Phan, Albert Lawrence, Yu Hao, Ziying Zhou, Ruijuan Chen, Yu Chen, Fa Zhang, Mark H Ellisman
Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless,verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment.This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise...
April 6, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28389569/parallel-adaptive-evolution-of-geographically-distant-herring-populations-on-both-sides-of-the-north-atlantic-ocean
#17
Sangeet Lamichhaney, Angela P Fuentes-Pardo, Nima Rafati, Nils Ryman, Gregory R McCracken, Christina Bourne, Rabindra Singh, Daniel E Ruzzante, Leif Andersson
Atlantic herring is an excellent species for studying the genetic basis of adaptation in geographically distant populations because of its characteristically large population sizes and low genetic drift. In this study we compared whole-genome resequencing data of Atlantic herring populations from both sides of the Atlantic Ocean. An important finding was the very low degree of genetic differentiation among geographically distant populations (fixation index = 0.026), suggesting lack of reproductive isolation across the ocean...
April 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28386181/analytical-fuzzy-approach-to-biological-data-analysis
#18
Weiping Zhang, Jingzhi Yang, Yanling Fang, Huanyu Chen, Yihua Mao, Mohit Kumar
The assessment of the physiological state of an individual requires an objective evaluation of biological data while taking into account both measurement noise and uncertainties arising from individual factors. We suggest to represent multi-dimensional medical data by means of an optimal fuzzy membership function. A carefully designed data model is introduced in a completely deterministic framework where uncertain variables are characterized by fuzzy membership functions. The study derives the analytical expressions of fuzzy membership functions on variables of the multivariate data model by maximizing the over-uncertainties-averaged-log-membership values of data samples around an initial guess...
March 2017: Saudi Journal of Biological Sciences
https://www.readbyqxmd.com/read/28384156/how-evolution-learns-to-generalise-using-the-principles-of-learning-theory-to-understand-the-evolution-of-developmental-organisation
#19
Kostas Kouvaris, Jeff Clune, Loizos Kounios, Markus Brede, Richard A Watson
One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments. Such variability is crucial for evolvability, but poorly understood. In particular, how can natural selection favour developmental organisations that facilitate adaptive evolution in previously unseen environments? Such a capacity suggests foresight that is incompatible with the short-sighted concept of natural selection. A potential resolution is provided by the idea that evolution may discover and exploit information not only about the particular phenotypes selected in the past, but their underlying structural regularities: new phenotypes, with the same underlying regularities, but novel particulars, may then be useful in new environments...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28379950/computation-and-measurement-of-cell-decision-making-errors-using-single-cell-data
#20
Iman Habibi, Raymond Cheong, Tomasz Lipniacki, Andre Levchenko, Effat S Emamian, Ali Abdi
In this study a new computational method is developed to quantify decision making errors in cells, caused by noise and signaling failures. Analysis of tumor necrosis factor (TNF) signaling pathway which regulates the transcription factor Nuclear Factor κB (NF-κB) using this method identifies two types of incorrect cell decisions called false alarm and miss. These two events represent, respectively, declaring a signal which is not present and missing a signal that does exist. Using single cell experimental data and the developed method, we compute false alarm and miss error probabilities in wild-type cells and provide a formulation which shows how these metrics depend on the signal transduction noise level...
April 2017: PLoS Computational Biology
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