Evaluating Purifying Selection in the Mitochondrial DNA of Various Mammalian Species

Mitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations.     

Influence of fire and mechanical sagebrush reduction treatments on restoration seedings in Utah,United States

Overabundance of woody plants in semiarid ecosystems can degrade understory herbaceous vegetation and often requires shrub reduction and seeding to recover ecosystem services. We used meta‐analysis techniques to assess the effects of fire and mechanical shrub reduction over two post‐treatment timeframes (1–4 and 5–10 years) on changes in cover and frequency of 15 seeded species at 63 restoration sites with high potential for recovery. Compared to mechanical treatments, fire resulted in greater increases in seeded species. Native shrubs did not increase, and forbs generally declined over time; however, large increases in perennial grasses were observed, suggesting that seeding efforts contributed to enhanced understory herbaceous conditions. We found greater increases in a few non‐native species than native species across all treatments, suggesting the possibility that interference among seeded species may have influenced results of this regional assessment. Differences among treatments and species were likely driven by seedbed conditions, which should be carefully considered in restoration planning. Site characteristics also dictated seeded species responses: while forbs showed greater increases in cover over the long term at higher elevation sites considered to be more resilient to disturbance, surprisingly, shrubs and grasses had greater increases in cover and frequency at lower elevation sites where resilience is typically much lower. Further research is needed to understand the causes of forb mortality over time, and to decipher how greater increases of non‐native relative to native seeded species will influence species diversity and successional trajectories of restoration sites.     

Biosynthesis of sialylated lipooligosaccharides in Haemophilus ducreyi is dependent on exogenous sialic acid and not mannosamine. Incorporation studies using N-acylmannosamine analogues, N-glycolylneuraminic acid, and 13C-labeled N-acetylneuraminic acid

Haemophilus ducreyi is a Gram-negative bacterium that causes chancroid, a sexually transmitted disease. Cell surface lipooligosaccharides (LOS) of H. ducreyi are thought to play important biological roles in host infection. The vast majority of H. ducreyi strains contain high levels of sialic acid (N-acetylneuraminic acid, NeuAc) in their LOS. Here we investigate the biosynthetic origin of H. ducreyi sialosides by metabolic incorporation studies using a panel of N-acylmannosamine and sialic acid analogues. Incorporation of sialosides into LOS was assessed by matrix-assisted laser desorption and electrospray ionization mass spectrometry. A Fourier transform ion cyclotron resonance mass spectrometer provided accurate mass measurements, and a quadrupole time-of-flight instrument was used to obtain characteristic fragment ions and partial carbohydrate sequences. Exogenously supplied N-acetylmannosamine analogues were not converted to LOS-associated sialosides at a detectable level. In contrast, exogenous (13)C-labeled N-acetylneuraminic acid ([(13)C]NeuAc) and N-glycolylneuraminic acid (NeuGc) were efficiently incorporated into LOS in a dose-dependent fashion. Moreover, approximately 1.3 microM total exogenous sialic acid was sufficient to obtain about 50% of the maximum production of sialic acid-containing glycoforms observed under in vitro growth conditions. Together, these data suggest that the expressed levels of sialylated LOS glycoforms observed in H. ducreyi are in large part controlled by the exogenous concentrations of sialic acid and at levels one might expect in vivo. Moreover, these studies show that to properly exploit the sialic acid biosynthetic pathway for metabolic oligosaccharide engineering in H. ducreyi and possibly other prokaryotes that share similar pathways, precursors based on sialic acid and not mannosamine must be used.     

DNA fingerprinting reveals polygyny in the subterranean rodent Ctenomys talarum

DNA fingerprinting was used to characterize patterns of paternity in two populations of Ctenomys talarum from Buenos Aires Province, Argentina. The multilocus probe PV47-2 was used to detect variation in genomic DNA extracted from 12 females, their 32 offspring, and 14 putative sires. For 11 out of 12 litters examined, a single male capable of providing all nonmaternal bands was identified. Within each study population, individual males sired more than one litter, suggesting that C. talarum is polygynous. No evidence of multiple paternity of litters was found. High band-sharing values among females suggest that further research is needed to assess the population genetic structure of this species.     

