Elevated CO2 decreases seed germination in Arabidopsis thaliana

The impact of elevated [CO₂] on seed germination was studied in different genotypes of Arabidopsis thaliana from natural populations. Two generations of seeds were studied: the maternal generation was produced in the greenhouse (present-day conditions), the offspring generation was produced in two chambers where the CO₂ concentration was either the present atmospheric concentration (about 350 ppm) or elevated (700 ppm). The seeds were tested for proportion of germinated seeds and mean germination time in both chambers to study the impact of elevated [CO₂] during seed production and germination. Elevated [CO₂] during maturation of seeds on the mother-plants decreased the proportion of germinated seeds, while elevated [CO₂] during germination had no effect on the proportion of germinated seeds. However, when seeds were both produced and germinated under elevated [CO₂] (situation expected by the end of next century), germination was slow and low. Moreover, the effect of the [CO₂] treatment differs among genotypes of Arabidopsis: there is a strong treatment × genotype interaction. This means that there is ample genetic variance for a selective response modiying the effects of high levels of [CO₂] in natural populations of Arabidopsis thaliana. The outcome at the community level will depend on what seeds are available, when they germinate and the resulting competition following germination.     

Synthesis of a biological active tumor growth factor from the predicted DNA sequence of Shope fibroma virus

A 55-residue peptide comprising the carboxyl portion (residues 26-80) of the Shope fibroma virus growth factor (SFGF), a predicted 80-residue DNA virus gene product that encoded a homologous sequence with the epidermal growth factor transforming growth factor alpha family, was synthesized by a stepwise solid-phase method. The synthetic SFGF (26-80) purified to homogeneity by reverse-phase HPLC was characterized by fission ionization mass spectrometry and amino acid analysis. The disulfide pairings were established by enzymatic digestion and mass spectrometry and were found to be similar to those of EGF and TGF alpha. Synthetic SFGF (26-80) was found to share about 10% of the activities as EGF in the radioreceptor binding to A431 cells, stimulation of [3H]thymidine uptake in NRK cells, and induction of colony formation in soft-agar assay. Our results therefore confirmed that SFGF contained the putative biological activities of the EGF-TGF alpha family and that production of SFGF by Shope fibroma virus infected cells may account for the proliferative diseases associated with this particular virus.     

PyCogent: a toolkit for making sense from sequence

We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent.     

Cicada ear geometry: species and sex effects

Many insect species rely on their sense of audition to find a mate, to localize prey or to escape from a predator. Cicadas are particularly known for their loud call and the conspicuous tympanal hearing system located in their abdomen. The vibration pattern of the tympanal membrane (TM) has been investigated recently revealing mechanical properties specific to species and sex. Although TM size and shape is likely to affect these patterns, the geometry of the cicada ear has never been examined per se. Focusing on three Mediterranean cicada species, namely Cicadatra atra, Cicada orni and Lyristes plebejus, we investigated the structure of TM shape variation at two levels, within and across species. Applying an elliptic Fourier analysis to the outlines of both male and female TMs, we estimated sexual dimorphism and species effects. Cicadatra atra showed a large TM compared with its small size, probably as a result of selective constraints related to the role of the TM in sound production. Sexual dimorphism seemed to be greater than interspecific variation, indicating that constraints operating on sex might be more selective than those acting on species identification. In addition, C. orni appeared to be significantly different from the two other species. This morphological peculiarity could be related to the unique vibrational pattern of its membrane. This would establish for the first time a direct link between the shape and mechanism of a hearing organ. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 922–934.     

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes

The severe environmental stresses of the Arctic may have promoted unique soil bacterial communities compared with those found in lower latitude environments. Here, we present a comprehensive analysis of the biogeography of soil bacterial communities in the Arctic using a high resolution bar‐coded pyrosequencing technique. We also compared arctic soils with soils from a wide range of more temperate biomes to characterize variability in soil bacterial communities across the globe. We show that arctic soil bacterial community composition and diversity are structured according to local variation in soil pH rather than geographical proximity to neighboring sites, suggesting that local environmental heterogeneity is far more important than dispersal limitation in determining community‐level differences. Furthermore, bacterial community composition had similar levels of variability, richness and phylogenetic diversity within arctic soils as across soils from a wide range of lower latitudes, strongly suggesting a common diversity structure within soil bacterial communities around the globe. These results contrast with the well‐established latitudinal gradients in animal and plant diversity, suggesting that the controls on bacterial community distributions are fundamentally different from those observed for macro‐organisms and that our biome definitions are not useful for predicting variability in soil bacterial communities across the globe.     

