Transgenic tobacco plants expressing Tarin 1 inhibit the growth of Pseudomonas syringae pv. tomato and the development of Spodoptera frugiperda

The protein Tarin 1, from Colocasia esculenta, was expressed in Nicotiana tabacum. Bioassays were done on plants expressing Tarin 1 at different levels using Spodoptera frugiperda larvae, various bacteria and fungi and the root‐knot nematode Meloidogyne javanica. It was found that S. frugiperda larvae fed on transformed plants had retarded and lower pupation, lower accumulated biomass and higher mortality rate than larvae fed on control plants. Also, Tarin 1 was found to inhibit the growth in vitro of Pseudomonas syringae pv. tomato. For Meloidogyne javanica, both relative replication and root damage were greater in control plants than in transformed plants, but the results were not statistically significant. This work illustrates the effects of plants expressing Tarin 1, on the growth and development of insects and bacteria, and shows its potential for pest management.     

Will Environmental Stewardship enhance small mammal abundance on intensively managed farmland?

• 1 The creation of grassy field margins, as part of the UK Government's Environmental Stewardship (ES) scheme, is one of a number of measures proposed to mitigate the adverse effects of arable intensification on wildlife. Widespread development of these margins will potentially increase the amount of habitat available to small mammals in arable landscapes, as many species do not inhabit the cropped area.
• 2 The aim of this study was to determine what impact ES-type margins might have on small mammals. We compared small mammal abundance and biomass in spring and autumn on 3-m-wide and 6-m-wide grassy margins with that on conventionally managed field edges that have no margin (0 m wide) and are intensively cultivated to the field edge.
• 3 Bank voles Clethrionomys glareolus, wood mice Apodemus sylvaticus and common shrews Sorex araneus were the most abundant species; few field voles Microtus agrestis were captured on any margin. In autumn, bank vole and common shrew numbers were higher on the grassy margins than on conventional field edges, and margin width per se was positively associated with bank vole abundance. The number of wood mice captured did not differ among the different margin types.
• 4 Total small mammal biomass increased between spring and autumn on the 3-m- and 6-m-wide grassy margins, but decreased on the 0-m-wide margins. Total biomass in autumn was three times higher on 6-m-wide margins compared with the conventional arable field edges.

     

Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling

Background  

Proteochemometrics is a new methodology that allows prediction of protein function directly from real interaction measurement data without the need of 3D structure information. Several reported proteochemometric models of ligand-receptor interactions have already yielded significant insights into various forms of bio-molecular interactions. The proteochemometric models are multivariate regression models that predict binding affinity for a particular combination of features of the ligand and protein. Although proteochemometric models have already offered interesting results in various studies, no detailed statistical evaluation of their average predictive power has been performed. In particular, variable subset selection performed to date has always relied on using all available examples, a situation also encountered in microarray gene expression data analysis.     

XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services

Background  

Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use.     

The fine structure of the adipose cell of the leech Glossiphonia complanata

The two distinct types of cytoplasm seen with the light microscope in the adipose cell of the leech Glossiphonia complanata have been identified in the electron microscope image of this cell. One of these, the basophil cytoplasm, contains many well oriented, paired membranes which are much more clearly evident when calcium ions are added to the fixative. The membranes sometimes appear as concentric arrays of lamellae and are thought to represent sections through a phospholipide-containing body. The paired membranes and the concentric lamellae have granules attached to them and resemble in size and structure the membranes of the endoplasmic reticulum encountered in many mammalian cells. Small dense cytoplasmic particles are present throughout the cell; they may be ferritin molecules, derived from the breakdown of haemoglobin taken in as food. On the basis of a previous histochemical study and the present electron microscope investigation, it is suggested that these paired membranes are similar to the organized type of mammalian ER and the results seem to confirm the belief that these membranes are composed of layers of phospholipoprotein together with attached particles of ribonucleoprotein.     

Summer distribution of Red-legged Partridges Alectoris rufa in relation to water availability on Mediterranean farmland

The suggestion that the summer distribution of Red-legged Partridges Alectoris rufa in the Mediterranean region is determined by the availability of surface water was examined on the agricultural farm, Alto Alentejo, southern Portugal. Partridge coveys were surveyed between 15 July and 15 August in 1993 and 1994. Using a vector-based Geographic Information System, we assessed, for each covey location and for the locations of a double number of random points, the distance to the nearest water point, distance to field boundaries, distance to water lines and land use classes. Univariate comparisons were made between the two groups of locations, and three multivariate logistic models were fitted through forward stepwise selection to the 1993, 1994 and pooled data sets to estimate the probability of sighting partridge coveys in the study area. Distance to water was significantly lower for partridge locations than for random points in both years and was the only variable selected for all logistic models. Apart from water availability, Red-legged Partridge locations were also affected by land use and distance to field boundaries.     

Zea ribosomal repeat evolution and substitution patterns

Zea and Tripsacum nuclear ribosomal internal transcribed spacer (ITS) sequences were used to evaluate patterns of concerted evolution, rates of substitutions, patterns of methylation-induced deamination, and structural constraints of the ITS. ITS pseudogenes were identified by their phylogenetic position, differences in nucleotide composition, extensive deamination at ancestral methylation sites, and substitutions resulting in low-stability secondary RNA structures. Selection was important in shaping the kinds of polymorphisms and substitutions observed in the ITS. ITS substitution rates were significantly different among the Zea taxa. Deamination of cytosines at methylation sites was a potent mutation source, but selection appeared to maintain high methylation site density throughout the ribosomal repeat except for the gene promoter. Nucleotide divergence statistics identified selectively constrained regions at the 5' ends of the ITS1 and ITS2.