Mutational robustness of ribosomal protein genes

The distribution of fitness effects (DFE) of mutations is of fundamental importance for understanding evolutionary dynamics and complex diseases and for conserving threatened species. DFEs estimated from DNA sequences have rarely been subject to direct experimental tests. We used a bacterial system in which the fitness effects of a large number of defined single mutations in two ribosomal proteins were measured with high sensitivity. The obtained DFE appears to be unimodal, where most mutations (120 out of 126) are weakly deleterious and the remaining ones are potentially neutral. The DFEs for synonymous and nonsynonymous substitutions are similar, suggesting that in some genes, strong fitness constraints are present at the level of the messenger RNA.     

Inhibitory effect of low partial pressures of acetylene on nitrification

The inhibiting effect of C₂H₂ on nitrification was investigated in two agricultural soils. Nitrification was totally inhibited at 10 Pa partial pressure of C₂H₂ which is lower than previously reported for soils. There were no differences in rates of nitrate production between flasks without C₂H₂ and flasks with C₂H₂ at 0.01 Pa, while there was an effect on nitrification at 0.1 PaC₂H₂. At 0.1 Pa no inhibition was noted during the first 3 days; after this period nitrification was partially inhibited. The inhibiting effect did not cease until 7 days after removal of C₂H₂. The sensitivity of nitrification to low concentrations of C₂H₂ should be noted when denitrification rates are determined by the use of the acetylene inhibition method (usually C₂H₂ at 10kPa).     

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.     

Comparison of biological activities of natural and recombinant chicken interferon-gamma

In recent years, chicken interferon-gamma (ChIFN-γ) has been identified and cloned from a chicken T cell line. In this study, recombinant ChIFN-γ produced in the baculovirus and prokaryotic (Escherichia coli) expression systems were characterized and their activity was compared to that of naturally ChIFN-γ produced by mitogen-activated splenic T cells. The baculovirus-derived ChIFN-γ protein (Bac-ChIFN-γ) proved to have physiochemical properties and biological activities similar to those of natural ChIFN-γ. Indeed, Bac-ChIFN-γ was able to inhibit the replication of cytolytic viruses in chicken embryo fibroblasts and to activate macrophages, as was determined by nitric oxide production. Levels ranging between 100 and 300 μg/ml of BacChIFN-γ could be obtained in the supernatants of infected insect cells. On the other hand, yields of the E. coli produced ChIFN-γ rarely exceeded 100 μg/ml after purification steps and although it was also able to activate the HD11 macrophage cell line in a specific manner, no anti-viral activity could be demonstrated. Therefore, the baculovirus expression system is an appropriate system for the high-level expression of biologically active ChIFN-γ and will allow further studies of the immunomodulatory and therapeutic effects of this cytokine in vivo.     

Environmental factors at different spatial scales governing soil fauna community patterns in fragmented forests

Spatial and temporal changes in community structure of soil organisms may result from a myriad of processes operating at a hierarchy of spatial scales, from small-scale habitat conditions to species movements among patches and large-sale landscape features. To disentangle the relative importance of spatial and environmental factors at different scales (plot, patch and landscape), we analyzed changes in Collembola community structure along a gradient of forest fragmentation, testing predictions of the Hierarchical Patch Dynamics Paradigm (HPDP) in different European biogeographic regions (Boreal, Continental, Atlantic, Mediterranean, Alpine). Using variance partitioning methods, based on partial CCAs, we observed that the independent effect of environmental processes was significantly explaining Collembola community variance in all regions, while the relative effect of spatial variables was not significant, due to the observed high levels of landscape heterogeneity along the gradient. Environmental factors at the patch and plot scales were generally significant and explained the larger part of community changes. Landscape variables were not significant across all study sites. Yet, at the landscape level, an increase in forest habitat and proximity of forest patches were showed to have an indirect influence on local community changes, by influencing microhabitat heterogeneity at lower spatial scales in all studied regions. In line with HPDP, large-scale landscape features influenced spatio-temporal changes in soil fauna communities by constraining small-scale environmental processes. In turn, these provided mechanistic understanding for diversity patterns operating at the patch scale, via shifts in community weighted mean of Collembola life-forms occurring in local communities along the fragmentation gradient.     