Theoretical habitat templets, species traits, and species richness: aquatic macrophytes in the Upper Rhône River and its floodplain

• 1 The objective of this study, which is based on forty-two species of hydrophytes and helophytes, is to investigate: (i) relationships among species traits; (ii) habitat utilization by species; (iii) the relationship between species traits and habitat utilization; (iv) trends in species traits in the framework of spatial–temporal habitat variability, and if trends match predictions from the river habitat templet; and (v) trends in species richness in the framework of spatial–temporal habitat variability, and if trends match predictions of the patch dynamics concept.
• 2 Two data sets were used for this analysis: species traits (mainly reproductive and morphological characteristics) were documented from the literature; and species distribution across eight habitat types was from field surveys conducted in the floodplain of the Upper Rhone River, France. This information was structured by a fuzzy coding technique and analysed by ordination methods.
• 3 Several species traits, which are related to disturbances and reflect resistance (e.g. attachment to soil or substrate) or resilience (e.g. potential for regeneration of an individual), are closely related for aquatic macrophytes.
• 4 Habitat utilization by aquatic macrophytes separates the habitat types along a gradient of connectivity with the main channel, which corresponds to a gradient in flood disturbance frequency and the permanence of the different water-bodies.
• 5 The relationship between species traits and habitat utilization is highly significant, indicating that a particular set of habitat types is used by taxa with a particular set of species trait modalities.
• 6 Observations in one habitat templet (in which scaling of the templet is primarily based on water level fluctuations for the temporal variability axis and on substrate characteristics for the spatial variability axis) generally do not support predictions on trends in species traits but do support predictions on trends in species richness.
• 7 Observations in an alternative habitat templet (in which scaling of the templet is based on frequency of flood scouring for the temporal variability axis and on heterogeneity of the substrate for the spatial variability axis) support theoretical predictions on trends for about half of the species traits for which predictions were available. However, trends in species richness in this alternative habitat templet are only partly in agreement with predictions.

     

Oxidative status in chronic hepatitis C: the influence of antiviral therapy and prognostic value of serum hydroperoxide assay

The effect of alpha-interferon (alpha-IFN) and ribavirin (RBV) treatment on oxidative status in chronic hepatitis C (CHC) is unknown. AIM: To study the time course of oxidative status in patients with CHC during alpha-IFN and RBV administration, and to evaluate the role of oxidative status in order to predict the therapeutic response. PATIENTS AND METHODS: Fifty one patients with CHC were studied. All received a combination of alpha-IFN and RBV for 6 or 12 months in relation to the type of response. The hydroperoxides concentration in serum test samples by D-ROM test was measured in all of the patients before therapy. In 27 patients, hydroperoxides were also measured during the treatment and during the 12 subsequent months. RESULTS: Cross-sectional analysis demonstrates that patients with a successive long-term response had a lower basal serum hydroperoxide concentration than non-responders (280 +/- 40.8 vs 337 +/- 83 CARR Units, p < 0.05). This resulted to be an independent factor predictive of long-term response in the multi-varied analysis. Longitudinal observation on 27 patients showed that the mean hydroperoxide concentration decreased significantly during treatment (T0 329 +/- 79.2 vs T12 272 +/- 34.5 CARR Units) and that the decrease in the mean values was mainly due to variations in the relapsers group. CONCLUSIONS: Normal basal hydroperoxide concentration helps to predict long-term response to combination therapy. The D-ROM test may be used for screening patients before treatment.     

Vestiges of an ancestral host plant: preference and performance in the butterfly Polygonia faunus and its sister species P. c‐album

1. In the study of the evolution of insect–host plant interactions, important information is provided by host ranking correspondences among female preference, offspring preference, and offspring performance. Here, we contrast such patterns in two polyphagous sister species in the butterfly family Nymphalidae, the Nearctic Polygonia faunus, and the Palearctic P. c‐album. 2. These two species have similar host ranges, but according to the literature P. faunus does not use the ancestral host plant clade – the ‘urticalean rosids’. Comparisons of the species can thus test the effects of a change in insect–plant associations over a long time scale. Cage experiments confirmed that P. faunus females avoid laying eggs on Urtica dioica (the preferred host of P. c‐album), instead preferring Salix, Betula, and Ribes. 3. However, newly hatched larvae of both species readily accept and grow well on U. dioica, supporting the general theory that evolutionary changes in host range are initiated through shifts in female host preferences, whereas larvae are more conservative and also can retain the capacity to perform well on ancestral hosts over long time spans. 4. Similar rankings of host plants among female preference, offspring preference, and offspring performance were observed in P. c‐album but not in P. faunus. This is probably a result of vestiges of larval adaptations to the lost ancestral host taxon in the latter species. 5. Female and larval preferences seem to be largely free to evolve independently, and consequently larval preferences warrant more attention.