incR: a new R package to analyse incubation behaviour

Incubation represents a life stage of crucial importance for the optimal development of avian embryos. For most birds, incubation poses a trade‐off between investing in self‐maintenance and offspring care. Furthermore, incubation is affected by environmental temperatures and, therefore, will be likely impacted by climate change. Despite its relevance and readily available temperature logging methods, avian incubation research is hindered by recognised limitations in available software. In this paper, a new quantitative approach to analyse incubation behaviour is presented. This new approach is embedded in a free R package, incR. The flexibility of the R environment eases the analysis, validation and visualisation of incubation temperature data. The core algorithm in incR is validated here and it is shown that the method extracts accurate metrics of incubation behaviour (e.g. number and duration of incubation bouts). This paper also presents a suggested workflow along with detailed R code to aid the practical implementation of incR.     

Inhibitory effects of Eucalyptus globulus on understorey plant growth and species richness are greater in non‐native regions

Aim

We studied the novel weapons hypothesis in the context of the broadly distributed tree species Eucalyptus globulus. We evaluated the hypothesis that this Australian species would produce stronger inhibitory effects on species from its non‐native range than on species from its native range.

Location

We worked in four countries where this species is exotic (U.S.A., Chile, India, Portugal) and one country where it is native (Australia).

Time period

2009–2012.

Major taxa studied

Plants.

Methods

We compared species composition, richness and height of plant communities in 20 paired plots underneath E. globulus individuals and open areas in two sites within its native range and each non‐native region. We also compared effects of litter leachates of E. globulus on root growth of seedlings in species from Australia, Chile, the U.S.A. and India.

Results

In all sites and countries, the plant community under E. globulus canopies had lower species richness than did the plant community in open areas. However, the reduction was much greater in the non‐native ranges: species richness declined by an average of 51% in the eight non‐native sites versus 8% in the two native Australian sites. The root growth of 15 out of 21 species from the non‐native range were highly suppressed by E. globulus litter leachates, whereas the effect of litter leachate varied from facilitation to suppression for six species native to Australia. The mean reduction in root growth for Australian plants was significantly lower than for plants from the U.S.A., Chile and India.

Main conclusions

Our results show biogeographical differences in the impact of an exotic species on understorey plant communities. Consistent with the novel weapons hypothesis, our findings suggest that different adaptations of species from the native and non‐native ranges to biochemical compounds produced by an exotic species may play a role in these biogeographical differences.     

Estimating dataset size requirements for classifying DNA microarray data.

A statistical methodology for estimating dataset size requirements for classifying microarray data using learning curves is introduced. The goal is to use existing classification results to estimate dataset size requirements for future classification experiments and to evaluate the gain in accuracy and significance of classifiers built with additional data. The method is based on fitting inverse power-law models to construct empirical learning curves. It also includes a permutation test procedure to assess the statistical significance of classification performance for a given dataset size. This procedure is applied to several molecular classification problems representing a broad spectrum of levels of complexity.     

Effects of selection for the timing of vegetative phase transition on corn borer (Lepidoptera: Noctuidae and Crambidae) damage

In maize, Zea mays L., the timing of vegetative phase transition from juvenile to adult vegetative phases can be modified through selection. A reduction in the juvenile vegetative phase has been associated with resistance to diseases and pests. The major maize pest in temperate areas is Ostrinia nubilalis (Hübner) and in Europe Sesamia nonagrioides Lefebvre. The objective of our study was to determine the effects of divergent selection for the timing of vegetative phase transition in maize on resistance to corn borers. Three cycles of divergent selection for early and late phase transition in a field corn synthetic and in a sweet corn population were evaluated separately under S. nonagrioides and O. nubilalis artificial infestation. For the field corn experiment, yield and moisture improved with selection for phase transition in both directions, but improvement was due to artifacts of selection, rather than to the change in phase transition. There were no correlated responses for corn borer damage, yield, or grain moisture due to selection for the timing of vegetative phase transition. In the sweet corn experiment, selection for the timing of vegetative phase transition had no significant effects on corn borer damage in sweet corn harvested at the fresh stage. Our results do not support the use of phase transition as an indirect criterion for improving resistance to corn borers in maize. The relationship between phase transition and pest resistance reported by other studies could depend on the genotypes or could be too weak to be detected in a selection program with wild-type maize.     

Immunocytochemical approach to the structure of human blood group B and H glycoconjugate antigens in the three days old rat cochlea

The possible structure of human blood-group antigens, as found in cochlear hair cells of 3-day-old rats, is suggested. Data were obtained from immunocytochemical studies using 77 antibodies against the major human blood group antigens of the ABO, H, I and Lewis genetic systems. Neither the anti-A-related nor the anti-Lewis-related antibodies showed any positive immunoreaction on hair cells. In contrast, anti-B, anti-AB and anti-H antibodies displayed specific positive immunoreactive patterns on the hair cells. The results suggest that, in immature hair cells, two main glycoconjugate structures of the lactoseries are present: H type 2 antigen, which is the precursor of the B type 2 antigen, and the B type 2 antigen itself. Similar H and B carbohydrate structures have been reported in rat olfactory receptors. The type 2 glycoconjugates carrying these H and B antigens of auditive and olfactory receptors are resistant to fixation and paraffin embedding, suggesting that they might be glycoproteins. These auditive and olfactory H and B antigens must be different from the B-related antigens that are expressed by pseudo-unipolar neurons of rat posterior root ganglia, that are built from type 4 core chains, and that are destroyed by routine paraffin embedding procedures.     

Pannexin1 channels act downstream of P2X7 receptors in ATP-induced murine T-cell death

Death of murine T cells induced by extracellular ATP is mainly triggered by activation of purinergic P2X₇ receptors (P2X₇Rs). However, a link between P2X₇Rs and pannexin1 (Panx1) channels, which are non-selective, has been recently demonstrated in other cell types. In this work, we characterized the expression and cellular distribution of pannexin family members (Panxs 1, 2 and 3) in isolated T cells. Panx1 was the main pannexin family member clearly detected in both helper (CD4⁺) and cytotoxic (CD8⁺) T cells, whereas low levels of Panx2 were found in both T-cell subsets. Using pharmacological and genetic approaches, Panx1 channels were found to mediate most ATP-induced ethidium uptake since this was drastically reduced by Panx1 channel blockers (¹⁰Panx1, Probenecid and low carbenoxolone concentration) and absent in T cells derived from Panx1^−/− mice. Moreover, electrophysiological measurements in wild-type CD4⁺ cells treated with ATP unitary current events and pharmacological sensitivity compatible with Panx1 channels were found. In addition, ATP release from T cells treated with 4Br-{"type":"entrez-nucleotide","attrs":{"text":"A23187","term_id":"833253","term_text":"A23187"}}A23187, a calcium ionophore, was completely blocked with inhibitors of both connexin hemichannels and Panx1 channels. Panx1 channel blockers drastically reduced the ATP-induced T-cell mortality, indicating that Panx1 channels mediate the ATP-induced T-cell death. However, mortality was not reduced in T cells of Panx1^−/− mice, in which levels of P2X₇Rs and ATP-induced intracellular free Ca²⁺ responses were enhanced suggesting that P2X₇Rs take over Panx1 channels lose-function in mediating the onset of cell death induced by extracellular ATP.