Alien and native plants show contrasting responses to climate and land use in Europe

Aim We tested whether the distribution and cover of alien plant species in Europe was related to human disturbance and microclimate. Location Surveys were conducted at 13 sites across Europe, each containing a pair of landscapes with different land‐use intensities. Methods Sampling locations were chosen based on land use and microclimate at two scales: land use was characterized at the patch and landscape scale; climate was expressed as regional and local temperature. The slope of each sample location was derived from a digital elevation model. Cover of plant species was measured using point counts and analysed using mixed effect models. Species were classified as native, archaeophytes and neophytes (pre‐ versus post‐ad 1500 immigrants). Due to the zero inflation observed in the alien groups, their cover was analysed conditional on their presence. Results Anthropogenic disturbance was a significant explanatory variable, increasing the presence and cover of alien species and decreasing the cover of native species. Alien presence was increased in sites under agricultural management, while their cover responded to land use at both local and landscape scales (and to their interaction), such that only natural habitats in semi‐natural landscapes had low alien cover. Microclimate was important for neophytes, with presence concentrated around mesic conditions. Slope was relevant for archaeophytes and native species, suppressing the former group and promoting the latter one. Main conclusions We found that, at the European scale, the distribution of alien plants is related to anthropogenic disturbance more than to microclimatic differences. The presence of neophytes, however, was influenced by climate at local and regional scales, with the highest incidence under mesic conditions. The different patterns observed for the presence and cover of alien species suggest different mechanisms acting during their establishment and spread. They also suggest that to counteract the expansion of alien species natural habitats may need to be maintained at landscape scales.     

GeneTRACE-reconstruction of gene content of ancestral species

While current computational methods allow the reconstruction of individual ancestral protein sequences, reconstruction of complete gene content of ancestral species is not yet an established task. In this paper, we describe GENETRACE, an efficient linear-time algorithm that allows the reconstruction of evolutionary history of individual protein families as well as the complete gene content of ancestral species. The performance of the method was validated with a simulated evolution program called SimulEv. Our results indicate that given a set of correct phylogenetic profiles and a correct species tree, ancestral gene content can be reconstructed with sensitivity and selectivity of more than 90%. SimulEv simulations were also used to evaluate performance of the reconstruction of gene content-based phylogenetic trees, suggesting that these trees may be accurate at the terminal branches but suffer from long branch attraction near the root of the tree.     

Myriads of protein families,and still counting

From the historical record of genome sequencing, we show that the rate of discovery of new families has remained constant over time, indicating that our knowledge of sequence space is far from complete.     

Bacteriophage Mu transposase contains a fragment with primary structure similar to that of protein VPg covalently linked with poliovirus RNA

A statistically valid similarity was found to exist between the amino acid sequences of poliovirus genome-linked protein VPg and a fragment of bacteriophage Mu transposase (Mu A protein). Based on this observation a hypothesis is proposed that the molecular mechanisms underlying the functions of the two proteins may be analogous. Both proteins are supposed to be site-specific endonucleases which form covalent linkage with the 5'-phosphate group of the nicked DNA or RNA strand. The amino acid residue participating in the formation of this linkage in MuA is tentatively identified as Tyr413.     

Quantitative Urine Culture Method Using a Plastic ?Paddle” Containing Dual Media

A new dip-inoculum method for quantitative urine culture is described which utilizes a dual-chambered plastic "paddle" housing both a general purpose and differential medium. Comparative bacterial counts of 1,000 clinical specimens using the pour plate and this device were identical in 82.9% and within a factor of five in 95.6%. The "paddle" detected all but 19 of 258 specimens (92.6%) with 100,000 or greater colonies per ml. This simple, convenient method should allow more extensive use of quantitative urine culture in the diagnosis and follow-up of patients with urinary tract infections in office practice. It should not be considered as a substitute for the more definitive pour plate method or for standard methods for characterization of bacteriological species when more exact information is required.