Low Success Rate in Re-Establishing European Perch in Some Highly Acidified Lakes in Southernmost Norway

In order to test whether major reductions in acid inputs had improved water quality sufficiently for fish populations to recover, we stocked wild European perch (Perca fluviatilis) in three highly acidified lakes that had previously supported this species, and in one limed lake. The fish, which were introduced from a local lake (donor lake), generally ranged from 12 to 16 cm in total length, and were stocked at densities of 117–177 fish ha^?1. The untreated lakes were highly acid, with minimum pH values and maximum inorganic aluminium concentrations (Al_i) during the spring of 4.6–4.7 and 118–151 µg L^?1 respectively. In the limed lake, the corresponding values for pH and Al_i ranged between 5.8 and 6.6 and 5 and 19 µg L^?1 respectively. Gill-netting in two subsequent years after the introduction yielded only a few recruits (0+) and one adult in one of the three acidified lakes in one year only. However, stocked perch reproduced successfully in both years in the limed lake. There was a significant linear relationship between the catches (CPUE) of juvenile perch (age 0+) in the different lakes in the autumn and the water quality in May (time of hatching), both in terms of Al_i (r ²=0.934, P<0.05) and pH (r ²=0.939, P<0.05). Our data suggest unsuccessful recruitment in waters of pH <5.1 and Al_i>60 µg L^?1.     

Fish communities in coastal freshwater ecosystems: the role of the physical and chemical setting

Background

We explored how embayment watershed inputs, morphometry, and hydrology influence fish community structure among eight embayments located along the southeastern shoreline of Lake Ontario, New York, USA. Embayments differed in surface area and depth, varied in their connections to Lake Ontario and their watersheds, and drained watersheds representing a gradient of agricultural to forested land use.

Results

We related various physicochemical factors, including total phosphorus load, embayment area, and submerged vegetation, to differences in fish species diversity and community relative abundance, biomass, and size structure both among and within embayments. Yellow perch (Perca flavescens) and centrarchids numerically dominated most embayment fish communities. Biomass was dominated by piscivorous fishes including brown bullhead (Ameiurus nebulosus), bowfin (Amia calva), and northern pike (Esox lucius). Phosphorus loading influenced relative biomass, but not species diversity or relative abundance. Fish relative abundance differed among embayments; within embayments, fish abundance at individual sampling stations increased significantly with submerged vegetative cover. Relative biomass differed among embayments and was positively related to total phophorus loading and embayment area. Fish community size structure, based on size spectra analysis, differed among embayments, with the frequency of smaller-bodied fishes positively related to percent vegetation.

Conclusion

The importance of total phosphorus loading and vegetation in structuring fish communities has implications for anthropogenic impacts to embayment fish communities through activities such as farming and residential development, reduction of cultural eutrophication, and shoreline development and maintenance.     

Evaluation of potential feed sources,and technical and economic considerations of small‐scale commercial striped catfish (Pangasius hypothalamus) pond farming systems in the Mekong Delta of Vietnam

A technical and socio‐economic survey was conducted in Dong Thap, Can Tho and An Giang, provinces of Vietnam in 2009. The results showed that most of the small scale farmers of striped catfish (Pangasius hypothalamus) carry out fish pond culture, developed and operated by self‐learned experience and from neighbours knowledge. The mean pond depth varied from 3.5 to 4.0 m, ranging from 2 to 6 m. Most of the fish farms have extremely high stocking density, with an average of about 40 fish m^?2, in some cases up to 70 fish per m². The average yields and net income of small‐scales pond farming is about 21–27 kg per m² crop^?1 and US$ 0.184–0.329 kg^?1 crop^?1 respectively. These figures are not significantly different compared with large‐scale pond farming. About 75%, 86% and 80% of fish farmers in Dong Thap, Can Tho and An Giang province, respectively, received positive net returns. Farm‐made feed is still playing an important role because of higher net profit compared with commercial pellet feeds. Rice bran and trash fish are the main feed ingredients for farm‐made feed formulations. Striped catfish farmers are now actively searching for locally produced plant protein sources as alternatives to marine trash fish or fish meal.     

Seasonal and diel effects on the activity of northern pike studied by high‐resolution positional telemetry

Abstract – Temperate lakes can be ice covered for several months each year, yet little is known about the behaviour and activity of the fish during the cold season. As northern pike represents the top of the food web in many northern temperate lakes and may structure the ecosystem both directly and indirectly, a detailed understanding of the behaviour of this species during winter is important. We continuously monitored the activity of adult northern pike (Esox lucius) in a small temperate lake from late summer to winter for two consecutive years using an automatic acoustic positional telemetry system. Four subsample periods representing different temperature regimes from each year were chosen for further investigation. The results revealed that pike activity was similar between seasons. In all periods, a distinct diel pattern, showing increased activity during day as compared to night, was evident. Our findings indicate that the fish component of temperate lentic ecosystems can be more active during the cold season than previously assumed. This may have implications for the structuring effect of pike on the lower trophic levels.