R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway

The RNA interference (RNAi) pathway is initiated by processing long double-stranded RNA into small interfering RNA (siRNA). The siRNA-generating enzyme was purified from Drosophila S2cells and consists of two stoichiometric subunits: Dicer-2(DCR-2) and a previously unknown protein that we named R2D2. R2D2 is homologous to the Caenorhabditis elegans RNAi protein RDE-4. Association with R2D2 does not affect the enzymatic activity of DCR-2. Rather, the DCR-2/R2D2 complex, but not DCR-2 alone, binds to siRNA and enhances sequence-specific messenger RNA degradation mediated by the RNA-initiated silencing complex (RISC). These results indicate that R2D2 bridges the initiation and effector steps of the Drosophila RNAi pathway by facilitating siRNA passage from Dicer to RISC.     

Age, sex, density, winter weather, and population crashes in Soay sheep

Quantifying the impact of density, extrinsic climatic fluctuations, and demography on population fluctuations is a persistent challenge in ecology. We analyzed the effect of these processes on the irregular pattern of population crashes of Soay sheep on the St. Kilda archipelago, United Kingdom. Because the age and sex structure of the population fluctuates independently of population size, and because animals of different age and sex respond in different ways to density and weather, identical weather conditions can result in different dynamics in populations of equal size. In addition, the strength of density-dependent processes is a function of the distribution of weather events. Incorporating demographic heterogeneities into population models can influence dynamics and their response to climate change.     

Influence of high temperature and terminal moisture stress on dormancy in wheat (Triticum aestivum L.)

Preharvest sprouting is common in cereals that lack grain dormancy if maturing grain is exposed to rain. Over three successive seasons wheat genotypes with a range of dormancy levels, were exposed to moisture stress and periods of high temperature stress (>30 °C) in controlled field trials. Dormancy assessments were based on a germination index of hand threshed grain throughout grain filling. There were three main results. First, moisture stress combined with consistently high temperature during grain filling was associated with induced dormancy in Cunderdin, (germination index of 0.41) in a normally non-dormant genotype (germination index normally >0.80), but no additional dormancy in DM 2001, a dormant genotype (germination index normally <0.10). In contrast sudden heat shocks (>30 °C max. for >12 days) at 30–50 days post-anthesis reduced dormancy, germination index increase of 0.42 on average across five genotypes. Secondly, whilst dormancy was affected by moisture and heat stress, genotypes maintained their relative rankings across environments and genotype had the most effect on dormancy (70–92% of the variation in germination index) with DM 2001 and DH 22 more dormant than DH 56, DH 45 and Cunderdin. Finally, the effect of environment was different for different genotypes; those with partial dormancy (germination index usually 0.20–0.50, DH 56 and DH 45) were most influenced by the environmental conditions with germination indexes ranging from 0.06 to 0.85 depending on environment. Consequently avoidance of high temperatures, moisture stress, and maturity × stress interactions, are important prerequisites in screening for genotypes with genetic differences in dormancy.     

A comparison of random draw and locally neutral models for the avifauna of an English woodland

Background

Extensive work has been done to identify and explain multi-year cycles in animal populations. Several attempts have been made to relate these to climatic cycles. We use advanced time series analysis methods to attribute cyclicities in several North-American mammal species to abiotic vs. biotic factors.

Results

We study eleven century-long time series of fur-counts and three climatic records – the North Atlantic Oscillation (NAO), the El-Niño-Southern Oscillation (ENSO), and Northern Hemisphere (NH) temperatures – that extend over the same time interval. Several complementary methods of spectral analysis are applied to these 14 times series, singly or jointly. These spectral analyses were applied to the leading principal components (PCs) of the data sets. The use of both PC analysis and spectral analysis helps distinguish external from intrinsic factors that influence the dynamics of the mammal populations.

Conclusions

Our results show that all three climatic indices influence the animal-population dynamics: they explain a substantial part of the variance in the fur-counts and share characteristic periods with the fur-count data set. In addition to the climate-related periods, the fur-count time series also contain a significant 3-year period that is, in all likelihood, caused by biological interactions.     

