Uncover Genetic Interactions in Caenorhabditis elegans by RNA Interference

RNA-mediated interference (RNAi) has emerged recently as one of the most powerful functional genomics tools. RNAi has been particularly effective in the nematode worm C. elegans where RNAi has been used to analyse the loss-of-function phenotypes of almost all predicted genes. In this review, we illustrate how RNAi has been used to analyse gene function in C. elegans as well as pointing to some future directions for using RNAi to examine genetic interactions in a systematic manner.     

BEHAVIOR OF RED-TAILED HAWKS IN A WIND TURBINE DEVELOPMENT

Abstract: Birds flying within windfarms can be killed when they collide with wind turbines. Raptors, especially red-tailed hawks (Buteo jamaicensis), are more susceptible to collisions than other birds, which may be attributable to their specific foraging and flight behavior. To more fully understand the problem, and to reduce raptor mortality, it is necessary to acquire more information on habitat use and flight behavior by raptors inhabiting windfarms. Between June 1999 and June 2000, we watched raptors for 346 hours in the Altamont Pass Wind Resource Area, the largest windfarm in North America. We recorded flight behavior in relation to characteristics of the topography such as slope aspect, elevation, and inclination and in relation to various weather variables including wind speed and wind direction. We found that red-tailed hawk behavior and their use of slope aspect differed according to wind speed. Hawks perched more often in weak winds than in strong. Red-tailed hawks were more likely to soar during low wind conditions and kite during strong wind, particularly on hillsides that faced into the wind as opposed to hillsides shielded from the wind. This is likely a result of their use of deflection updrafts for lift during flight. During our study, when winds were strong and from the south-southwest, kiting behavior occurred on south-southwestern facing slopes with inclines of greater than 20% and peak elevations greater than adjacent slopes. Accordingly, mitigation measures to decrease red-tailed hawk fatalities should be directed specifically to these areas and others fitting this general model. Wind farm managers can power down turbines at the top of these hazardous slopes when they pose the greatest danger—when winds are strong and facing perpendicularly to the slope.     

Environmental signals from leaves--a physiognomic analysis of European vegetation

Leaf physiognomic traits vary predictably along climatic and environmental gradients. The relationships between leaf physiognomy and climate have been investigated on different continents, but so far an investigation based on European vegetation has been missing. A grid data set (0.5 degrees x 0.5 degrees latitude/longitude) has been compiled in order to determine spatial patterns of leaf physiognomy across Europe. Based on distribution maps of native European hardwoods, synthetic chorologic flora lists were compiled for all grid cells. Every synthetic chorologic flora was characterised by 25 leaf physiognomic traits and correlated with 16 climatic parameters. Clear spatial patterns of leaf physiognomy have been observed, which are statistically significant related to certain, temperature-related climate parameters. Transfer functions for several climatic parameters have been established, based on the observed relationships. The study provides evidence that synthetically generated floras represent a powerful tool for analysing spatial patterns of leaf physiognomy and their relationships to climate. The transfer functions from the European data set indicate slightly different relationships of leaf physiognomy and environment compared with results obtained from other continents.     

Effects of N-deficiency and timing of N supply on the recovery and distribution of labeled 15N in contrasting maize hybrids

Little information exists on the pattern of nitrogen (N) uptake, remobilization and N use efficiency (NUE) in Leafy and stay-green (SG) maize (Zea mays L.) genotypes. A pot experiment was conducted under controlled nutrition and growing conditions to determine the response of Leafy and SG maize genotypes to different levels of N-deficiency and timing of N supply. Three contrasting maize hybrids, Pioneer 3905 (a conventional hybrid with moderate SG characteristics), Pioneer 39F06 Bt (with a high score of SG trait) and Maizex LF850-RR (with a Leafy trait) were grown in 6 L plastic pots. Five different N treatments [no supply of N until V8 (N₁), no supply of N after V8 (N₂), no supply of N after silking (N₃), no supply of N beyond 3 weeks after silking (N₄), and continuous N supply from emergence to physiological maturity (N₅; standard check)] were imposed through modified Hoagland solution applied manually. Labeled ¹⁵N of 5% ¹⁵N₂–NH₄NO₃fertilizer was applied at 3 g per pot at the start of each schedule N treatment. Total amounts of N applied in different treatments were 3.13, 1.32, 1.90, 2.63 and 3.40 g, respectively in N₁, N₂, N₃, N₄ and N₅. Dry matter, N concentration, ¹⁵N (atom% enrichment) and NUE were determined in roots, stalk, leaves and grains at crop maturity. The three contrasting hybrids did not differ in grain yield, total N acquisition, partitioning of ¹⁵N and NUE. Restriction of N supply until V8, and from V8 to physiological maturity significantly reduced grain yield and N-uptake in all hybrids. Irrespective of the level of N-deficiency in plant and timing when the labeled fertilizer was applied, the amount of ¹⁵N recovered in the matured plant was the same in all N treatments. It has been evident that maize continued to take up N beyond 3 weeks after silking and the later N was applied during the development, the higher proportion of it was partitioned to grains. Of the total ¹⁵N uptake, 78% was partitioned to kernels in the N₄ treatment compared to only 61% in the control. Our data showed no evidence of differential N uptake, remobilization and NUE in the SG or Leafy hybrids tested, but the timing of N application and level of N-deficiency in plant significantly influenced N uptake, remobilization and N-dynamics in maize.     

