Automated pre-processing strategies for species occurrence data used in biodiversity modelling

To construct Biodiversity richness maps from Environmental Niche Models (ENMs) of thousands of species is time consuming. A separate species occurrence data pre-processing phase enables the experimenter to control test AUC score variance due to species dataset size. Besides, removing duplicate occurrences and points with missing environmental data, we discuss the need for coordinate precision, wide dispersion, temporal and synonymity filters. After species data filtering, the final task of a pre-processing phase should be the automatic generation of species occurrence datasets which can then be directly ’plugged-in’ to the ENM. A software application capable of carrying out all these tasks will be a valuable time-saver particularly for large scale biodiversity studies.

Effects of biosolids from tomato processing on soil fertility and wheat growth in a Greek alfisol

The effects of biosolids from tomato processing on soil properties and wheat growth were investigated in an Alfisol from central Greece. Biosolids were mixed with soil from the surface (Ap) or subsurface (Bt) horizon in plastic containers at rates of 1%, 5%, and 10% by dry weight (d.w.; equivalent to 10, 50, and 100 Mg ha–1). Biosolid treatments were compared to an NH4Cl application (50 mg N kg–1) and an untreated control in (1) a 102 d incubation experiment at 28°C to determine biosolid nitrification potential and (2) a 45 d outdoor experiment to evaluate effects on soil fertility and wheat growth. Mineralization of biosolids in the incubation experiment resulted in accumulation of nitrate-N and indicated that biosolids were able to supply N that was in excess of crop needs in treatments of 5% and 10%. After 45 d of wheat growth, available soil nutrients (N, P) and P uptake by wheat were distinctly lower in the Bt than in the Ap horizon. However, soil pH, electrical conductivity, organic matter, total N, nitrate-N, extractable P, and exchangeable K increased with increasing rate of biosolid application in both soils. These were followed by corresponding increases in wheat nutrient uptake and biomass production, thus demonstrating the importance of this organic material for sustaining production in soils of low immediate fertility. Compared to the NH4Cl treatment (50 kg N ha–1 equivalent), biosolid application rates of 5% and 10% had higher available soil nutrients, similar or higher nutrient uptake and higher wheat biomass. But only an application of 10% biosolids provided sufficient N levels for wheat in the surface soil, and even higher applications were required for providing sufficient N and P in the Bt horizon.

Ionic calcium and pH as predictors of stability of milk to UHT processing

This paper describes the use of pH and calcium ion electrodes for investigating factors affecting the heat stability of UHT milk with added calcium chloride. Calcium chloride was added to raw milk to manipulate ionic calcium and pH to within the range that may be typically encountered in raw milk of different compositions and microbial quality. Addition of only 5 mM calcium chloride was sufficient to induce considerable changes in pH, ionic calcium and ethanol stability and alter its stability to UHT treatment. There was a strong relationship between pH decrease and increase in ionic calcium when pH was reduced, whether by addition of calcium chloride or by acidification. Calcium chloride addition was found to increase sediment formation in UHT treated milk. However, sediment could be reduced by addition of stabilizers. Those most effective were ones which decreased ionic calcium and increased pH, such as trisodium citrate and disodium hydrogen phosphate. Sediment formation following UHT treatment was only slight for milk samples whose ethanol stability was greater than 80%.

A platform for supporting micro-collaborations in a diverse device environment

Collaborative software is usually thought of as providing audio-video conferencing services, application/desktop sharing, and access to large content repositories. However mobile device usage is characterized by users carrying out short and intermittent tasks sometimes referred to as 'micro-tasking'. Micro-collaborations are not well supported by traditional groupware systems and the work in this paper seeks out to address this. Mico is a system that provides a set of application level peer-to-peer services for the ad-hoc formation and facilitation of collaborative groups across a diverse mobile device domain. The system builds on the Java ME bindings of the JXTA P2P protocols, and is designed with an approach to use the lowest common denominators that are required for collaboration between varying degrees of mobile device capability. To demonstrate how our platform facilitates application development, we built an exemplary set of demonstration applications and include code examples here to illustrate the ease and speed afforded when developing collaborative software with Mico.

