The kinome of Phytophthora infestans reveals oomycete-specific innovations and links to other taxonomic groups

Background

Paracoccidioides brasiliensis (Eukaryota, Fungi, Ascomycota) is a thermodimorphic fungus, the etiological agent of paracoccidioidomycosis, the most important systemic mycoses in Latin America. Three isolates corresponding to distinct phylogenetic lineages of the Paracoccidioides species complex had their genomes sequenced. In this study the identification and characterization of class II transposable elements in the genomes of these fungi was carried out.

Results

A genomic survey for DNA transposons in the sequence assemblies of Paracoccidioides, a genus recently proposed to encompass species P. brasiliensis (harboring phylogenetic lineages S1, PS2, PS3) and P. lutzii (Pb01-like isolates), has been completed. Eight new Tc1/mariner families, referred to as Trem (Tr ansposable e lement m ariner), labeled A through H were identified. Elements from each family have 65-80% sequence similarity with other Tc1/mariner elements. They are flanked by 2-bp TA target site duplications and different termini. Encoded DDD-transposases, some of which have complete ORFs, indicated that they could be functionally active. The distribution of Trem elements varied between the genomic sequences characterized as belonging to P. brasiliensis (S1 and PS2) and P. lutzii. TremC and H elements would have been present in a hypothetical ancestor common to P. brasiliensis and P. lutzii, while TremA, B and F elements were either acquired by P. brasiliensis or lost by P. lutzii after speciation. Although TremD and TremE share about 70% similarity, they are specific to P. brasiliensis and P. lutzii, respectively. This suggests that these elements could either have been present in a hypothetical common ancestor and have evolved divergently after the split between P. brasiliensis and P. Lutzii, or have been independently acquired by horizontal transfer.

Conclusions

New families of Tc1/mariner DNA transposons in the genomic assemblies of the Paracoccidioides species complex are described. Families were distinguished based on significant BLAST identities between transposases and/or TIRs. The expansion of Trem in a putative ancestor common to the species P. brasiliensis and P. lutzii would have given origin to TremC and TremH, while other elements could have been acquired or lost after speciation had occurred. The results may contribute to our understanding of the organization and architecture of genomes in the genus Paracoccidioides.     

Combined prime-boost vaccination against tick-borne encephalitis (TBE) using a recombinant vaccinia virus and a bacterial plasmid both expressing TBE virus non-structural NS1 protein

Background  

Heterologous prime-boost immunization protocols using different gene expression systems have proven to be successful tools in protecting against various diseases in experimental animal models. The main reason for using this approach is to exploit the ability of expression cassettes to prime or boost the immune system in different ways during vaccination procedures. The purpose of the project was to study the ability of recombinant vaccinia virus (VV) and bacterial plasmid, both carrying the NS1 gene from tick-borne encephalitis (TBE) virus under the control of different promoters, to protect mice against lethal challenge using a heterologous prime-boost vaccination protocol.     

Ectodermal FGFs induce perinodular inhibition of limb chondrogenesis in vitro and in vivo via FGF receptor 2

The formation of cartilage elements in the developing vertebrate limb, where they serve as primordia for the appendicular skeleton, is preceded by the appearance of discrete cellular condensations. Control of the size and spacing of these condensations is a key aspect of skeletal pattern formation. Limb bud cell cultures grown in the absence of ectoderm formed continuous sheet-like masses of cartilage. With the inclusion of ectoderm, these cultures produced one or more cartilage nodules surrounded by zones of noncartilaginous mesenchyme. Ectodermal fibroblast growth factors (FGF2 and FGF8), but not a mesodermal FGF (FGF7), substituted for ectoderm in inhibiting chondrogenic gene expression, with some combinations of the two ectodermal factors leading to well-spaced cartilage nodules of relatively uniform size. Treatment of cultures with SU5402, an inhibitor FGF receptor tyrosine kinase activity, rendered FGFs ineffective in inducing perinodular inhibition. Inhibition of production of FGF receptor 2 (FGFR2) by transfection of wing and leg cell cultures with antisense oligodeoxynucleotides blocked appearance of ectoderm- or FGF-induced zones of perinodular inhibition of chondrogenesis and, when introduced into the limb buds of developing embryos, led to shorter, thicker, and fused cartilage elements. Because FGFR2 is expressed mainly at sites of precartilage condensation during limb development in vivo and in vitro, these results suggest that activation of FGFR2 by FGFs during development elicits a lateral inhibitor of chondrogenesis that limits the expansion of developing skeletal elements.     

