Targeted identification of genomic regions using TAGdb

Background

The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes.

Results

We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome.

Conclusions

The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly.     

Crop species differ in root plasticity response to localised P supply

The effect of localised phosphorus (P) fertiliser placement and in particular, deep P fertiliser placement, on the comparative root growth and P uptake of fibrous vs tap‐rooted crops is not known. In this study, we examined the root growth and P uptake of wheat (Triticum aestivum L.), canola (Brassica napus L.), and narrow‐leaf lupin (Lupinus angustifolius L.) in a split‐root system and in columns with deep (19 cm) or shallow (5 cm) P fertiliser sources in glasshouse conditions. In the split‐root system, plants of all three species grown under heterogeneous soil P conditions absorbed more P and produced greater root and shoot biomass than those under homogeneous P supply. Root plasticity differed between species under heterogeneous soil P supply: canola and wheat allocated relatively more root biomass and root length to the high P zone than narrow‐leaf lupin. In the column experiment, there was no difference in the amount of P accumulated in shoots of any crops grown in the deep vs shallow P fertiliser treatments. Root proliferation occurred within the shallow and deep‐P fertiliser bands in all three species; however, root distribution above or below the bands did not differ between deep or shallow P fertiliser treatments in any species. Whilst root plasticity responses to heterogeneous soil P supply differed among species, root architecture (fibrous vs taproot) did not confer any advantage or disadvantage to the acquisition of P from deep vs shallow P fertiliser bands. Moreover, whilst roots proliferate in the vicinity of P fertiliser bands, root distribution outside of the bands appears to remain unaltered in both fibrous and tap‐rooted crops during early growth.     

Linking nest histories,remotely sensed land use data and wildlife crime records to explore the impact of grouse moor management on peregrine falcon populations

Wildlife crime can be difficult to quantify, and its true impact on populations can be underestimated if rates are under-recorded. The illegal killing of birds of prey is an important form of wildlife crime, which in the UK, is often associated with land managed for the recreational shooting of red grouse Lagopus lagopus scoticus. In the UK, increases in peregrine falcons Falco peregrinus following recovery from organo-chlorine pesticides have not been uniform, with slow growth and localised declines in some areas, including those managed for red grouse shooting. In this study, we combined 1081 peregrine nest histories across northern England between 1980 and 2006 with a remotely sensed map of grouse moor management, to test whether breeding performance was lower in areas with active management for grouse shooting. Productivity of pairs on grouse moors was 50% lower than pairs breeding on non-grouse moor habitat. However, clutch size and brood size of successful nests did not differ between habitat types, suggesting that food constraints were unlikely to explain this difference. Population models suggested source-sink dynamics, with populations on grouse moors unable to sustain themselves without immigration. Population data confirmed that growth rates were indeed lower on grouse moors than on non-grouse moor sites. Analysis of wildlife crime data confirmed that persecution of the species was more frequent on grouse moors than in other habitat types. This population will be more secure, and better able to function as a barometer of environmental health and climate change, if illegal persecution of the species ceases on areas of land managed for grouse shooting.     

A TWO-STAGE TECHNIQUE FOR THE IN VITRO DIGESTION OF FORAGE CROPS

A simple technique for the determination in vitro of the dry- or organic-matter digestibility of small (0·5 g) samples of dried forages is described. It involves incubation first with rumen liquor and then with acid pepsin. Using 146 samples of grass, clover and lucerne of known in vivo digestibility ( Y ), the regression equation Y = 0·99 X– 1·01 (S.E. ± 2·31) has been calculated, where X = in vitro dry-matter digestibility. This technique has been used for the study of the digestibilities of plant breeder's material, of the leaf and stem fractions of herbage and of herbage consumed by animals.     

Evaluation of methods of rapid mass killing of segregated early weaned piglets

The operational logistics of mass killing of healthy, surplus piglets by manual blunt force trauma, controlled blunt force trauma, intraperitoneal injection of barbiturate, and free bullet were recorded. Objective performance variables evaluated were, speed of application, human resource and input cost, animal restraint required, and failure rate. Subjective evaluation of esthetics and difficulty of application indicated manual blunt force trauma is an unacceptable technique. Under field conditions, physical methods of killing were superior to intraperitoneal injection of concentrated pentobarbital. Considering animal welfare metrics in isolation, controlled blunt force trauma was superior to all other techniques attempted.     