Polymethyleneamine Alkaloids of Animal Origin: I. Metabolites of Marine and Microbial Organisms

This review, issued in two parts, describes the information on the structure and biological activity of animal alkaloids derived from polymethyleneamines and produced by marine organisms, wasps, spiders, and microorganisms. Animal alkaloids are outstanding models for developing methods and drugs for the treatment of many human diseases. In the first part, we consider compounds produced by marine and microbial organisms. Some promising synthetic analogues of these alkaloids are used in developing modern preparations for the chelate therapy of excessive blood iron content and antituberculosis, antiproliferative, and immunosuppressive drugs.     

High level expression of a recombinant acid phytase gene in Pichia pastoris

AIMS: To achieve high phytase yield with improved enzymatic activity in Pichia pastoris. METHODS AND RESULTS: The 1347-bp phytase gene of Aspergillus niger SK-57 was synthesized using a successive polymerase chain reaction and was altered by deleting intronic sequences, optimizing codon usage and replacing its original signal sequence with a synthetic signal peptide (designated MF4I) that is a codon-modified Saccharomyces cerevisiae mating factor alpha-prepro-leader sequence. The gene constructs containing wild type or modified phytase gene coding sequences under the control of the highly-inducible alcohol oxidase gene promoter with the MF4I- or wild type alpha-signal sequence were used to transform Pichia pastoris. The P. pastoris strain that expressed the modified phytase gene (phyA-sh) with MF4I sequence produced 6.1 g purified phytase per litre of culture fluid, with the phytase activity of 865 U ml(-1). The expressed phytase varied in size (64, 67, 87, 110 and 120 kDa), but could be deglycosylated to produce a homogeneous 64 kDa protein. The recombinant phytase had two pH optima (pH 2.5 and pH 5.5) and an optimum temperature of 60 degrees C. CONCLUSIONS: The P. pastoris strain with the genetically engineered phytase gene produced 6.1 g l(-1) of phytase or 865 U ml(-1) phytase activity, a 14.5-fold increase compared with the P. pastoris strain with the wild type phytase gene. SIGNIFICANCE AND IMPACT OF THE STUDY: The P. pastoris strain expressing the modified phytase gene with the MF4I signal peptide showed great potential as a commercial phytase production system.     

Hunter Self-monitoring by the Isoseño-Guaraní in the Bolivian Chaco

Declared in 1995, the 34,400 km² Kaa-Iya del Gran Chaco National Park is the first protected area in South America co-managed by an indigenous organization, the Capitanía del Alto y Bajo Isoso (CABI). In 1997, based on historical occupation by the Isoseño-Guaraní over the past 300 years, CABI formally demanded a 19,000 km² `Tierra Comunitaria de Orígen' (TCO) that adjoins, but does not overlap, the national park. The creation of TCOs and the co-administration of protected areas are elements of decentralization processes in Bolivia, whereby the management of land and natural resources is devolving to departmental and municipal levels of government. This paper examines biodiversity monitoring in the context of a community wildlife management program developed with CABI. Hunter self-monitoring (100–150 hunters per month) combined with monthly activity records for potential hunters (7637 observed hunter-months) permit estimations of total offtakes of subsistence game species for 1996–2003, as well as catch-per-unit-effort over the same time period. These data show considerable fluctuations from year to year and no declining trends that would suggest over-hunting. Monitoring populations of multiple game species can be relatively expensive, even with the voluntary support of hunters, considering data collection and analysis, as well as presentation and discussion through community meetings. At the same time, monitoring does not provide highly accurate assessments of short-term changes in wildlife resources. However, relatively simple participatory methods are important for generating information on long-term trends and for creating a context for community discussion of formal wildlife management.     

