174 research outputs found
CplexA: a Mathematica package to study macromolecular-assembly control of gene expression
Summary: Macromolecular assembly vertebrates essential cellular processes,
such as gene regulation and signal transduction. A major challenge for
conventional computational methods to study these processes is tackling the
exponential increase of the number of configurational states with the number of
components. CplexA is a Mathematica package that uses functional programming to
efficiently compute probabilities and average properties over such
exponentially large number of states from the energetics of the interactions.
The package is particularly suited to study gene expression at complex
promoters controlled by multiple, local and distal, DNA binding sites for
transcription factors. Availability: CplexA is freely available together with
documentation at http://sourceforge.net/projects/cplexa/.Comment: 28 pages. Includes Mathematica, Matlab, and Python implementation
tutorials. Software can be downloaded at http://cplexa.sourceforge.net
Stochastic dynamics of macromolecular-assembly networks
The formation and regulation of macromolecular complexes provides the
backbone of most cellular processes, including gene regulation and signal
transduction. The inherent complexity of assembling macromolecular structures
makes current computational methods strongly limited for understanding how the
physical interactions between cellular components give rise to systemic
properties of cells. Here we present a stochastic approach to study the
dynamics of networks formed by macromolecular complexes in terms of the
molecular interactions of their components. Exploiting key thermodynamic
concepts, this approach makes it possible to both estimate reaction rates and
incorporate the resulting assembly dynamics into the stochastic kinetics of
cellular networks. As prototype systems, we consider the lac operon and phage
lambda induction switches, which rely on the formation of DNA loops by proteins
and on the integration of these protein-DNA complexes into intracellular
networks. This cross-scale approach offers an effective starting point to move
forward from network diagrams, such as those of protein-protein and DNA-protein
interaction networks, to the actual dynamics of cellular processes.Comment: Open Access article available at
http://www.nature.com/msb/journal/v2/n1/full/msb4100061.htm
Dynamics-informed deconvolutional neural networks for super-resolution identification of regime changes in epidemiological time series
Inferring the timing and amplitude of perturbations in epidemiological
systems from their stochastically spread low-resolution outcomes is as relevant
as challenging. It is a requirement for current approaches to overcome the need
to know the details of the perturbations to proceed with the analyses. However,
the general problem of connecting epidemiological curves with the underlying
incidence lacks the highly effective methodology present in other inverse
problems, such as super-resolution and dehazing from computer vision. Here, we
develop an unsupervised physics-informed convolutional neural network approach
in reverse to connect death records with incidence that allows the
identification of regime changes at single-day resolution. Applied to COVID-19
data with proper regularization and model-selection criteria, the approach can
identify the implementation and removal of lockdowns and other
nonpharmaceutical interventions with 0.93-day accuracy over the time span of a
year.Comment: 18 pages, 5 figure
Multiprotein DNA looping
DNA looping plays a fundamental role in a wide variety of biological
processes, providing the backbone for long range interactions on DNA. Here we
develop the first model for DNA looping by an arbitrarily large number of
proteins and solve it analytically in the case of identical binding. We uncover
a switch-like transition between looped and unlooped phases and identify the
key parameters that control this transition. Our results establish the basis
for the quantitative understanding of fundamental cellular processes like DNA
recombination, gene silencing, and telomere maintenance.Comment: 11 pages, 4 figure
Ab initio thermodynamic modeling of distal multisite transcription regulation
Transcription regulation typically involves the binding of proteins over long distances on multiple DNA sites that are brought close to each other by the formation of DNA loops. The inherent complexity of assembling regulatory complexes on looped DNA challenges the understanding of even the simplest genetic systems, including the prototypical lac operon. Here we implement a scalable approach based on thermodynamic molecular properties to model ab initio systems regulated through multiple DNA sites with looping. We show that this approach applied to the lac operon accurately predicts the system behavior for a wide range of cellular conditions, which include the transcription rate over five orders of magnitude as a function of the repressor concentration for wild type and all seven combinations of deletions of three operators, as well as the observed induction curves for cells with and without active catabolite activator protein. Our results provide new insights into the detailed functioning of the lac operon and reveal an efficient avenue to incorporate the required underlying molecular complexity into fully predictive models of gene regulation
Bitter, Sweet, Salty, Sour and Umami Taste Perception Decreases with Age: Sex-Specific Analysis, Modulation by Genetic Variants and Taste-Preference Associations in 18 to 80 Year-Old Subjects
There is growing interest in relating taste perception to diet and healthy aging. However, there is still limited information on the influence of age, sex and genetics on taste acuity as well as on the relationship between taste perception and taste preferences. We have analysed the influence of age on the intensity rating of the five basic tastes: sweet, salty, bitter, sour and umami (separately and jointly in a ``total taste score´´) and their modulation by sex and genetics in a relatively healthy population (men and women) aged 18-80 years (n = 1020 Caucasian European participants). Taste perception was determined by challenging subjects with solutions of the five basic tastes using standard prototypical tastants (6-n-propylthiouracil (PROP), NaCl, sucrose, monopotassium glutamate and citric acid) at 5 increasing concentrations (I to V). We also measured taste preferences and determined the polymorphisms of the genes taste 2 receptor member 38 (TAS2R38), taste 1 receptor member 2 (TAS2R38) and sodium channel epithelial 1 beta subunit (SCNN1B), as TAS2R38-rs713598, TAS1R2-rs35874116 and SCNN1B-rs239345 respectively. We found a statistically significant decrease in taste perception (total taste score) with increasing age for all the concentrations analysed. This association was stronger for the higher concentrations (p = 0.028; p = 0.012; p = 0.005; p = 4.20 x 10(-5) and p = 1.48 x 10(-7), for I to V in the multivariable-adjusted models). When we analysed taste qualities (using concentration V), the intensity rating of all the 5 tastes was diminished with age (p < 0.05 for all). This inverse association differed depending on the test quality, being higher for bitter (PROP) and sour. Women perceived taste significantly more intense than men (p = 1.4 x 10(-8) for ``total taste score´´). However, there were differences depending on the taste, umami being the lowest (p = 0.069). There was a complex association between the ability to perceive a taste and the preference for the same. Significant associations were, nevertheless, found between a higher perception of sour taste and a higher preference for it in women. In contrast, the higher perception of sweet was significantly associated with a higher preference for bitter in both, men and women. The TAS2R38-rs713598 was strongly associated with bitter (PROP) taste (p = 1.38 x 10(-50)), having a significant interaction with sex (p = 0.030). The TAS1R2-rs35874116 was not significantly associated with sweet, whereas the SCNN1B-rs239345 was associated (p = 0.040) with salty taste. In conclusion, the inverse association between age and perceived taste intensity as well as the additional influence of sex and some genetic polymorphisms give rise to large inter-individual differences in taste perception and taste preferences that should be taken into account in future studies and for applications in precision nutrition for healthy aging.This study was partially funded, by the Spanish Ministry of Health (Instituto de Salud Carlos III) and the Ministerio de Economia y Competitividad-Fondo Europeo de Desarrollo Regional (FEDER) (grants CIBER 06/03, PRX17/00500, PI16/00366, PI06/1326 and SAF2016-80532-R); the University Jaume I (grants P1-1B2013-54 and COGRUP/2016/06); the Fundacio La Marato de TV3 (grant 538/U/2016); the Real Colegio Complutense at Harvard University and the Generalitat Valenciana (grant PROMETEO2017/017).S
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