ASPP1 and ASPP2: common activators of p53 family members

We recently showed that ASPP1 and ASPP2 stimulate the apoptotic function of p53. We show here that ASPP1 and ASPP2 also induce apoptosis independently of p53. By binding to p63 and p73 in vitro and in vivo, ASPP1 and ASPP2 stimulate the transactivation function of p63 and p73 on the promoters of Bax, PIG3, and PUMA but not mdm2 or p21(WAF-1/CIP1). The expression of ASPP1 and ASPP2 also enhances the apoptotic function of p63 and p73 by selectively inducing the expression of endogenous p53 target genes, such as PIG3 and PUMA, but not mdm2 or p21(WAF-1/CIP1). Removal of endogenous p63 or p73 with RNA interference demonstrated that (16) the p53-independent apoptotic function of ASPP1 and ASPP2 is mediated mainly by p63 and p73. Hence, ASPP1 and ASPP2 are the first two identified common activators of all p53 family members. All these results suggest that ASPP1 and ASPP2 could suppress tumor growth even in tumors expressing mutant p53.     

The activation of the [NiFe]-hydrogenase from<Emphasis Type="Italic"> Allochromatium vinosum</Emphasis>. An infrared spectro-electrochemical study

The membrane-bound [NiFe]-hydrogenase from Allochromatium vinosum can occur in several inactive or active states. This study presents the first systematic infrared characterisation of the A. vinosum enzyme, with emphasis on the spectro-electrochemical properties of the inactive/active transition. This transition involves an energy barrier, which can be overcome at elevated temperatures. The reduced Ready enzyme can exist in two different inactive states, which are in an apparent acid–base equilibrium. It is proposed that a hydroxyl ligand in a bridging position in the Ni-Fe site is protonated and that the formed water molecule is subsequently removed. This enables the active site to bind hydrogen in a bridging position, allowing the formation of the fully active state of the enzyme. It is further shown that the active site in enzyme reduced by 1 bar H₂ can occur in three different electron paramagnetic resonance (EPR)-silent states with a different degree of protonation.Abbreviations BV benzyl viologen - MB methylene blue - MBH membrane-bound hydrogenase - SHE standard hydrogen electrode     

Two direct repeats cause most human mtDNA deletions

Mitochondrial DNA (mtDNA) deletions are a common cause of human mitochondrial disease and also occur as part of normal aging. However, it is unknown how the deletions actually occur. To gain further insight, we studied the sequences that flank 263 different human mtDNA deletions. The distribution of deletion breakpoints did not correspond to the basic parameters of wild-type mtDNA that are thought to predispose to deletion formation. But there was a striking correspondence to the position of two 13-bp direct repeats beginning at nucleotides 8470 and 13 447. The vast majority of different mtDNA deletions appear to be related to these two repeats, suggesting a common mechanism related to mtDNA replication.     

<Emphasis Type="Italic">Hypocrea phyllostachydis</Emphasis> and its <Emphasis Type="Italic">Trichoderma</Emphasis> anamorph,a new bambusicolous species from France

Hypocrea phyllostachydis was collected from the bamboo species Phyllostachys bambusoides in southwestern France (Dept. Pyréneés Atlantiques). It can be distinguished from other morphologically similar species by the small subglobose or broadly ellipsoidal conidia and small ascospores. Conidiophores of the Trichoderma state of H. phyllostachydis do not branch in a pyramidal fashion, as is typical of most species of Trichoderma. Rather, it has an irregular branching pattern, with a long central axis and relatively short lateral secondary branches. A key to species of Hypocrea with green ascospores from France is presented.