Urban Domestic Gardens (IV): The Extent of the Resource and its Associated Features

Domestic (‘private’) gardens constitute a substantial proportion of ‘green space’ in urban areas and hence are of potential significance for the maintenance of biodiversity in such areas. However, the size and nature of this resource and its associated features are poorly known. In this study, we provide the first detailed audit, using domestic gardens in the city of Sheffield as a model study system. Domestic gardens, the mean area of which was 151 m², cover approximately 33 km² or 23% of the predominantly urban area of the city. The smaller gardens contribute disproportionately to this total because, although individually they add little, they are large in number. Conversely, the regions of the city with proportionately more garden area contribute most to the total garden area of the city, although such regions are limited in number. Based on the findings of a telephone based survey, 14.4% of dwellings with gardens were estimated to have ponds, 26% to have nest-boxes, 29% to have compost heaps, 48% to hold trees more than 3 m tall, and 14% of dwellings were estimated to be home to one or more cats. Whilst the absolute frequency of these features is low to moderate, by extrapolation they nonetheless yield estimates for domestic gardens in Sheffield of a total of 25,200 ponds, 45,500 nest boxes, 50,750 compost heaps, 360,000 trees, and a population of 52,000 domestic cats. These results are considered in the context of the role of gardens in urban areas as habitats for wildlife and the implications for housing policy.     

Fractal analysis of plant spatial patterns: a monitoring tool for vegetation transition shifts

Spatial heterogeneity, like species diversity, is an important ecosystem property. We examine the effects of land use on the diversity and spatial distribution of plants in five semi-arid communities of eastern Spain using non-linear methods to assess the spatialtemporal dynamics of plant populations. Specifically, we are interested in detecting long-term structural changes or drift in an ecosystem before it is too late to prevent irreversible degradation. Fractal analysis is used to characterize the complexity of plant spatial patterns and Information Theory indices are used to measure change in information flow with land use changes and soil substrate. We found that grazing favored diversity and heterogeneity of species distribution on the impoverished gypsum and saline substrate community, as opposed to the detrimental effect of grazing in the Alpha steppe community. Indeed, old-field succession after 30 years of abandonment showed a recovery of species diversity but not the spatial structure of the vegetation. Further, Information Fractal Dimension, representing the unpredictability of plant spatial patterns in the landscape, increased as we moved from a highly diverse to a less diverse community, revealing the change to a more scattered and homogeneous spatial plant distribution. The Information Fractal Dimension is a good estimator of ecosystem disturbance, independent of scale, and thus can be used to monitor ecosystem dynamics.     

Soil seed banks of two montane riparian areas: implications for restoration

Understanding the role of seed banks can be important for designing restoration projects. Using the seedling emergence method, we investigated the soil seed banks of two montane, deciduous riparian forest ecosystems of southeastern Arizona. We contrasted the seed banks and extant vegetation of Ramsey Canyon, which is the site of riparian restoration activities, with that of Garden Canyon, which has been less affected by human land uses. Fewer plant species were found at Ramsey Canyon than Garden Canyon, for both the seed bank and extant vegetation, and the vegetation at Ramsey Canyon (seed bank and extant) had consistently drier wetland indicator scores. As well, vegetation patterns within sampling zones (channel margins and adjacent riparian forests) differed between canyons. At Garden Canyon channel margins, the seed bank and extant vegetation had relatively high similarity, with herbaceous wetland perennial species dominating. Extant vegetation in the floodplain riparian forest zone at Garden Canyon had a drier wetland indicator score than the seed bank, suggesting that the floodplains are storing seeds dispersed from wetter fluvial surfaces. Vegetation patterns for Ramsey Canyon channel margins were similar to those for Garden Canyon floodplains. Vegetation patterns in the Ramsey Canyon riparian forest zone were indicative of non-flooded conditions with an abundance of upland species in the soil seed bank and extant vegetation. Channel geomorphology measurements indicated that much of the riparian forest zone at Ramsey Canyon is functionally a terrace, a condition that may be a legacy of channel erosion from historic land uses. Steep, erodible channel slopes may contribute to the low seed bank germinant density at Ramsey Canyon channel margins, and narrower flood-prone area may explain the greater terrestrialization of the vegetation in both sampling zones. We recommend testing the use of donor soils from more diverse stream reaches to restore biodiversity levels at Ramsey Canyon, following restoration activities such as channel-widening. Seed banks from Garden Canyon, for example, although predominantly consisting of herbaceous perennials, would supply species with a range of moisture tolerances, life spans, and growth forms. We also recommend that restorationists take care not to harm seed banks exposed during removal of introduced species; at Ramsey Canyon, soil seed banks were equally diverse in areas with high and low cover of the introduced Vinca major (a legacy of Ramsey Canyon land use).