Understanding the mathematical properties of graphs underling biological systems could give hints on the evolutionary mechanisms behind these structures. In this article we perform a complete statistical analysis over thousands of graphs representing
metabolic and protein-protein interaction (PPI) networks. First, we investigate the quality of fits obtained for the nodes degree distributions to power-law functions. This analysis suggests that a power-law distribution poorly describes the data except for the far right tail in the case of PPI networks. Next we obtain descriptive statistics for the main graph parameters and try to identify the properties that deviate from the expected values had the networks been built by randomly linking nodes with the same degree distribution. This survey identifies the properties of biological networks which are not solely the result of their degree distribution, but emerge from yet unidentified mechanisms other than those that drive these distributions. The findings suggest that, while PPI networks have properties that differ from their expected values in their randomiz
We study odd-parity baryonic resonances with one heavy and three light flavors, dynamically generated by meson-baryon interactions. Special attention is paid to Heavy Quark Spin Symmetry (HQSS), hence pseudoscalar and vector mesons and baryons with J
^P = 1/2+ and 3/2+ are considered as constituent hadrons. For the hidden-charm sector (N-c-quarks = N-c-antiquarks = 1), the meson-baryon Lagrangian with Heavy Flavor Symmetry is constructed by a minimal extension of the SU(3) Weinberg-Tomozawa (WT) Lagrangian to fulfill HQSS, such that not new parameters are needed. This interaction can be presented in different formal ways: as a Field Lagrangian, as Hadron creation-annihilation operators, as SU(6)xHQSS group projectors and as multichannel matrices. The multichannel Bethe-Salpeter equation is solved for odd-parity light baryons, hidden-charm N and Delta and Beauty Baryons (Lambda-b). Results of calculations with this model are shown in comparison with other models and experimental values for baryonic resonances.
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an essential elemen
t in their research. Therefore there is a strong need of efficient and versatile computational tools for the research in this area. Results: In this manuscript we present PyNetMet, a Python library of tools to work with networks and metabolic models. These are open-source free tools for use in a Python platform, which adds considerably versatility to them when compared with their desktop software similars. On the other hand these tools allow one to work with different standards of metabolic models (OptGene and SBML) and the fact that they are programmed in Python opens the possibility of efficient integration with any other already existing Python tool. Conclusions: PyNetMet is, therefore, a collection of computational tools that will facilitate the research work with metabolic models and networks.
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this comparison in ord
er to infer evolutionary distances between different organisms. Our methodology allows a quantification of the metabolic differences between different species from a broad range of families and even kingdoms. This quantification is then applied in order to reconstruct phylogenetic trees for sets of various organisms.
Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one persons work in order to satisfactory collect, a
nalyze and validate the list of all metabolic reactions present in a specific organism. In order to write this list, one manually has to go through a huge amount of genomic, metabolomic and physiological information. Currently, there is no optimal algorithm that allows one to automatically go through all this information and generate the models taking into account probabilistic criteria of unicity and completeness that a biologist would consider. Results: This work presents the automation of a methodology for the reconstruction of genome scale metabolic models for any organism. The methodology that follows is the automatized version of the steps implemented manually for the reconstruction of the genome scale metabolic model of a photosynthetic organism, {it Synechocystis sp. PCC6803}. The steps for the reconstruction are implemented in a computational platform (COPABI) that generates the models from the probabilistic algorithms that have been developed. Conclusions: For validation of the developed algorithm robustness, the metabolic models of several organisms generated by the platform have been studied together with published models that have been manually curated. Network properties of the models like connectivity and average shortest mean path of the different models have been compared and analyzed.
In this contribution, a design of a synthetic calibration genetic circuit to characterize the relative strength of different sensing promoters is proposed and its specifications and performance are analyzed via an effective mathematical model. Our ca
librator device possesses certain novel and useful features like modularity (and thus the possibility of being used in many different biological contexts), simplicity, being based on a single cell, high sensitivity and fast response. To uncover the critical model parameters and the corresponding parameter domain at which the calibrator performance will be optimal, a sensitivity analysis of the model parameters was carried out over a given range of sensing protein concentrations (acting as input). Our analysis suggests that the half saturation constants for repression, sensing and difference in binding cooperativity (Hill coefficients) for repression are the key to the performance of the proposed device. They furthermore are determinant for the sensing speed of the device, showing that it is possible to produce detectable differences in the repression protein concentrations and in turn in the corresponding fluorescence in less than two hours. This analysis paves the way for the design, experimental construction and validation of a new family of functional genetic circuits for the purpose of calibrating promoters.
We use a consistent SU(6) extension of the meson-baryon chiral Lagrangian within a coupled channel unitary approach in order to calculate the T-matrix for meson-baryon scattering in s-wave. The building blocks of the scheme are the pion and nucleon o
ctets, the rho nonet and the Delta decuplet. We identify poles in this unitary T-matrix and interpret them as resonances. We study here the non exotic sectors with strangeness S=0,-1,-2,-3 and spin J=1/2, 3/2 and 5/2. Many of the poles generated can be associated with known N, Delta, Sigma, Lambda and Xi resonances with negative parity. We show that most of the low-lying three and four star odd parity baryon resonances with spin 1/2 and 3/2 can be related to multiplets of the spin-flavor symmetry group SU(6). This study allows us to predict the spin-parity of the Xi(1620), Xi(1690), Xi(1950), Xi(2250), Omega(2250) and Omega(2380) resonances, which have not been determined experimentally yet.
We report on some ideas concerning the nature of the X(3872) resonance and the need for approximately equal charged and neutral components of $D bar{D}^* +cc$. Then we discuss how some hidden charm states are obtained from the interaction between vec
tor mesons with charm and can be associated to some of the charmonium-like X,Y,Z states. Finally we discuss how the nature of these states could be investigated through different types of radiative decay.
In this work we study the radiative decay of dynamically generated $J^P=oh^-$ charm baryons into the ground state $J^P=oh^+$ baryons. Since different theoretical interpretations of these baryonic resonances, and in particular of the $Lambda_c(2595)$,
give different predictions, a precise experimental measurement of these decays would be an important step for understanding their nature.
We study the renormalization of the properties of low lying charm and hidden charm scalar mesons in a nuclear medium, concretely of the D_{s0}(2317) and the theoretical hidden charm state X(3700). We find that for the D_{s0}(2317), with negligible wi
dth at zero density, the width becomes about 100 MeV at normal nuclear matter density, while in the case of the X(3700) the width becomes as large as 200 MeV. We discuss the origin of this new width and trace it to reactions occurring in the nucleus, while offering a guideline for future experiments testing these changes. We also show how those medium modifications will bring valuable information on the nature of the scalar resonances and the mechanisms of the interaction of D mesons with nucleons and nuclei.
