Emulsifying, rheological and physicochemical properties of exopolysaccharide produced by Bifidobacterium longum subsp. infantis CCUG 52486 and Bifidobacterium infantis NCIMB 702205

The rheological, emulsification and certain physicochemical properties of purified exopolysaccharides (EPS) of Bifidobacterium longum subsp. infantis CCUG 52486 and Bifidobacterium infantis NCIMB 702205 were studied and compared with those of guar gum and xanthan gum. The two strains were grown in skim milk supplemented with 1.5% (w/v) casein hydrolysate at 37 ◦C for 24 h; they both produced heteropolysaccharides with different molecular mass and composition. The carbohydrate content of both polymers was more than 92% and no protein was detected. The EPS of B. longum subsp. infantis CCUG 52486 showed highly branched entangled porous structure under scanning electron microscopy. Higher intrinsic viscosity was observed for the EPS of B. longum subsp. infantis CCUG 52486 compared to the EPS of B. infantis NCIMB 702205 and guar gum. Both polymers showed pseudoplastic non-Newtonian fluid behaviour in an aqueous solution. The EPS of B. infantis NCIMB 702205 and B. longum subsp. infantis CCUG 52486 produced more stable emulsions with orange oil, sunflower seed oil, coconut oil and xylene compared to guar and xanthan gum. The EPS of B. longum subsp. infantis CCUG 52486 is the most promising one for applications in the food industry, as it had higher intrinsic viscosity, higher apparent viscosity in aqueous solution, porous dense entangled structure and good emulsification activity.

Identification and validation of candidate genes associated with domesticated and improved traits in soybean

Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 traitassociated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.

Production of haploids and doubled haploids in oil palm

Background: Oil palm is the world’s most productive oil-food crop despite yielding well below its theoretical maximum. This maximum could be approached with the introduction of elite F1 varieties. The development of such elite lines has thus far been prevented by difficulties in generating homozygous parental types for F1 generation. Results: Here we present the first high-throughput screen to identify spontaneously-formed haploid (H) and doubled haploid (DH) palms. We secured over 1,000 Hs and one DH from genetically diverse material and derived further DH/mixoploid palms from Hs using colchicine. We demonstrated viability of pollen from H plants and expect to generate 100% homogeneous F1 seed from intercrosses between DH/mixoploids once they develop female inflorescences. Conclusions: This study has generated genetically diverse H/DH palms from which parental clones can be selected in sufficient numbers to enable the commercial-scale breeding of F1 varieties. The anticipated step increase in productivity may help to relieve pressure to extend palm cultivation, and limit further expansion into biodiverse rainforest.

Storm prediction research and its application to the oil/gas industry

The accurate prediction of storms is vital to the oil and gas sector for the management of their operations. An overview of research exploring the prediction of storms by ensemble prediction systems is presented and its application to the oil and gas sector is discussed. The analysis method used requires larger amounts of data storage and computer processing time than other more conventional analysis methods. To overcome these difficulties eScience techniques have been utilised. These techniques potentially have applications to the oil and gas sector to help incorporate environmental data into their information systems

A preliminary investigation of the release of oil from contaminated clays and other fine-grained sediments during consolidation

Fine-grained sediments on land, or in a freshwater or marine environment, may become contaminated with a wide range of pollutants including hydrocarbons. This paper is concerned with preliminary studies of the mobilization and transportation of hydrocarbons, during the process of consolidation, to adjacent sediments or water bodies. A modified Rowe Cell was used to measure the consolidation properties of prepared kaolinite and bentonite clay-water slurries, with and without the addition of oil, along with hydrocarbon-bearing drill-cuttings samples taken from the sea-bed adjacent to two North Sea oil-well platforms. The consolidation properties of the kaolinite and bentonite clay slurries were little altered by the addition of oil, which was present at concentrations of between 8073 and 59 572 mg kg(-1). During each consolidation stage, samples of the expelled pore-fluids were collected and analysed for oil content. These values were very low in comparison with the original oil concentration in the samples and changed little between each consolidation stage. Analysis of the slurry samples both before and after consolidation confirms that, proportionally, little oil is removed as a result of consolidation. The implication of these results is that, for the range of samples tested, the very high hydraulic gradients and particle rearrangements that occur during the process of consolidation are capable of releasing only proportionally small amounts of oil bound to the fine-grained clay and silt particles.

