12,078 research outputs found
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
Cavity approach for modeling and fitting polymer stretching
The mechanical properties of molecules are today captured by single molecule
manipulation experiments, so that polymer features are tested at a nanometric
scale. Yet devising mathematical models to get further insight beyond the
commonly studied force--elongation relation is typically hard. Here we draw
from techniques developed in the context of disordered systems to solve models
for single and double--stranded DNA stretching in the limit of a long polymeric
chain. Since we directly derive the marginals for the molecule local
orientation, our approach allows us to readily calculate the experimental
elongation as well as other observables at wish. As an example, we evaluate the
correlation length as a function of the stretching force. Furthermore, we are
able to fit successfully our solution to real experimental data. Although the
model is admittedly phenomenological, our findings are very sound. For
single--stranded DNA our solution yields the correct (monomer) scale and, yet
more importantly, the right persistence length of the molecule. In the
double--stranded case, our model reproduces the well-known overstretching
transition and correctly captures the ratio between native DNA and
overstretched DNA. Also in this case the model yields a persistence length in
good agreement with consensus, and it gives interesting insights into the
bending stiffness of the native and overstretched molecule, respectively.Comment: 12 pages; 3 figures; 1 tabl
Guide to the classics: Don Quixote, the world’s first novel – and one of the best
Completed by Cervantes when he was in prison, Don Quixote is the tale of a man so passionate about reading he leaves home to live the life of his fictional heroes
DĂ©cimas
Copia digital. Valladolid : Junta de Castilla y LeĂłn. ConsejerĂa de Cultura y Turismo, 2009-201
Comparative analysis of two genomic regions among four strains of Buchnera aphidicola, primary endosymbiont of aphids.
Preliminary analysis of two selected genomic regions of Buchnera aphidicola BCc, the primary endosymbiont of the cedar aphid Cinara cedri, has revealed a number of interesting features when compared with the corresponding homologous regions of the three B. aphidicola genomes previously sequenced, that are associated with different aphid species. Both regions exhibit a significant reduction in length and gene number in B. aphidicola BCc, as it could be expected since it possess the smallest bacterial genome. However, the observed genome reduction is not even in both regions, as it appears to be dependent on the nature of their gene content. The region fpr-trxA, that contains mainly metabolic genes, has lost almost half of its genes (45.6%) and has reduced 52.9% its length. The reductive process in the region rrl-aroK, that contains mainly ribosomal protein genes, is less dramatic, since it has lost 9.3% of genes and has reduced 15.5% of its length. Length reduction is mainly due to the loss of protein-coding genes, not to the shortening of ORFs or intergenic regions. In both regions, G+C content is about 4% lower in BCc than in the other B. aphidicola strains. However, when only conserved genes and intergenic regions of the four B. aphidicola strains are compared, the G+C reduction is higher in the fpr-trxA region
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
- …