Conformational and hydration effects of site-selective sodium, calcium and strontium ion binding to the DNA Holliday junction structure d(TCGGTACCGA)(4)

The role of metal ions in determining the solution conformation of the Holliday junction is well established, but to date the picture of metal ion binding from structural studies of the four-way DNA junction is very incomplete. Here we present two refined structures of the Holliday junction formed by the sequence d(TCGGTACCGA) in the presence of Na+ and Ca2+, and separately with Sr2+ to resolutions of 1.85 Angstrom and 1.65 Angstrom, respectively. This sequence includes the ACC core found to promote spontaneous junction formation, but its structure has not previously been reported. Almost complete hydration spheres can be defined for each metal cation. The Na+ sites, the most convincing observation of such sites in junctions to date, are one on either face of the junction crossover region, and stabilise the ordered hydration inside the junction arms. The four Ca2+ sites in the same structure are at the CG/CG steps in the minor groove. The Sr2+ ions occupy the TC/AG, GG/CC, and TA/TA sites in the minor groove, giving ten positions forming two spines of ions, spiralling through the minor grooves within each arm of the stacked-X structure. The two structures were solved in the two different C2 lattices previously observed, with the Sr2+ derivative crystallising in the more highly symmetrical form with two-fold symmetry at its centre. Both structures show an opening of the minor groove face of the junction of 8.4degrees in the Ca2+ and Na+ containing structure, and 13.4degrees in the Sr2+ containing structure. The crossover angles at the junction are 39.3degrees and 43.3degrees, respectively. In addition to this, a relative shift in the base pair stack alignment of the arms of 2.3 Angstrom is observed for the Sr2+ containing structure only. Overall these results provide an insight into the so-far elusive stabilising ion structure for the DNA Holliday junction. (C) 2003 Elsevier Science Ltd. All rights reserved.

Nutrient sensing and signalling in plants: Potassium and phosphorus

Potassium and phosphorus are important macronutrients for crops but are often deficient in the field. Very little is known about how plants sense fluctuations in K and P and how information about K and P availability is integrated at the whole plant level into physiological and metabolic adaptations. This chapter reviews recent advances in discovering molecular responses of plants to K and P deficiency by microarray experiments. These studies provide us not only with a comprehensive picture of adaptive mechanisms, but also with a large number of transcriptional markers that can be used to identify upstream components of K and P signalling pathways. On the basis of the available information we discuss putative receptors and signals involved in the sensing and integration of K and P status both at the cellular and at the whole plant level. These involve membrane potential, voltage-dependent ion channels, intracellular Ca and pH, and transcription factors, as well as hormones and metabolites for systemic signalling. Genetic screens of reporter lines for transcriptional markers and metabolome analysis of K- and P-deficient plants are likely to further advance our knowledge in this area in the near future.

Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence

This study quantifies the influence of Poa alpina on the soil microbial community in primary succession of alpine ecosystems, and whether these effects are controlled by the successional stage. Four successional sites representative of four stages of grassland development (initial, 4 years (non-vegetated); pioneer, 20 years; transition, 75 years; mature, 9500 years old) on the Rotmoos glacier foreland, Austria, were sampled. The size, composition and activity of the microbial community in the rhizosphere and bulk soil were characterized using the chloroform-fumigation extraction procedure, phospholipid fatty acid (PLFA) analysis and measurements of the enzymes beta-glucosidase, beta-xylosidase, N-acetyl-beta-glucosaminidase, leucine aminopeptidase, acid phosphatase and sulfatase. The interplay between the host plant and the successional stage was quantified using principal component (PCA) and multidimensional scaling analyses. Correlation analyses were applied to evaluate the relationship between soil factors (C-org, N-t, C/N ratio, pH, ammonium, phosphorus, potassium) and microbial properties in the bulk soil. In the pioneer stage microbial colonization of the rhizosphere of P. alpina was dependent on the reservoir of microbial species in the bulk soil. As a consequence, the rhizosphere and bulk soil were similar in microbial biomass (ninhydrin-reactive nitrogen (NHR-N)), community composition (PLFA), and enzyme activity. In the transition and mature grassland stage, more benign soil conditions stimulated microbial growth (NHR-N, total amount of PLFA, bacterial PLFA, Gram-positive bacteria, Gram-negative bacteria), and microbial diversity (Shannon index H) in the rhizosphere either directly or indirectly through enhanced carbon allocation. In the same period, the rhizosphere microflora shifted from a G(-) to a more G(+), and from a fungal to a more bacteria-dominated community. Rhizosphere beta-xylosidase, N-acetyl-beta-glucosaminidase, and sulfatase activity peaked in the mature grassland soil, whereas rhizosphere leucine aminopeptidase, beta-glucosidase, and phosphatase activity were highest in the transition stage, probably because of enhanced carbon and nutrient allocation into the rhizosphere due to better growth conditions. Soil organic matter appeared to be the most important driver of microbial colonization in the bulk soil. The decrease in soil pH and soil C/N ratio mediated the shifts in the soil microbial community composition (bacPLFA, bacPLFA/fungPLFA, G(-), G(+)/G(-)). The activities of beta-glucosidase, beta-xylosidase and phosphatase were related to soil ammonium and phosphorus, indicating that higher decomposition rates enhanced the nutrient availability in the bulk soil. We conclude that the major determinants of the microllora vary along the successional gradient: in the pioneer stage the rhizosphere microflora was primarily determined by the harsh soil environment; under more favourable environmental conditions, however, the host plant selected for a specific microbial community that was related to the dynamic interplay between soil properties and carbon supply. (C) 2004 Elsevier Ltd. All rights reserved.

Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence

This study quantifies the influence of Poa alpina on the soil microbial community in primary succession of alpine ecosystems, and whether these effects are controlled by the successional stage. Four successional sites representative of four stages of grassland development (initial, 4 years (non-vegetated); pioneer, 20 years; transition, 75 years; mature, 9500 years old) on the Rotmoos glacier foreland, Austria, were sampled. The size, composition and activity of the microbial community in the rhizosphere and bulk soil were characterized using the chloroform-fumigation extraction procedure, phospholipid fatty acid (PLFA) analysis and measurements of the enzymes beta-glucosidase, beta-xylosidase, N-acetyl-beta-glucosaminidase, leucine aminopeptidase, acid phosphatase and sulfatase. The interplay between the host plant and the successional stage was quantified using principal component (PCA) and multidimensional scaling analyses. Correlation analyses were applied to evaluate the relationship between soil factors (C-org, N-t, C/N ratio, pH, ammonium, phosphorus, potassium) and microbial properties in the bulk soil. In the pioneer stage microbial colonization of the rhizosphere of P. alpina was dependent on the reservoir of microbial species in the bulk soil. As a consequence, the rhizosphere and bulk soil were similar in microbial biomass (ninhydrin-reactive nitrogen (NHR-N)), community composition (PLFA), and enzyme activity. In the transition and mature grassland stage, more benign soil conditions stimulated microbial growth (NHR-N, total amount of PLFA, bacterial PLFA, Gram-positive bacteria, Gram-negative bacteria), and microbial diversity (Shannon index H) in the rhizosphere either directly or indirectly through enhanced carbon allocation. In the same period, the rhizosphere microflora shifted from a G(-) to a more G(+), and from a fungal to a more bacteria-dominated community. Rhizosphere beta-xylosidase, N-acetyl-beta-glucosaminidase, and sulfatase activity peaked in the mature grassland soil, whereas rhizosphere leucine aminopeptidase, beta-glucosidase, and phosphatase activity were highest in the transition stage, probably because of enhanced carbon and nutrient allocation into the rhizosphere due to better growth conditions. Soil organic matter appeared to be the most important driver of microbial colonization in the bulk soil. The decrease in soil pH and soil C/N ratio mediated the shifts in the soil microbial community composition (bacPLFA, bacPLFA/fungPLFA, G(-), G(+)/G(-)). The activities of beta-glucosidase, beta-xylosidase and phosphatase were related to soil ammonium and phosphorus, indicating that higher decomposition rates enhanced the nutrient availability in the bulk soil. We conclude that the major determinants of the microllora vary along the successional gradient: in the pioneer stage the rhizosphere microflora was primarily determined by the harsh soil environment; under more favourable environmental conditions, however, the host plant selected for a specific microbial community that was related to the dynamic interplay between soil properties and carbon supply. (C) 2004 Elsevier Ltd. All rights reserved.

The effect of calcium removal from milk on casein micelle stability and structure

The total calcium level of raw skimmed milk was reduced by 10, 19, 29, 40 and 51% using Duolite® ion-exchange resin. The products were examined for concentrations of ionic calcium, sodium and potassium and the pH, ethanol stability, micelle diameter and ζ-potential were also measured. Ionic calcium decreased with removal of calcium and pH increased. Calcium removal resulted in an increase in the ethanol stability from 88% to above 100%. Casein micelle diameter increased as calcium was removed. The ζ-potential of the skimmed bulk milk was -24.4 mV, gradually becoming more negative with calcium removal to -30.6 mV after 51% calcium removal. The milk became more translucent as calcium was removed. To investigate the reversibility of this process, calcium chloride was added back to the depleted samples to restore their original total calcium content. At 51% removal, restoration of the total calcium level resulted in formation of clots. At levels of 10 and 19% calcium removal, the ethanol stability remained above 100%, but at higher levels of calcium removal the alcohol stability was adversely affected when the calcium was added back. Adding back calcium resulted in partial restoration of the original casein micelle diameter.