In situ mineral <Superscript>15</Superscript>N dynamics and fate of added <Superscript>15</Superscript>NH<Subscript>4</Subscript><Superscript>+</Superscript> in hoop pine plantation and adjacent native forest in subtropical Australia

Background, aim, and scope  Hoop pine (Araucaria cunninghamii) is a nitrogen (N) demanding indigenous Australia softwood species with plantations in Southeast Queensland, Australia. Soil fertility has declined with increasing rotations and comparison study of N cycling between hoop pine plantations, and adjacent native forest (NF) is required to develop effective forest management for enhancing sustainable forest production and promoting environmental benefits. Field in situ mineral ¹⁵N transformations in these two forest ecosystems have not been studied. Hence, the present study was to compare the differences in soil nutrients, N transformations, ¹⁵N fluxes, and fate between the hoop pine plantation and the adjacent native forest. Materials and methods  The study sites were in Yarraman State Forest (26°52′ S, 151°51′ E), Southeastern Queensland, Australia. The in situ core incubation method was used in the field experiments. Mineral N was determined using a LACHAT Quickchem Automated Ion Analyzer. ¹⁵N were performed using an isotope ratio mass spectrometer with a Eurovector elemental analyzer. All statistical tests were carried out by the SPSS 11.0 for Windows statistical software package. Results  Soil total C and N were significantly higher in the NF than in the 53-year-old hoop pine plantation. Concentrations of NO₃ ^– were significantly higher in the NF soil than in the plantation soil. The plantation soil had significantly higher ¹⁵N and ¹³C natural abundances than the NF soil. The NF soil had significantly lower C/N ratios than the plantation soil. NO₃ ^––N was dominated in mineral N pools in both NF and plantation soils, accounting for 91.6% and 70.3% of the total mineral N pools, respectively. Rates of net nitrification and net N mineralization were, respectively, four and three times higher in the NF soil than in the plantation soil. The ¹⁵NO₃ ^––N and mineral ¹⁵N were significantly higher in the NF soil than in the plantation soil. Significant difference in ¹⁵NH₄ ⁺–N was found in the NF soil before and after the incubation. Discussion  The NF soil had significantly higher NO₃ ^––N, mineral N, total N and C but lower δ¹⁵N, δ¹³C, and C/N ratios than the plantation soil. Moreover, the rates of soil net N mineralization and nitrification were significantly higher, but ammonification rate was lower in the NF than in the plantation. The NF soil had many more dynamic N transformations than the plantation soil due to the combination of multiple species and layers and, thus, stimulation of microbial activity and alteration of C and N pool sizes in favor of the N transformations by soil microbes. The net rate of N and ¹⁵N transformation demonstrated differences in N dynamic related to the variation in tree species between the two ecosystems. Conclusions  The change of land use and trees species had significant impacts on soil nutrients and N cycling processes. The plantation had larger losses of N than the NF. The NO₃ ^––N and ¹⁵NO₃ ^––N dominated in the mineral N and ¹⁵N pools in both forest ecosystems. Recommendations and perspectives  Native forest soil had strong N dynamic compared with the plantation soil. Composition of multiple tree species with different ecological niches in the plantation could promote the soil ecosystem sustainability. The ¹⁵N isotope dilution technique in the field can be quite useful for studying in situ mineral ¹⁵N transformations and fate to further understand actual N dynamics in natural forest soils.     

Measurement, management and mitigation of operational interactions between the South Australian Sardine Fishery and short-beaked common dolphins (Delphinus delphis)

This study arose from recommendations given in response to a legislated ecological assessment of the South Australian Sardine Fishery in 2004, urging it to: (i) attempt to mitigate operational interactions with marine mammals if excessive levels were detected; and (ii) improve the accuracy of their reporting of these events.An initial observer program revealed high rates of encirclement and mortality (1.78 and 0.39 dolphins per net-set, respectively) of short-beaked common dolphins (Delphinus delphis). This equated to an estimate of 1728 encirclements and 377 mortalities across the entire fleet over the same period. The average time taken for fishers to respond to encirclements was 135.93 ± 3.72 min and 21.3% of encircled animals subsequently died. During that time, fishers only reported 3.6% of encirclements and 1.9% of mortalities recorded by observers.A code of practice (CoP) was subsequently introduced aimed at mitigating operational interactions. A second observer program revealed a significant reductions in the observed rates of dolphin encirclement (0.22; down 87.3%) and mortality (0.01; down 97.1%) with an estimate of 169 and eight, respectively. The average time taken for fishers to respond to dolphin encirclements also reduced to 16.33 ± 4.67 min (down 76.9%) and the proportion of encircled animals that subsequently died reduced to 5.0%. Agreement between industry reports and observer records improved, with the fishery reporting 57.9% and 58.9% of the rate of encirclements and mortalities, respectively, recorded by observers.A number of avoidance and release strategies in the CoP may have been responsible for these improvements. In particular, fishers were required to delay or relocate their activities if dolphins were observed prior to fishing and to release encircled dolphins immediately or abort the fishing event if release procedures were unsuccessful. Future improvements to the CoP include: (i) improved response times when an encircled dolphin is detected; (ii) better use of behavioural cues for deciding when to abort a net-set; (iii) ceasing fishing during rough weather; and (iv) continuing to increase reporting accuracy by fishers. It is also recommended that the abundance, movements and boundaries of the common dolphin population in the region be determined, so that the impact of fishing activities on their status can be established.