Preventing highly pathogenic avian influenza (HPAI) at the rural community level: a case study from Cambodia

Poultry is an integral part of the rural livelihoods in Cambodia, with more than half of the households keeping poultry in their small-scale, traditional, and extensive backyards. More than 20 highly pathogenic avian influenza (HPAI) outbreaks have been reported since 2004 with deaths of over 21,000 birds. During the HPAI outbreaks, some of the flocks in the rural areas were culled without compensation and producers were not allowed to sell outside of the community. Heifer International worked with 2,000 rural families through local project partners in the target communities to develop an effective intervention mechanism to mitigate the impact of the HPAI crisis. Heifer International provided training, public education, and networking as well as promoting model farms based on improved scavenging poultry management. Each community selected one farm family to serve as a model farm. They were trained in Heifer's working approach and committed to practicing integrated farming systems based on scavenging poultry management. One Village Animal Health Worker (VAHW) in each community participated during the project implementation, playing a key role in the information exchange and the interaction between the communities and the avian influenza experts. Formal and informal trainings were conducted for all project partners and project recipients through experts and VAHWs, respectively. There have been no outbreaks reported in the communities in the project areas. Farmers have started using appropriate techniques to maintain biosecurity. They are passing on the knowledge and the skills to the surrounding communities. This participatory approach in educating rural farmers can serve as a model to mitigate HPAI in the developing countries around the world.     

Spatial Distribution and Temporal Trends of Polycyclic Aromatic Hydrocarbons (PAHs) in Sediments from Lake Maryut, Alexandria, Egypt

Surface and core sediments from Lake Maryut, Egypt, one of the most polluted lakes in Egypt, were analyzed for polycyclic aromatic hydrocarbons (PAHs) using gas chromatography?Cmass spectrometry. This investigation represents the first extensive study of the distribution and sources of PAHs in sediments from Lake Maryut. The total PAHs concentrations (sum of 39 PAH compounds) in surface sediments varied greatly depending on the sampling location and ranged from 106 to 57,800 ng/g dry weight with a mean concentration of 6,950 ng/g. The most polluted areas are distributed in areas which are mainly influenced by municipal sewage and industrial effluent discharges, suggesting a direct influence of these sources on the pollutant distribution patterns. PAH concentrations were one to two orders of magnitude higher in comparison with those reported for riverine/estuaries systems around the world. Molecular indices, such as pyrogenic index (PI), methylphenanthrenes to phenanthrene ratio, HMW_PAH/LMW_PAH, A-PAHs/P-PAHs, FL/FL?+?PY, BaP/BaP?+?C, IP/IP?+?BgP, and Per/??(penta-aromatics) were calculated to evaluate different hydrocarbon origins and their relative importance. In general, sediments from the main basin and northwest basin of Lake Maryut showed the highest PAH concentrations with petrogenic signatures, indicating major sources of petrogenic PAHs in the city. On the other hand, lower levels of PAHs with a pyrogenic signature were widely recorded in areas that are distant from anthropogenic sources. At other locations, both petrogenic and pyrogenic inputs were significant. The concentrations of perylene relative to the penta-aromatic isomers are dominant especially in locations associated with terrestrial inputs and in the deepest core sediments, indicating diagenetic origin for the presence of perylene. Temporal trends of PAH concentrations in both cores sediments were influenced by input pathways and followed the economic development and the environmental policies of the Egyptian Government in the last 15 years. Finally, PAH levels in sediments were compared with Sediments Quality Guidelines (effects range median?Ceffects range low) for evaluation probable toxic effects on organism. Results suggest an ecotoxicological risk for benthic organisms mainly in the main basin area, where high concentrations of PAHs were found in sediments influenced by anthropogenic activities.     

Influence of nitrogen and other nutrients on the growth of Agave deserti

Although agaves are commercially important worldwide and ecologically interesting, their nutrient responses have not been extensively studied under controlled conditions. Here, nutrient responses of seedlings and adult plants of Agave deserti were examined, with particular emphasis on nitrogen. Growth of seedlings in hydroponics was enhanced by increasing potassium, phosphate, and especially nitrate. Seedling growth in sand culture was also enhanced by adding nitrate, leading to just over 2% N by dry weight in the leaves. Seedlings had optimal growth in soil having about 0.1% N by dry weight and a pH between 6 and 8. In going from irrigation with no added nutrients to full‐strength Hoagland solution for mature plants in soil, leaf unfolding (a non‐destructive measure of productivity) approximately doubled. The rate of leaf unfolding in the field was also doubled by adding 100 kg N hectare^‐1, higher levels proving inhibitory.