Supplementation with fruit and vegetable soups and beverages increases plasma carotenoid concentrations but does not alter markers of oxidative stress or cardiovascular risk factors

This study was aimed at determining whether an increase of 5 portions of fruits and vegetables in the form of soups and beverages has a beneficial effect on markers of oxidative stress and cardiovascular disease risk factors. The study was a single blind, randomized, controlled, crossover dietary intervention study. After a 2-wk run-in period with fish oil supplementation, which continued throughout the dietary intervention to increase oxidative stress, the volunteers consumed carotenoid-rich or control vegetable soups and beverages for 4 wk. After a 10-wk wash-out period, the volunteers repeated the above protocol, consuming the other intervention foods. Both test and control interventions significantly increased the % energy from carbohydrates and decreased dietary protein and vitamin B-12 intakes. Compared with the control treatment, consumption of the carotenoid-rich soups and beverages increased dietary carotenoids, vitamin C, alpha-tocopherol, potassium, and folate, and the plasma concentrations of alpha-carotene (362%), beta-carotene (250%) and lycopene (31%) (P < 0.01) and decreased the plasma homocysteine concentration by 8.8% (P < 0.01). The reduction in plasma homocysteine correlated weakly with the increase in dietary folate during the test intervention (r = -0.35, P = 0.04). The plasma antioxidant status and markers of oxidative stress were not affected by treatment. Consumption of fruit and vegetable soups and beverages makes a useful contribution to meeting dietary recommendations for fruit and vegetable consumption.

Fertilisers and insect herbivores: a meta-analysis

Despite the importance of a thorough understanding of the effect of synthetic fertiliser on insect population dynamics, existing literature is conflicting and an area of intense debate. Here, a categorical random-effects meta-analysis and a vote count meta-analysis are employed to examine the effects of nitrogen(N), phosphorus (P), potassium (K) and NPK fertiliser on insect population dynamics. In agreement with the general consensus, insects were found to respond positively, overall, to fertilisers. Sucking insects showed a much stronger response to fertilisers than chewing insects. The environment in which a study is conducted can have a marked effect on insect responses to fertiliser, with natural environments showing the potential for buffering effects of nitrogen fertilisers in particular. As well as highlighting the potential shortfall in the amount of research investigating particularly the effects of potassium and phosphorus, this study provides an invaluable flag post in the ongoing research investigating fertiliser effects on ecosystems.

Effects of phytate and minerals on the bioavailability of oxalate from food

Phytate and mineral cations are both considered as important dietary factors for inhibiting the crystallisation of calcium oxalate kidney stones in susceptible individuals. In this paper, the phytate and mineral composition of whole bran cereals (wheat, barley and oat) and legumes were determined together with their soluble and insoluble oxalate concentrations in order to investigate the effects on oxalate solubility. The oat bran sample had the highest soluble oxalate concentration at 79 ± 1.3 mg/100 g, while total and soluble oxalate concentrations in the food samples studied range from 33 to 199 mg/100 g and 14 to 79 mg/100 g, respectively. The phytate concentration was in the range from 227 to 4393 mg/100 g and the concentrations of cations were in the range 54–70 mg/100 g for calcium, 75–398 mg/100 g for magnesium, 244–1529 mg/100 g for potassium and 4–11 mg/100 g for iron. Soluble oxalate concentration did not increase in proportion to total oxalate, and the phytate concentration in all foods was sufficient to contribute to an increase in soluble oxalate concentration by binding calcium.

The late Roman field army in Northern Britain? Mobility, material culture and multi-isotope analysis at Scorton (N. Yorks)

At Hollow Banks Quarry, Scorton, located just north of Catterick (N Yorks.), a highly unusual group of 15 late Roman burials was excavated between 1998 and 2000. The small cemetery consists of almost exclusively male burials, dated to the fourth century. An unusually large proportion of these individuals was buried with crossbow brooches and belt fittings, suggesting that they may have been serving in the late Roman army or administration and may have come to Scorton from the Continent. Multi-isotope analyses (carbon, nitrogen, oxygen and strontium) of nine sufficiently well-preserved individuals indicate that seven males, all equipped with crossbow brooches and/or belt fittings, were not local to the Catterick area and that at least six of them probably came from the European mainland. Dietary (carbon and nitrogen isotope) analysis only of a tenth individual also suggests a non-local origin. At Scorton it appears that the presence of crossbow brooches and belts in the grave was more important for suggesting non-British origins than whether or not they were worn. This paper argues that cultural and social factors played a crucial part in the creation of funerary identities and highlights the need for both multi-proxy analyses and the careful contextual study of artefacts.