The tissue-specific processing of pro-opiomelanocortin

It is just over 30 years since the definitive identification of the adrenocorticotrophin (ACTH) precursor, pro-opiomelanocotin (POMC). Although first characterised in the anterior and intermediate lobes of the pituitary, POMC is also expressed in a number of both central and peripheral tissues including the skin, central nervous tissue and placenta. Following synthesis, POMC undergoes extensive post-translational processing producing not only ACTH, but also a number of other biologically active peptides. The extent and pattern of this processing is tissue-specific, the end result being the tissue dependent production of different combinations of peptides from the same precursor. These peptides have a diverse range of biological roles ranging from pigmentation to adrenal function to the regulation of feeding. This level of complexity has resulted in POMC becoming the archetypal model for prohormone processing, illustrating how a single protein combined with post-translational modification can have a diverse number of roles.

An unusual choanoflagellate protein released by hedgehog autocatalytic processing

Hedgehog proteins are important cell-cell signalling proteins utilized during the development of multicellular animals. Members of the hedgehog gene family have not been detected outside the Metazoa, raising unanswered questions about their evolutionary origin. Here we report a highly unusual hedgehog-related gene from a choanoflagellate, a close unicellular relative of the animals. The deduced C-terminal domain, Hoglet-C, is homologous to the autocatalytic domain of Hedgehog proteins and is predicted to function in autocatalytic cleavage of the precursor peptide. In contrast, the N-terminal Hoglet-N peptide has no similarity to the signalling peptide of Hedgehog (Hh-N). Instead, Hoglet-N is deduced to be a secreted protein with an enormous threonine-rich domain of unprecedented size and purity (over 200 threonine residues) and two polysaccharide-binding domains. Structural modelling reveals that these domains have a novel combination of features found in cellulose-binding domains (CBD) of types IIa and IIb, and are expected to bind cellulose. We propose that the two CBD domains enable Hoglet-N to bind to plant matter, tethering an amorphous nucleophilic anchor, facilitating transient adhesion of the choanoflagellate cell. Since HhC and Hoglet-C are homologous, but Hh-N and Hoglet-N are not, we argue that metazoan hedgehog genes evolved by fusion of two distinct genes.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye and analysed by two-dimensional difference gel electrophoresis. Gel images analysed off-line, using the DeCyder image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

The role of satellite image-processing for national-scale estimates of gene flow from genetically modified crops: rapeseed in the UK as a model

1.There is concern over the possibility of unwanted environmental change following transgene movement from genetically modified (GM) rapeseed Brassica napus to its wild and weedy relatives. 2. The aim of this research was to develop a remote sensing-assisted methodology to help quantify gene flow from crops to their wild relatives over wide areas. Emphasis was placed on locating sites of sympatry, where the frequency of gene flow is likely to be highest, and on measuring the size of rapeseed fields to allow spatially explicit modelling of wind-mediated pollen-dispersal patterns. 3. Remote sensing was used as a tool to locate rapeseed fields, and a variety of image-processing techniques was adopted to facilitate the compilation of a spatially explicit profile of sympatry between the crop and Brassica rapa. 4. Classified satellite images containing rapeseed fields were first used to infer the spatial relationship between donor rapeseed fields and recipient riverside B. rapa populations. Such images also have utility for improving the efficiency of ground surveys by identifying probable sites of sympatry. The same data were then also used for the calculation of mean field size. 5. This paper forms a companion paper to Wilkinson et al. (2003), in which these elements were combined to produce a spatially explicit profile of hybrid formation over the UK. The current paper demonstrates the value of remote sensing and image processing for large-scale studies of gene flow, and describes a generic method that could be applied to a variety of crops in many countries. 6.Synthesis and applications. The decision to approve or prevent the release of a GM cultivar is made at a national rather than regional level. It is highly desirable that data relating to the decision-making process are collected at the same scale, rather than relying on extrapolation from smaller experiments designed at the plot, field or even regional scale. It would be extremely difficult and labour intensive to attempt to carry out such large-scale investigations without the use of remote-sensing technology. This study used rapeseed in the UK as a model to demonstrate the value of remote sensing in assembling empirical information at a national level.

