Conserved motifs in nuclear genes encoding predicted mitochondrial proteins in Trypanosoma cruzi

Trypanosoma cruzi, the protozoan parasite that causes Chagas’ disease, exhibits peculiar biological features. Among them, the presence of a unique mitochondrion is remarkable. Even though the mitochondrial DNA constitutes up to 25% of total cellular DNA, the structure and functionality of the mitochondrion are dependent on the expression of the nuclear genome. As in other eukaryotes, specific peptide signals have been proposed to drive the mitochondrial localization of a subset of trypanosomatid proteins. However, there are mitochondrial proteins encoded in the nuclear genome that lack of a peptide signal. In other eukaryotes, alternative protein targeting to subcellular organelles via mRNA localization has also been recognized and specific mRNA localization towards the mitochondria has been described. With the aim of seeking for mitochondrial localization signals in T. cruzi, we developed a strategy to build a comprehensive database of nuclear genes encoding predicted mitochondrial proteins (MiNT) in the TriTryps (T. cruzi, T. brucei and L. major). We found that approximately 15% of their nuclear genome encodes mitochondrial products. In T. cruzi the MiNT database reaches 1438 genes and a conserved peptide signal, M(L/F) R (R/S) SS, named TryM-TaPe is found in 60% of these genes, suggesting that the canonical mRNA guidance mechanism is present. In addition, the search for compositional signals in the transcripts of T. cruzi MiNT genes produce a list, being worth to note a conserved nontranslated element represented by the consensus sequence DARRVSG. Taking into account its reported interaction with the T. brucei TRRM3 protein which is enriched in the mitochondrial membrane fraction, we here suggest a putative zip code role for this element. Globally, here we provide an inventory of the mitochondrial proteins in T. cruzi and give evidence for the existence of both peptide and mRNA signals specific to nuclear encoded mitochondrial proteins

Distribution of aminogenic activity among potential autochthonous starter cultures for dry fermented sausages

Any bacterial strain to be used as starter culture should have suitable characteristics, including a lack of amino acid decarboxylase activity. In this study, the decarboxylase activity of 76 bacterial strains, including lactic acid bacteria and gram-positive, catalase-positive cocci, was investigated. These strains were previously isolated from European traditional fermented sausages to develop autochthonous starter cultures. Of all the strains tested, 48% of the lactic acid bacteria strains and 13% of gram-positive, catalase-positive cocci decarboxylated one or more amino acids. Aminogenic potential was strain dependent, although some species had a higher proportion of aminogenic strains than did others. Thus, all Lactobacillus curvatus strains and 70% of Lactobacillus brevis strains had the capacity to produce tyramine and beta-phenylethylamine. Some strains also produced other aromatic amines, such as tryptamine and the diamines putrescine and cadaverine. All the enterococcal strains tested were decarboxylase positive, producing high amounts of tyramine and considerable amounts of beta-phenylethylamine. None of the staphylococcal strains had tyrosine-decarboxylase activity, but some produced other amines. From the aminogenic point of view, Lactobacillus plantarum, Lactobacillus sakei, and Staphylococcus xylosus strains would be the most suitable for use as autochthonous starter cultures for traditional fermented sausages

On the equivalence between Implicit Regularization and Constrained Differential Renormalization

Constrained Differential Renormalization (CDR) and the constrained version of Implicit Regularization (IR) are two regularization independent techniques that do not rely on dimensional continuation of the space-time. These two methods which have rather distinct basis have been successfully applied to several calculations which show that they can be trusted as practical, symmetry invariant frameworks (gauge and supersymmetry included) in perturbative computations even beyond one-loop order. In this paper, we show the equivalence between these two methods at one-loop order. We show that the configuration space rules of CDR can be mapped into the momentum space procedures of Implicit Regularization, the major principle behind this equivalence being the extension of the properties of regular distributions to the regularized ones.Comment: 16 page

Thin-Film Metamaterials called Sculptured Thin Films

Morphology and performance are conjointed attributes of metamaterials, of which sculptured thin films (STFs) are examples. STFs are assemblies of nanowires that can be fabricated from many different materials, typically via physical vapor deposition onto rotating substrates. The curvilinear--nanowire morphology of STFs is determined by the substrate motions during fabrication. The optical properties, especially, can be tailored by varying the morphology of STFs. In many cases prototype devices have been fabricated for various optical, thermal, chemical, and biological applications.Comment: to be published in Proc. ICTP School on Metamaterials (Augsut 2009, Sibiu, Romania

Nickel and platinum group metal nanoparticle production by <i>Desulfovibrio alaskensis</i> G20

Desulfovibrio alaskensis G20 is an anaerobic sulfate reducing bacteria. While Desulfovibrio species have previously been shown to reduce palladium and platinum to the zero-state, forming nanoparticles in the process; there have been no reports that D. alaskensis is able to form these nanoparticles. Metal nanoparticles have properties that make them ideal for use in many industrial and medical applications, such as their size and shape giving them higher catalytic activity than the bulk form of the same metal. Nanoparticles of the platinum group metals in particular are highly sought after for their catalytic ability and herein we report the formation of both palladium and platinum nanoparticles by D. alaskensis and the biotransformation of solvated nickel ions to nanoparticle form

Scoping prediction of re-radiated ground-borne noise and vibration near high speed rail lines with variable soils

This paper outlines a vibration prediction tool, ScopeRail, capable of predicting in-door noise and vibration, within structures in close proximity to high speed railway lines. The tool is designed to rapidly predict vibration levels over large track distances, while using historical soil information to increase accuracy. Model results are compared to an alternative, commonly used, scoping model and it is found that ScopeRail offers higher accuracy predictions. This increased accuracy can potentially reduce the cost of vibration environmental impact assessments for new high speed rail lines. To develop the tool, a three-dimensional finite element model is first outlined capable of simulating vibration generation and propagation from high speed rail lines. A vast array of model permutations are computed to assess the effect of each input parameter on absolute ground vibration levels. These relations are analysed using a machine learning approach, resulting in a model that can instantly predict ground vibration levels in the presence of different train speeds and soil profiles. Then a collection of empirical factors are coupled with the model to allow for the prediction of structural vibration and in-door noise in buildings located near high speed lines. Additional factors are also used to enable the prediction of vibrations in the presence of abatement measures (e.g. ballast mats and floating slab tracks) and additional excitation mechanisms (e.g. wheelflats and switches/crossings)