Patterns of pollen and seed dispersal in a small, fragmented population of the wind-pollinated tree Araucaria angustifolia in southern Brazil

Paternity analysis based on eight microsatellite loci was used to investigate pollen and seed dispersal patterns of the dioecious wind- pollinated tree, Araucaria angustifolia. The study sites were a 5.4 ha isolated forest fragment and a small tree group situated 1.7 km away, located in Paran alpha State, Brazil. In the forest fragment, 121 males, 99 females, 66 seedlings and 92 juveniles were mapped and genotyped, together with 210 seeds. In the tree group, nine male and two female adults were mapped and genotyped, together with 20 seeds. Paternity analysis within the forest fragment indicated that at least 4% of the seeds, 3% of the seedlings and 7% of the juveniles were fertilized by pollen from trees in the adjacent group, and 6% of the seeds were fertilized by pollen from trees outside these stands. The average pollination distance within the forest fragment was 83 m; when the tree group was included the pollination distance was 2006m. The average number of effective pollen donors was estimated as 12.6. Mother- trees within the fragment could be assigned to all seedlings and juveniles, suggesting an absence of seed immigration. The distance of seedlings and juveniles from their assigned mother- trees ranged from 0.35 to 291m ( with an average of 83m). Significant spatial genetic structure among adult trees, seedlings, and juveniles was detected up to 50m, indicating seed dispersal over a short distance. The effective pollination neighborhood ranged from 0.4 to 3.3 ha. The results suggest that seed dispersal is restricted but that there is longdistance pollen dispersal between the forest fragment and the tree group; thus, the two stands of trees are not isolated.

Influence of sodium chloride on seed germination and seedling root growth of cotton (Gossypium hirsutum L.)

Response of cotton (Gossypium hirsutum L. cv. NIAB-78) to salinity, in terms of seed germination, seedling root growth and root Na+ and K+ content was determined in a laboratory experiment. Cotton seeds were exposed to increasing salinity levels using germination water with Sodium chloride concentrations of 0, 50, 100, 150 and 200 mM, to provide different degrees of salt stress. Germinated seeds were counted and roots were harvested at 24, 48, 72 and 96 h after the start of the experiment. It appeared that seed germination was only slightly affected by an increase in salinity (in most cases the differences between treatment were non-significant), whereas root length, root growth rate, root fresh and dry weights were severely affected, generally highly significant differences in these variables were found for comparisons involving most combinations of salinity levels, in particular with increased incubation period. K+ contents decreased with increasing salinity levels, although differences in K+ content were only significant when comparing the control and the 4 salinity levels. Na+ content of the roots increased with increasing levels of NaCl in the germination water, suggesting an exchange of K+ for Na+. The ratio K+/Na+ strongly decreased with rising levels of salinity from around 4.5 for the control to similar to 1 at 200 mM NaCl.

Potential for clean yam minisett production by resource-poor farmers in the middle-belt of Nigeria

Yarn minisett technique (YMT) has been promoted throughout West Africa since the 1980s as a sustainable means of producing clean yarn planting material, but adoption of the technique is Often reported as being patchy at best. While there has been much research Oil the factors that influence adoption of the technique, there have been no attempts to assess its economic viability under 'farmer-managed' as distinct from 'on station' conditions. The present paper describes the results of farmer-managed trials employing the YMT (white yarn: Dioscorea rotundata) at two villages in Igalaland, Kogi State, Nigeria. One of the villages (Edeke) is on the banks of the River Niger and represents it specialist yarn environment, whereas the other village (Ekwuloko) is inland, where farmers employ a more general cropping system. Four farmers were selected in each of the two villages and asked to plant a trial comprising two varieties of yam, their popular local variety its well its another variety grown in other parts of Igalaland, and to treat yarn setts (80-100 g) with either woodash or insecticide/nematicide + fungicide mix (chemical treatment). Results suggest that while chemical sett treatment increased yield and hence gross margin compared with woodash, if household labour is costed then YMT is not economically viable. However, the specialist yarn growers of Edeke were far more positive about the use of YMT as they tended to keep the yarn seed tubers for planting rather than sell them. Thus, great care needs to be taken with planning adoption surveys on the assumption that all farmers should adopt a technology.

A preliminary investigation of the release of oil from contaminated clays and other fine-grained sediments during consolidation

Fine-grained sediments on land, or in a freshwater or marine environment, may become contaminated with a wide range of pollutants including hydrocarbons. This paper is concerned with preliminary studies of the mobilization and transportation of hydrocarbons, during the process of consolidation, to adjacent sediments or water bodies. A modified Rowe Cell was used to measure the consolidation properties of prepared kaolinite and bentonite clay-water slurries, with and without the addition of oil, along with hydrocarbon-bearing drill-cuttings samples taken from the sea-bed adjacent to two North Sea oil-well platforms. The consolidation properties of the kaolinite and bentonite clay slurries were little altered by the addition of oil, which was present at concentrations of between 8073 and 59 572 mg kg(-1). During each consolidation stage, samples of the expelled pore-fluids were collected and analysed for oil content. These values were very low in comparison with the original oil concentration in the samples and changed little between each consolidation stage. Analysis of the slurry samples both before and after consolidation confirms that, proportionally, little oil is removed as a result of consolidation. The implication of these results is that, for the range of samples tested, the very high hydraulic gradients and particle rearrangements that occur during the process of consolidation are capable of releasing only proportionally small amounts of oil bound to the fine-grained clay and silt particles.