A novel approach to processing high-performance polymers that exploits entropically driven ring-opening polymerization

Blends of the poly(ether sulfone) derived from 4,4'-biphenol and 4,4'-dichlorodiphenylsulfone (Radel-R(TM)) with its homologous macrocyclic oligomers show greatly lowered melt viscosities relative to that of the parent polymer, potentially enabling more facile production and fabrication of fiber-reinforced composite materials. The macrocycles can then undergo entropically driven ring-opening polymerization in situ. The required blends can be obtained easily in one step, by carrying out polycondensations at concentrations lower than those usually used for polymer synthesis.

The oxadiazolyldiazenido(1-) ligand: a remarkably versatile platform for the synthesis of heteropolynuclear transition metal complexes

Cyclo-condensation of aroyl hydrazides with the cationic tungsten-dichlorodiazomethane complex [BrW(dppe)(2)(N2CCI2)](+) affords neutral oxadiazolyldiazenido(1-) complexes which react readily with a wide range of transition and non-transition metal species to afford a novel series of crystallographically-characterised heteropolynuclear complexes containing bridging oxadiazolyldiazenido(1-) ligands.

Changes in milk composition and processing properties during the spring flush period

The period, known to UK farmers and processors as the "spring flush", when the cows' diet changes from dry feed to spring pasture, has long been established as a time of change in milk properties and processing characteristics. Although it is believed to be a time when problems in processing are most likely to occur (e.g. milk that does not form clots or forms weak gels during cheesemaking), there is little evidence in the literature of detailed changes in milk composition and their impact on product manufacture. In this study, a range of physicochemical properties were analysed in milk collected from five commercial dairy herds before, during and after the spring flush period of 2006. In particular, total and ionic calcium contents of milk were studied in relation to other parameters including rennet clotting, acid gel properties, heat coagulation, alcohol stability, micelle size and zeta potential. Total divalent cations were significantly reduced from 35.4 to 33.4 mmol.L-1 during the study, while ionic calcium was reduced from 1.48 to 1.40 mmol.L-1 over the same period. Many parameters varied significantly between the sample dates. However, there was no evidence to suggest that any of the milk samples would have been unsuitable for processing - e.g. there were no samples that did not form clots with chymosin within a reasonable time or formed especially weak rennet or acid gels. A number of statistically significant correlations were found within the data, including ionic calcium concentration and pH; rennet clotting time (RCT) and micelle diameter; and RCT and ethanol stability. Overall, while there were clear variations in milk composition and properties over this period, there was no evidence to support the view that serious processing problems are likely during the change from dry feed to spring pasture.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye (TM) and analysed by two-dimensional difference gel. electrophoresis. Gel images analysed off-line, using the DeCyder (TM) image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Multivariate analysis of phenol mineralisation by combined hydrodynamic cavitation and heterogeneous advanced Fenton processing

Phenolic compounds in wastewaters are difficult to treat using the conventional biological techniques such as activated sludge processes because of their bio-toxic and recalcitrant properties and the high volumes released from various chemical, pharmaceutical and other industries. In the current work, a modified heterogeneous advanced Fenton process (AFP) is presented as a novel methodology for the treatment of phenolic wastewater. The modified AFP, which is a combination of hydrodynamic cavitation generated using a liquid whistle reactor and the AFP is a promising technology for wastewaters containing high organic content. The presence of hydrodynamic cavitation in the treatment scheme intensifies the Fenton process by generation of additional free radicals. Also, the turbulence produced during the hydrodynamic cavitation process increases the mass transfer rates as well as providing better contact between the pseudo-catalyst surfaces and the reactants. A multivariate design of experiments has been used to ascertain the influence of hydrogen peroxide dosage and iron catalyst loadings on the oxidation performance of the modified AFP. High er TOC removal rates were achieved with increased concentrations of hydrogen peroxide. In contrast, the effect of catalyst loadings was less important on the TOC removal rate under conditions used in this work although there is an optimum value of this parameter. The concentration of iron species in the reaction solution was measured at 105 min and its relationship with the catalyst loadings and hydrogen peroxide level is presented.