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%.

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.

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.

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.

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.

Predictions of some product parameters based on the processing conditions of ultra-high-temperature milk plants

The temperature-time profiles of 22 Australian industrial ultra-high-temperature (UHT) plants and 3 pilot plants, using both indirect and direct heating, were surveyed. From these data, the operating parameters of each plant, the chemical index C*, the bacteriological index B* and the predicted changes in the levels of beta-lactoglobulin, alpha-lactalbumin, lactulose, furosine and browning were determined using a simulation program based on published formulae and reaction kinetics data. There was a wide spread of heating conditions used, some of which resulted in a large margin of bacteriological safety and high chemical indices. However, no conditions were severe enough to cause browning during processing. The data showed a clear distinction between the indirect and direct heating plants. They also indicated that degree of denaturation of alpha-lactalbumin varied over a wide range and may be a useful discriminatory index of heat treatment. Application of the program to pilot plants illustrated its value in determining processing conditions in these plants to simulate the conditions in industrial UHT plants. (C) 2008 Elsevier Ltd. All rights reserved.

Opportunities and challenges in high pressure processing of foods

Consumers increasingly demand convenience foods of the highest quality in terms of natural flavor and taste, and which are freedom additives and preservatives. This demand has triggered the need for the development of a number of nonthermal approaches to food processing, of which high-pressure technology has proven to be very valuable. A number of recent publications have demonstrated novel and diverse uses of this technology. Its novel features, which include destruction of microorganisms at room temperature or lower, have made the technology commerically attractive. Enzymes forming bacteria can be by the application of pressure-thermal combinations. This review aims to identify the opportunities and challenges associated with this technology. In addition to discussing the effects of high pressure on food components, this review covers the combined effects of high pressure processing with: gamma irradiation, alternating current, ultrasound, and carbon dioxide or anti-microbial treatment. Further, the applications of this technology in various sectors-fruits and vegetables, dairy and meat processing-have been dealt with extensively. The integration of high-pressure with other matured processing operations such as blanching, dehydration, osmotic dehydration, rehyrdration, frying, freezing/thawing and solid-liquid extraction has been shown to open up new processing options. The key challenges identified include: heat transfer problems and resulting non-uniformity in processing, obtaining reliable and reproducible data, for process validation, lack of detailed knowledge about the interaction between high pressure, and a number of food constituents, packaging and statutory issues.

Formation of high levels of acrylamide during the processing of flour derived from sulfate-deprived wheat

When wheat was grown under conditions of severe sulfate depletion, dramatic increases in the concentration of free asparagine were found in the grain of up to 30 times as compared to samples receiving the normal levels of sulfate fertilizer. The effect was observed both in plants grown in pots, where the levels of nutrients were carefully controlled, and in plants grown in field trials on soil with poor levels of natural nutrients where sulfate fertilizer was applied at levels from 0 to 40 kg sulfur/Ha. Many of the other free amino acids were present at higher levels in the sulfate-deprived wheat, but the levels of free glutamine showed increases similar to those observed for asparagine. In baked cereal products, asparagine is the precursor of the suspect carcinogen acrylamide, and when flours from the sulfate-deprived wheat were heated at 160 degrees C for 20 min, levels of acrylamide between 2600 and 5200 mu g/kg were found as compared to 600-900 mu g/kg in wheat grown with normal levels of sulfate fertilization.