Comparative modeling of DNA and RNA polymerases from Moniliophthora perniciosa mitochondrial plasmid

<p>Abstract</p> <p>Background</p> <p>The filamentous fungus <it>Moniliophthora perniciosa </it>(Stahel) Aime & Phillips-Mora is a hemibiotrophic Basidiomycota that causes witches' broom disease of cocoa (<it>Theobroma cacao </it>L.). This disease has resulted in a severe decrease in Brazilian cocoa production, which changed the position of Brazil in the market from the second largest cocoa exporter to a cocoa importer. Fungal mitochondrial plasmids are usually invertrons encoding DNA and RNA polymerases. Plasmid insertions into host mitochondrial genomes are probably associated with modifications in host generation time, which can be involved in fungal aging. This association suggests activity of polymerases, and these can be used as new targets for drugs against mitochondrial activity of fungi, more specifically against witches' broom disease. Sequencing and modeling: DNA and RNA polymerases of <it>M. perniciosa </it>mitochondrial plasmid were completely sequenced and their models were carried out by Comparative Homology approach. The sequences of DNA and RNA polymerase showed 25% of identity to 1XHX and 1ARO (pdb code) using BLASTp, which were used as templates. The models were constructed using Swiss PDB-Viewer and refined with a set of Molecular Mechanics (MM) and Molecular Dynamics (MD) in water carried out with AMBER 8.0, both working under the ff99 force fields, respectively. Ramachandran plots were generated by Procheck 3.0 and exhibited models with 97% and 98% for DNA and RNA polymerases, respectively. MD simulations in water showed models with thermodynamic stability after 2000 ps and 300 K of simulation.</p> <p>Conclusion</p> <p>This work contributes to the development of new alternatives for controlling the fungal agent of witches' broom disease.</p

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Short-term population differences in the genetic architecture of life history traits related to sexuality in an aphid species.

One of the most important factors that determine the evolutionary trajectory of a suite of traits in a population is the structure of the genetic variance-covariance matrix (G). We studied the cyclically parthenogenetic aphid Rhopalosiphum padi, whose populations exhibit two types of reproductive lineages respectively specialized in sexuality (that is, cyclically parthenogenetic lineages) and in asexuality (that is, obligate parthenogenetic lineages). We compared the quantitative genetics of life histories in these two lineage types. Our results suggest that both, the elements and the whole structure of the resulting G matrices differ in the very short term, between lineage types. This would involve the evolution toward different evolutionary optima in the same population, depending on whether sexual or asexual lineages predominate. Since sexual and asexual lineages vary seasonally in their abundance, a fluctuating selective regime has been proposed for this species, which would contribute to the maintenance of the reproductive polymorphism that these populations exhibit

Induction of chiral porous solids containing only achiral building blocks

In many areas of chemistry the synthesis of chiral compounds is a target of increasing importance. They play a vital role in biological function and in many areas of society and science, including biology, medicine, biotechnology, chemistry and agriculture. Many pharmaceutical molecules, like their biological targets, are chiral and it is therefore easy to understand the growing demand for efficient methods of producing enantiomerically pure compounds. This is equally true for the preparation of chiral solids, which have potential applications in asymmetric catalysis, chiral separations and the like. In this Review we will consider recent progress and future potential in the development of methods for the preparation of chirally pure solids, in particular where the building blocks of the structure are achiral themselves. We will discuss strategies for the synthesis of both inorganic (for example, zeolites) and inorganic-organic hybrid (for example, metal organic framework) chiral porous solids.</p