TIP: Protein backtranslation aided by genetic algorithms

Summary: Several applications require the backtranslation of a protein sequence into a nucleic acid sequence. The degeneracy of the genetic code makes this process ambiguous; moreover, not every translation is equally viable. The usual answer is to mimic the codon usage of the target species; however, this does not capture all the relevant features of the 'genomic styles' from different taxa. The program TIP ('Traducción Inversa de Proteínas') applies genetic algorithms to improve the backtranslation, by minimizing the difference of some coding statistics with respect to their average value in the target. © Oxford University Press 2004; all rights reserved

Finite-rank Bratteli-Vershik diagrams are expansive

The representation of Cantor minimal systems by Bratteli-Vershik diagrams has been extensively used to study particular aspects of their dynamics. A main role has been played by the symbolic factors induced by the way vertices of a fixed level of the diagram are visited by the dynamics. The main result of this paper states that Cantor minimal systems that can be represented by Bratteli-Vershik diagrams with a uniformly bounded number of vertices at each level (called finite-rank systems) are either expansive or topologically conjugate to an odometer. More precisely, when expansive, they are topologically conjugate to one of their symbolic factors

Directional dynamical cubes for minimal -systems

We introduce the notions of directional dynamical cubes and directional regionally proximal relation defined via these cubes for a minimal -system. We study the structural properties of systems that satisfy the so-called unique closing parallelepiped property and we characterize them in several ways. In the distal case, we build the maximal factor of a -system that satisfies this property by taking the quotient with respect to the directional regionally proximal relation. Finally, we completely describe distal -systems that enjoy the unique closing parallelepiped property and provide explicit examples

Limit measures for affine cellular automata on topological Markov subgroups

Consider a topological Markov subgroup which is p(s)-torsion (with p prime) and an affine cellular automaton defined on it. We show that the Cesaro mean of the iterates, by the automaton of a probability measure with complete connections and summable memory decay that is compatible with the topological Markov subgroup, converges to the Haar measure

Wandering intervals in affine extensions of self-similar interval exchange maps: The cubic Arnoux-Yoccoz map

In this article, we provide sufficient conditions on a self-similar interval exchange map, whose renormalization matrix has complex eigenvalues of modulus greater than one, for the existence of affine interval exchange maps with wandering intervals that are semi-conjugate with it. These conditions are based on the algebraic properties of the complex eigenvalues and the complex fractals built from the natural substitution emerging from self-similarity. We show that the cubic Arnoux–Yoccoz interval exchange map satisfies these conditions

Characterization of minimal sequences associated with self similar interval exchange maps

The construction of affine interval exchange maps (IEMs) with wandering intervals that are semi-conjugate to a given self-similar IEM is strongly related to the existence of the so-called minimal sequences associated with local potentials, which are certain elements of the substitution subshift arising from the given IEM. In this article, under the condition called unique representation property, we characterize such minimal sequences for potentials coming from non-real eigenvalues of the substitution matrix. We also give conditions on the slopes of the affine extensions of a self-similar IEM that determine whether it exhibits a wandering interval or not.MathAmsud grant DCS-2017 CMM-Basal grant PFB-0

Draft genome sequence of the sulfobacillus thermosulfidooxidans cutipay strain, an indigenous bacterium isolated from a naturally extreme mining environment in northern Chile

Sulfobacillus thermosulfidooxidans strain Cutipay is a mixotrophic, acidophilic, moderately thermophilic bacterium isolated from mining environments of the north of Chile, making it an interesting subject for studying the bioleaching of copper. We introduce the draft genome sequence and annotation of this strain, which provide insights into its mechanisms for heavy metal resistance. © 2012, American Society for Microbiology

Generation and robustness of Boolean networks to model Clostridium difficile infection

One of the more common healthcare associated infection is Chronic diarrhea. This disease is caused by the bacterium Clostridium difficile which alters the normal composition of the human gut flora. The most successful therapy against this infection is the fecal microbial transplant (FMT). They displace C. difficile and contribute to gut microbiome resilience, stability and prevent further episodes of diarrhea. The microorganisms in the FMT their interactions and inner dynamics reshape the gut microbiome to a healthy state. Even though microbial interactions play a key role in the development of the disease, currently, little is known about their dynamics and properties. In this context, a Boolean network model for C. difficile infection (CDI) describing one set of possible interactions was recently presented. To further explore the space of possible microbial interactions, we propose the construction of a neutral space conformed by a set of models that dif

A mathematical model for copper homeostasis in Enterococcus hirae

Copper is an essential micronutrient for life. It is required by a wide range of species, from bacteria to yeast, plants and mammals including humans. To prevent the consequences of the excess or deficit of copper, living organisms have developed molecular mechanisms that regulate the uptake, efflux, storage and use of the metal. However, the limits of homeostatic regulation are not known. Here, we take advantage of a simple biological mechanism involved in copper metabolism of Enterococcus hirae, to explore how the regulation is achieved by using a set of four proteins codified in the cop operon: two P-type ATP-ases copper transporters, one copper chaper-one and one Cu-response transcription factor. We propose a mathematical model, based on differential equations and the power-law formalism (see M.A. Savageau, Chaos 11(1) (2001) 142-159), for the behavior of the cop operon and we show that homeostasis is a result of transient dynamics. The results derived from the mathematical model allow to measure qualitatively the adaptability of the system to its environment. This detailed model has been possible thanks to the available experimental biological information provided in a sequence of recent works by Solioz and co-workers

Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies

Design and selection of efficient metabolic pathways is critical for the success of metabolic engineering endeavors. Convenient pathways should not only produce the target metabolite in high yields but also are required to be thermodynamically feasible under production conditions, and to prefer efficient enzymes. To support the design and selection of such pathways, different computational approaches have been proposed for exploring the feasible pathway space under many of the above constraints. In this review, an overview of recent constraint-based optimization frameworks for metabolic pathway prediction, as well as relevant pathway engineering case studies that highlight the importance of rational metabolic designs is presented. Despite the availability and suitability of in silico design tools for metabolic pathway engineering, scarce—although increasing—application of computational outcomes is found. Finally, challenges and limitations hindering the broad adoption and successful application of these tools in metabolic engineering projects are discussed