Effects of patch size and density on flower visitation and seed set of wild plants: a pan-European approach

1. Habitat fragmentation can affect pollinator and plant population structure in terms of species composition, abundance, area covered and density of flowering plants. This, in turn, may affect pollinator visitation frequency, pollen deposition, seed set and plant fitness. 2. A reduction in the quantity of flower visits can be coupled with a reduction in the quality of pollination service and hence the plants’ overall reproductive success and long-term survival. Understanding the relationship between plant population size and⁄ or isolation and pollination limitation is of fundamental importance for plant conservation. 3. Weexamined flower visitation and seed set of 10 different plant species fromfive European countries to investigate the general effects of plant populations size and density, both within (patch level) and between populations (population level), on seed set and pollination limitation. 4. Wefound evidence that the effects of area and density of flowering plant assemblages were generally more pronounced at the patch level than at the population level. We also found that patch and population level together influenced flower visitation and seed set, and the latter increased with increasing patch area and density, but this effect was only apparent in small populations. 5. Synthesis. By using an extensive pan-European data set on flower visitation and seed set we have identified a general pattern in the interplay between the attractiveness of flowering plant patches for pollinators and density dependence of flower visitation, and also a strong plant species-specific response to habitat fragmentation effects. This can guide efforts to conserve plant–pollinator interactions, ecosystem functioning and plant fitness in fragmented habitats.

Nitrogen management is essential to prevent tropical oil palm plantations from causing ozone pollution

More than half the world's rainforest has been lost to agriculture since the Industrial Revolution. Among the most widespread tropical crops is oil palm (Elaeis guineensis): global production now exceeds 35 million tonnes per year. In Malaysia, for example, 13% of land area is now oil palm plantation, compared with 1% in 1974. There are enormous pressures to increase palm oil production for food, domestic products, and, especially, biofuels. Greater use of palm oil for biofuel production is predicated on the assumption that palm oil is an “environmentally friendly” fuel feedstock. Here we show, using measurements and models, that oil palm plantations in Malaysia directly emit more oxides of nitrogen and volatile organic compounds than rainforest. These compounds lead to the production of ground-level ozone (O3), an air pollutant that damages human health, plants, and materials, reduces crop productivity, and has effects on the Earth's climate. Our measurements show that, at present, O3 concentrations do not differ significantly over rainforest and adjacent oil palm plantation landscapes. However, our model calculations predict that if concentrations of oxides of nitrogen in Borneo are allowed to reach those currently seen over rural North America and Europe, ground-level O3 concentrations will reach 100 parts per billion (109) volume (ppbv) and exceed levels known to be harmful to human health. Our study provides an early warning of the urgent need to develop policies that manage nitrogen emissions if the detrimental effects of palm oil production on air quality and climate are to be avoided.

Global transcript analysis of rice leaf and seed using SAGE technology.

We have compiled two comprehensive gene expression profiles from mature leaf and immature seed tissue of rice (Oryza sativa ssp. japonica cultivar Nipponbare) using Serial Analysis of Gene Expression (SAGE) technology. Analysis revealed a total of 50 519 SAGE tags, corresponding to 15 131 unique transcripts. Of these, the large majority (approximately 70%) occur only once in both libraries. Unexpectedly, the most abundant transcript (approximately 3% of the total) in the leaf library was derived from a type 3 metallothionein gene. The overall frequency profiles of the abundant tag species from both tissues differ greatly and reveal seed tissue as exhibiting a non-typical pattern of gene expression characterized by an over abundance of a small number of transcripts coding for storage proteins. A high proportion ( approximately 80%) of the abundant tags (> or = 9) matched entries in our reference rice EST database, with many fewer matches for low abundant tags. Singleton transcripts that are common to both tissues were collated to generate a summary of low abundant transcripts that are expressed constitutively in rice tissues. Finally and most surprisingly, a significant number of tags were found to code for antisense transcripts, a finding that suggests a novel mechanism of gene regulation, and may have implications for the use of antisense constructs in transgenic technology.

Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily.

This review summarizes the recent discovery of the cupin superfamily (from the Latin term "cupa," a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic beta-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1, 2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.