Biology subjects

Luis Diambra

Publications and source records attributed to Luis Diambra.

3 recordsLinked to original sources

bioRxiv2016

Coding translational rates: the hidden genetic code

In this paper we propose that translational rate is modulated by pairs of consecutive codons or bicodons. By a statistical analysis of coding sequences, associated with low or with high abundant proteins, we found some bicodons with significant preference usage for either of these sets. These usage preferences cannot be explained by the frequency usage of the single codons. We compute a pause propensity measure of all bicodons in nine organisms, which reveals that in many cases bicodon preference is shared between related organisms. We found that bicodons associated with sequences encoding low abundant proteins are involved in translational attenuation reported in SufIprotein in E. coli. Furthermore, we observe that the misfolding in the drug-transport protein, encoded by MDR1 gene, is better explained by a big change in the pause propensity due to the synonymous bicodon variant, rather than by a relatively small change in the codon usage. These findings suggest that bicodon usage can be a more powerful framework to understand translational speed, protein folding efficiency, and to improve protocols to optimize heterologous gene expression.

Genomics↗

bioRxiv2015

Mesoscopic oscillations in a single-gene circuit without delay

It is well known that single-gene circuits with negative feedback loop can lead to oscillatory gene expression when they operate with time delay. In order to generate these oscillations many processes can contribute to properly timing such delay. Here we show that the time delay coming from the transitions between internal states of the cis-regulatory system (CRS) can drive sustained oscillations in an auto-repressive single-gene circuit operating in a small volume like a cell. We found that the cooperative binding of repressor molecules is not mandatory for a oscillatory behavior if there are enough binding sites in the CRS. These oscillations depend on an adequate balance between the CRS kinetic, and the synthesis/degradation rates of repressor molecules. This finding suggest that the multi-site CRS architecture plays a key role for oscillatory behavior of gene expression.\n\nPACS numbers: 82.40.Bj,87.10.Mn,87.16.-b,87.16.Yc,87.18.Tt,87.18.Vf

Systems Biology↗

bioRxiv2015

Systems Biology Approach to Model the Life Cycle of Trypanosoma cruzi

Due to recent advances in reprogramming cell phenotypes, many efforts have been dedicated to developing reverse engineering procedures for the identification of gene regulatory networks that emulate dynamical properties associated with the cell fates of a given biological system. In this work, we propose a systems biology approach for the reconstruction of the gene regulatory network underlying the dynamics of the Trypanosoma cruzis life cycle. By means of an optimisation procedure, we embedded the steady state maintenance, and the known phenotypic transitions between these steady states in response to environmental cues, into the dynamics of a gene network model. In the resulting network architecture we identified a small subnetwork, formed by seven interconnected nodes, that controls the parasites life cycle. The present approach could be useful for better understanding other single cell organisms with multiple developmental stages.\n\nAbbreviations

Systems Biology↗