The effect of nutrient fortification of sauces on product stability, sensory properties and subsequent liking by older adults

There are potential nutritional and sensory benefits of adding sauces to hospital meals. The aim of this study was to develop nutrient fortified sauces with acceptable sensory properties suitable for older people at risk of under-nutrition. Tomato, gravy and white sauce were fortified with macro and micro-nutrients using food ingredients rich in energy and protein as well as vitamin and mineral premixes. Sensory profile was assessed by a trained panel. Hedonic liking of fortified compared with standard sauces was evaluated by healthy older volunteers. The fortified sauces had higher nutritional value than the conventional ones, for example the energy content of the fortified tomato, white sauce and gravy formulations were increased between 2.5 and 4 fold compared to their control formulations. Healthy older consumers preferred the fortified tomato sauce compared with unfortified. There were no significant differences in liking between the fortified and standard option for gravy. There were limitations in the extent of fortification with protein, potassium and magnesium, as excessive inclusion resulted in bitterness, undesired flavours or textural issues. This was particularly marked in the white sauce to the extent that their sensory characteristics were not sufficiently optimised for hedonic testing. It is proposed that the development of fortified sauces is a simple approach to improving energy intake for hospitalised older people, both through the nutrient composition of the sauce itself and due to the benefits of increasing sensorial taste and lubrication in the mouth.

Effect of minerals on casein micelle stability of cows' milk

The effects of minerals on casein micelle stability of individual cows' milk, throughout a complete lactation, were investigated. Calcium and calcium ions, magnesium, phosphorus, sodium, potassium and citrate contents were analysed, together with the following physical properties of milk; pH, ethanol stability, rennet clotting time and coagulum firmness. There was an inverse non-linear relationship between free calcium ion concentration and ethanol stability (ES; r=0.84). Rennet coagulation time showed a weaker relationship with free calcium ion concentration (r=0.44) but a stronger relationship with pH (r=0.66). In addition, samples containing higher amounts of free calcium ions produced a firmer gel. Citrate in natural samples acts as a stabilizing factor, as it slightly improves milk stability. Potassium, on the other hand, exhibited a negative correlation, but only with rennet clotting time (r=-0.52). Throughout lactation the average values were; free Ca 21 concentration 1.88 mm,, pH 6.63, ES 83.2% and clotting time 13.6 min. The equilibrium relationship between pH and free Ca2+ concentration was investigated by adjusting milk pH from 5.9 to 7.1, using acid and alkali. There was a good inverse linear relationship between pH and log (free Ca 21) for individual milk samples, with a gradient of -0.62 and a standard deviation of 0.042.

Cosmopolitan Catterick? Isotopic evidence for population mobility on Rome’s Northern frontier

In order to investigate how the population diversity at major Romano-British urban centres compared to small towns and military outposts, we conducted multi-isotope (carbon, nitrogen, oxygen and strontium) analyses of bones (42 individuals) and teeth (26 individuals) of human skeletons from Cataractonium/ Roman Catterick in North Yorkshire (U.K.). The results suggest a markedly less diverse population at Catterick than at the larger towns. Significant differences are observed between burials from the town and fort area and the suburb of Bainesse to the south, and it is suggested that these reflect a shift to more localised recruitment for the Roman army in the Late Roman period. Isotope data for the ‘Bainesse Eunuch’, an unusual 4th century burial that has been interpreted as the remains of a ‘transvestite’ priest of Cybele, are not ultimately conclusive but consistent with origins in Southern Britain or areas with a similar climate abroad. This paper also presents strontium isotope data for modern vegetation samples from 17 sites in the Catterick/northern Vale of York area which contribute to a continuing effort to map the biosphere 87Sr/86Sr variation in Britain.

How do plants respond to nutrient shortage by biomass allocation?

Plants constantly sense the changes in their environment; when mineral elements are scarce, they often allocate a greater proportion of their biomass to the root system. This acclimatory response is a consequence of metabolic changes in the shoot and an adjustment of carbohydrate transport to the root. It has long been known that deficiencies of essential macronutrients (nitrogen, phosphorus, potassium and magnesium) result in an accumulation of carbohydrates in leaves and roots, and modify the shoot-to-root biomass ratio. Here, we present an update on the effects of mineral deficiencies on the expression of genes involved in primary metabolism in the shoot, the evidence for increased carbohydrate concentrations and altered biomass allocation between shoot and root, and the consequences of these changes on the growth and morphology of the plant root system.