<Emphasis Type="Italic">M. tuberculosis</Emphasis> genotypic diversity and drug susceptibility pattern in HIV- infected and non-HIV-infected patients in northern Tanzania

Background  

Tuberculosis (TB) is a major health problem and HIV is the major cause of the increase in TB. Sub-Saharan Africa is endemic for both TB and HIV infection. Determination of the prevalence of M. tuberculosis strains and their drug susceptibility is important for TB control.     

Analysis of stability of different regimes of heart rate dynamics by computer modeling

Computer modeling revealed the following three regimes of heart rate dynamics: linear dynamics, “1st degree chaos,” and “2nd degree chaos.” This study investigated a stability of these regimes with respect to changes in initial conditions. The results show that the greatest stability is notable for the linear regime. For this regime small errors in values of initial conditions can not sharply change the initial dynamics of RR intervals. Both nonlinear regimes of heart rate dynamics are unstable, and a degree of instability of regime “2nd degree chaos” is higher in comparison with regime “1st degree chaos.” The results of computer modeling are in agreement with experimental data pointing to the existence of a relationship between the degree of heart rate irregularity and cardiac electrical stability.     

Parameters of atrioventricular conduction and stability of different regimes of heart rate dynamics

By method of computer modeling we investigated a stability of different regimes of heart rate dynamics in relation to the change in the atrioventricular conduction parameters: refractory period, minimum atrioventricular delay and curvatures of delay functions in sinoatrial and atrioventricular nodes. It is shown that curvatures of delay functions in sinoatrial and atrioventricular nodes have the most significant influence on the stability of different regimes of heart rate dynamics. The minimum delays in sinoatrial and atrioventricular nodes have smaller impact. The parameters determining the refractory periods of sinoatrial and atrioventricular nodes are least significant in terms of stability of heart rate dynamics.     

Effect of substance P on catecholamine levels in the hypothalamus and midbrain in the rat during immobilization stress

Single intraperitoneal injection of substance P in a dose of 125 mcg/kg induced a significant increase of noradrenaline and dopamine level in the hypothalamus and the midbrain of intact rats. Under conditions of immobilization emotional stress, the substance P eliminated the stress induced decrease of hypothalamic noradrenaline and increase of its level in the midbrain; in other words the substance P normalized the noradrenaline level. Modulatory effect of a single injection of the substance P had a long-term character and was synchronized with an earlier found increase of resistability of rats to chronic emotional stress.     

Bayesian DNA copy number analysis

Background  

Some diseases, like tumors, can be related to chromosomal aberrations, leading to changes of DNA copy number. The copy number of an aberrant genome can be represented as a piecewise constant function, since it can exhibit regions of deletions or gains. Instead, in a healthy cell the copy number is two because we inherit one copy of each chromosome from each our parents.     

Analysis of the nonlinear heart rate dynamics by two-contour mathematical model

Using a two-contour mathematical model, changes in the degree of heart rate variability induced by an increased extracardial impulsation in the sinoatrial node have been studied. The model is based on quantitative characteristics of impulse conduction in the cardiac conduction system. A mathematical and computer modeling revealed the following three regimes of heart rate variability: linear dynamics, the 1st-degree chaos, and the 2nd-degree chaos. Transitions between these regimes have been studied. A comparative analysis of the one- and two-contour models of heart rate regulation has been performed.