Sampling properties of DNA sequence data in phylogenetic analysis

We inferred phylogenetic trees from individual genes and random samples of nucleotides from the mitochondrial genomes of 10 vertebrates and compared the results to those obtained by analyzing the whole genomes. Individual genes are poor samples in that they infrequently lead to the whole-genome tree. A large number of nucleotide sites is needed to exactly determine the whole-genome tree. A relatively small number of sites, however, often results in a tree close to the whole-genome tree. We found that blocks of contiguous sites were less likely to lead to the whole-genome tree than samples composed of sites drawn individually from throughout the genome. Samples of contiguous sites are not representative of the entire genome, a condition that violates a basic assumption of the bootstrap method as it is applied in phylogenetic studies.      

Is the association between optimistic cardiovascular risk perceptions and lower rates of cardiovascular disease mortality explained by biomarkers of systemic inflammation or endothelial function? A case-cohort study

Background  

More optimistic perceptions of cardiovascular disease risk are associated with substantively lower rates of cardiovascular death among men. It remains unknown whether this association represents causality (i.e. perception leads to actions/conditions that influence cardiovascular disease occurrence) or residual confounding by unmeasured factors that associate with risk perceptions and with physiological processes that promote cardiovascular disease (i.e. inflammation or endothelial dysfunction).     

The promoter of filamentation (POF1) protein from <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> is an ATPase involved in the protein quality control process

Background

The gene YCL047C, which has been renamed promoter of filamentation gene (POF1), has recently been described as a cell component involved in yeast filamentous growth. The objective of this work is to understand the molecular and biological function of this gene.

Results

Here, we report that the protein encoded by the POF1 gene, Pof1p, is an ATPase that may be part of the Saccharomyces cerevisiae protein quality control pathway. According to the results, Δpof1 cells showed increased sensitivity to hydrogen peroxide, tert-butyl hydroperoxide, heat shock and protein unfolding agents, such as dithiothreitol and tunicamycin. Besides, the overexpression of POF1 suppressed the sensitivity of Δpct1, a strain that lacks a gene that encodes a phosphocholine cytidylyltransferase, to heat shock. In vitro analysis showed, however, that the purified Pof1p enzyme had no cytidylyltransferase activity but does have ATPase activity, with catalytic efficiency comparable to other ATPases involved in endoplasmic reticulum-associated degradation of proteins (ERAD). Supporting these findings, co-immunoprecipitation experiments showed a physical interaction between Pof1p and Ubc7p (an ubiquitin conjugating enzyme) in vivo.

Conclusions

Taken together, the results strongly suggest that the biological function of Pof1p is related to the regulation of protein degradation.

     

Nimodipine maintains in vivo the increase in GFAP and enhances the astroglial ensheathment of surviving motoneurons in the rat following permanent target deprivation

Facial and hypoglossal nerves were resected unilaterally in a total of 108 rats. Rats were divided into two groups; one group received standard food pellets (placebo), the other received food pellets containing the Ca2+-blocking agent nimodipine. The expression of glial fibrillary acidic protein was examined in paraffin sections of the brainstem using light microscopical immunocytochemistry, and the degree of glial process ensheathment of the surviving neuronal perikarya in the hypoglossal and facial nuclei quantified on electron micrographs. Up to 28 days post-axotomy no differences in glial fibrillary acidic protein-immunoreactivity were observed between placebo and nimodipine-treated animals. By 42–days, glial fibrillary acid protein-immunoreactivity was stronger in the nimodipine treated animals and by 112 days, glial fibrillary acid protein-immunoreactive astrocytes occured only in nimodipine-treated animals. Thin astrocytic processes were seen to ensheath neurons in both placebo and nimodipine-treated animals. By 28 days post axotomy, lesioned neurons in nimodipine treated animals were covered by a mean of 2.6 (hypoglossal) and 2.9 (facial nucleus) astrocytic lamellae, compared with 1.7 lamellae in the placebo group. This relatively greater ensheathment of hypoglossal and facial neurons was maintained up to 112 days post-lesion, but reduced in the placebo-treated group to ～ 1.4 lamellae. It is concluded that nimodipine enhances the formation of astrocytic lamellae on lesioned neurons and that this process may be associated with a protective role for activated astrocytes directed towards motoneurons suffering from permanent target-deprivation.     

Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus Nicrophorus (Coleoptera: Silphidae)

Three satellite DNA families were identified in three species of burying beetles, Nicrophorus orbicollis, N. marginatus, and N. americanus. Southern hybridization and nucleotide sequence analysis of individual randomly cloned repeats shows that these satellite DNA families are highly abundant in the genome, are composed of unique repeats, and are species-specific. The repeats do not have identifiable core elements or substructures that are similar in all three families, and most interspecific sequence similarity is confined to homopolymeric runs of A and T. Satellite DNA from N. marginatus and N. americanus show single-base-pair indels among repeats, but single-nucleotide substitutions characterize most of the repeat variability. Although the repeat units are of similar lengths (342, 350, and 354 bp) and A + T composition (65%, 71%, and 71%, respectively), the average nucleotide divergence among sequenced repeats is very low (0.18%, 1.22%, and 0.71%, respectively). Transition/transversion ratios from the consensus sequence are 0.20, 0.69, and 0.70, respectively.      

Photodynamic inactivation of Aeromonas hydrophila by cationic phthalocyanines with different hydrophobicity

Antibacterial photodynamic therapy is a pioneering method for the inactivation of pathogenic bacteria. Four tetra alkyl-substituted cationic phthalocyanines with different hydrocarbon chains attached to the pyridyloxy group were synthesized. These photodynamic sensitizers were studied for antibacterial inactivation of a multidrug-resistant strain of Gram-negative bacterium Aeromonas hydrophila. Aeromonas species are recognized as etiological agents of a wide spectrum of diseases in humans and animals. The uptake of phthalocyanines by the bacterial cells decreased with an increase in cell density. Following the phthalocyanine solubility from hydrophilic to hydrophobic complexes, the accumulation capacity increased. Full inactivation was achieved with phthalocyanine with (methoxy) pyridyloxy substitution following a short exposure time, low drug concentration and mild irradiation. Although the phthalocyanine with the longest hydrocarbon chain (C12) has some toxic effect in the absence of light, substantial phototoxic effect was obtained with the optimal combination of drug-irradiation parameters.