Analysis of two genomes from the mitochondrion-like organelle of the intestinal parasite Blastocystis: complete sequences, gene content, and genome organization.

Acquisition of mitochondria by the ancestor of all living eukaryotes represented a crucial milestone in the evolution of the eukaryotic cell. Nevertheless, a number of anaerobic unicellular eukaryotes have secondarily discarded certain mitochondrial features, leading to modified organelles such as hydrogenosomes and mitosomes via degenerative evolution. These mitochondrion-derived organelles have lost many of the typical characteristics of aerobic mitochondria, including certain metabolic pathways, morphological traits, and, in most cases, the organellar genome. So far, the evolutionary pathway leading from aerobic mitochondria to anaerobic degenerate organelles has remained unclear due to the lack of examples representing intermediate stages. The human parasitic stramenopile Blastocystis is a rare example of an anaerobic eukaryote with organelles that have retained some mitochondrial characteristics, including a genome, whereas they lack others, such as cytochromes. Here we report the sequence and comparative analysis of the organellar genome from two different Blastocystis isolates as well as a comparison to other genomes from stramenopile mitochondria. Analysis of the characteristics displayed by the unique Blastocystis organelle genome gives us an insight into the initial evolutionary steps that may have led from mitochondria to hydrogenosomes and mitosomes

Generating functional analysis of complex formation and dissociation in large protein interaction networks

We analyze large systems of interacting proteins, using techniques from the non-equilibrium statistical mechanics of disordered many-particle systems. Apart from protein production and removal, the most relevant microscopic processes in the proteome are complex formation and dissociation, and the microscopic degrees of freedom are the evolving concentrations of unbound proteins (in multiple post-translational states) and of protein complexes. Here we only include dimer-complexes, for mathematical simplicity, and we draw the network that describes which proteins are reaction partners from an ensemble of random graphs with an arbitrary degree distribution. We show how generating functional analysis methods can be used successfully to derive closed equations for dynamical order parameters, representing an exact macroscopic description of the complex formation and dissociation dynamics in the infinite system limit. We end this paper with a discussion of the possible routes towards solving the nontrivial order parameter equations, either exactly (in specific limits) or approximately.Comment: 14 pages, to be published in Proc of IW-SMI-2009 in Kyoto (Journal of Phys Conference Series

Advancing towards a Practical Magnesium Ion Battery

A post-lithium battery era is envisaged, and it is urgent to find new and sustainable systems for energy storage. Multivalent metals, such as magnesium, are very promising to replace lithium, but the low mobility of magnesium ion and the lack of suitable electrolytes are serious concerns. This review mainly discusses the advantages and shortcomings of the new rechargeable magnesium batteries, the future directions and the possibility of using solid electrolytes. Special emphasis is put on the diversity of structures, and on the theoretical calculations about voltage and structures. A critical issue is to select the combination of the positive and negative electrode materials to achieve an optimum battery voltage. The theoretical calculations of the structure, intercalation voltage and diffusion path can be very useful for evaluating the materials and for comparison with the experimental results of the magnesium batteries which are not hassle-free

A Linear Molecule with Two Large Inverted Repeats: The Mitochondrial Genome of the Stramenopile Proteromonas lacertae

Mitochondrial evolution has given rise to a complex array of organelles, ranging from classical aerobic mitochondria to mitochondrial remnants known as hydrogenosomes and mitosomes. The latter are found in anaerobic eukaryotes, and these highly derived organelles often retain only scant evidence of their mitochondrial origins. Intermediate evolutionary stages have also been reported as facultatively or even strictly anaerobic mitochondria, and hydrogenosomes that still retain some mitochondrial features. However, the diversity among these organelles with transitional features remains rather unclear and barely studied. Here, we report the sequence, structure, and gene content of the mitochondrial DNA of the anaerobic stramenopile Proteromonas lacertae. It has a linear genome with a unique central region flanked by two identical large inverted repeats containing numerous genes and “telomeres” with short inverted repeats. Comparison with the organelle genome of the strictly anaerobic human parasite Blastocystis reveals that, despite the close similarity of the sequences, features such as the genome structure display striking differences. It remains unclear whether the virtually identical gene repertoires are the result of convergence or descent

Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure

We study the tailoring of structured random graph ensembles to real networks, with the objective of generating precise and practical mathematical tools for quantifying and comparing network topologies macroscopically, beyond the level of degree statistics. Our family of ensembles can produce graphs with any prescribed degree distribution and any degree-degree correlation function, its control parameters can be calculated fully analytically, and as a result we can calculate (asymptotically) formulae for entropies and complexities, and for information-theoretic distances between networks, expressed directly and explicitly in terms of their measured degree distribution and degree correlations.Comment: 25 pages, 3 figure

Structural characterization and electrochemical behavior of transition metal carbonates

III Encuentro sobre Nanociencia y Nanotecnología de Investigadores y Tecnólogos Andaluce

Un nuevo método de sintesis del carbonato de manganeso como electrodo negativo en baterías de ión-litio

III Encuentro sobre Nanociencia y Nanotecnología de Investigadores y Tecnólogos Andaluce

Magnesium Deintercalation From the Spinel-Type MgMn2-yFeyO4 (0.4≤y≤2.0) by Acid-Treatment and Electrochemistry

Rechargeable magnesium batteries attract lots of attention because of their high safety and low cost compared to lithium batteries, and it is needed to develop more efficient electrode materials. Although MgMn2O4 is a promising material for the positive electrode in Mg rechargeable batteries, it usually exhibits poor cyclability. To improve the electrochemical behavior, we have prepared nanoparticles of MgMn2-yFeyO4. The XRD results have confirmed that when Mn3+ (Jahn-Teller ion) ions are replaced by Fe3+ (non-Jahn-Teller ion), the resulting MgMn2-yFeyO4 is a cubic phase. The structure and theoretical voltage are theoretically calculated by using the DFT method. The obtained samples have been chemically treated in acid solution for partial demagnesiation, and it is observed that the presence of iron inhibits the deinsertion of Mg through disproportionation and favors the exchange reaction. The electrochemical behavior in non-aqueous magnesium cells has been explored

Diffusion dynamics on multiplex networks

We study the time scales associated to diffusion processes that take place on multiplex networks, i.e. on a set of networks linked through interconnected layers. To this end, we propose the construction of a supra-Laplacian matrix, which consists of a dimensional lifting of the Laplacian matrix of each layer of the multiplex network. We use perturbative analysis to reveal analytically the structure of eigenvectors and eigenvalues of the complete network in terms of the spectral properties of the individual layers. The spectrum of the supra-Laplacian allows us to understand the physics of diffusion-like processes on top of multiplex networks.Comment: 6 Pages including supplemental material. To appear in Physical Review Letter