bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil fertility changes in a red-brown earth under irrigated pastures. III Water relations of the mat and surface soil
Authors: Rixon AJ , Bridge BJ
Published: November 2004

The water relations of the surface mat of organic matter and the underlying 2.5 cm of soil from three annual and three perennial pastures of the same age were examined before and after mixing by cultivation. In either circumstance, the water relations of the 0–2.5 cm soil horizon did not differ significantly between the various pastures. The mats retained a considerable amount of water over a wide range of matric potentials. The organic carbon contents and amounts of water retained in the mats at –1520 J/kg matric potential were linearly related; at –9.8 J/kg and at –0.098 J/kg matric potentials they were linearly related, but the regression coefficients for mats from annual pastures were significantly greater than for mats from perennial pastures. Incorporation of the mat into the soil slightly increased the total porosity of the 0–2.5 cm soil horizon and changed the pore size distribution towards larger pores. Available water capacity (AWC) was defined as the depth of water held between the limits –0.098 and –1520 J/kg matric potentials. The AWC of the 0–7.6 cm soil horizon plus overlying pasture mat was less than that of the equivalent depth of cultivated soil with incorporated mat for all pastures. With the more conventional limits of AWC between –9.8 and –1520 J/kg matric potential, more water was available in the 0-7.6 cm soil plus mat than in the equivalent depth of cultivated soil, except in the case of an annual grass pasture.
Failure of sperm transport in relation to ewe infertility following prolonged grazing on oestrogenic pastures
Authors: Lightfoot RJ , Croker KP , Neil HG
Published: November 2004

Sixteen ewes were drawn from each of two ewe flocks, one of which had grazed on oestrogenic pastures for annual periods over the previous 5 years ("clover" treatment) while the other grazed on green oats ("oats" treatment). Fertility of ewes on the clover treatment had decreased progressively, whereas in those on the oats treatment it had remained high. Oestrous ewes were allocated alternately to receive either two or eight services then killed 24 hr post coitus and the numbers of sperm in the cervix, uterus, and fallopian tubes determined. There was no difference in ovarian activity between the two groups; however, highly significant differences were found in the numbers of sperm recovered from the cervix, uterus, and fallopian tubes. Average sperm numbers per fallopian tube were 17,160 and 350 for ewes on the oats and clover treatments respectively. In addition to the reduction in sperm numbers, both the percentage of motile sperm flushed from the cervix and the proportion of recovered ova with sperm attached to the zona pellucida were lower in ewes on the clover treatment. The results suggest that primary failure of sperm transport in ewes on the clover treatment occurred when sperm did not enter the cervix in adequate numbers following service. The significance of these observations in relation to possible causal mechanisms is discussed.
Developmental growth and body weight loss of cattle. I. Experimental design, body weight growth, and the effects of developmental growth and body weight loss on the dressed carcass and the offal
Authors: Seebeck RM
Published: November 2004

At the age of approximately 11 months, 19 Angus steers were allotted to two experimental groups, namely, 10 to group A and 9 to group B. Group A animals were grown in pens and fed ad libitum. They were killed, two at each of the following of body weights: 250, 281, 316, 356, 400 kg. Group B animals were grown under similar conditions and killed at the same body weights as corresponding animals in group A; however, they were grown to weights 15% above their killing weights (growing-on phase) and then made to lose weight at 0.5 kg per day by restricting food intake until they reached their planned killing weights (weight loss phase). Huxley's (1932) allometric equation was used in logarithmic form as the basis for covariance analyses of the data. Empty body weight (EBW) increased as a proportion of full body weight as full body weight increased. EBW was higher in group A animals than in group B animals at the same full body weight, reflecting differences in weight of contents of the digestive tract. Dressed carcass weight increased as a proportion of EBW as EBW increased. Dressed carcass weight was higher in group B animals than in group A animals at the same EBW, indicating that the increase in carcass weight that occurred during the growing-on phase was not completely lost during the weight loss phase. During developmental growth, the weights of hide, feet, head, liver, gall bladder, heart, lungs, kidneys, and gut tissue decreased as proportions of EBW. The weight of abdominal fat increased as a proportion of EBW, while the weights of tail, spleen, and blood did not change significantly as proportions of EBW. During body weight loss, the weights of the feet, head, and tail remained close to the weights they had reached at the end of the growing-on phase, although, with the head, this varied considerably with the size of the animal before undergoing body weight loss. All other components lost weight during the weight loss phase. The hide, heart, lungs, and abdominal fat all reversed, approximately, the pattern of development that occurred during body weight growth. The liver, gall bladder, kidneys, gut tissue, spleen, blood, and thymus gland all lost more weight during the weight loss phase than they put on during the growing-on phase. With the liver, kidneys, and gut tissue, the proportion of weight lost varied according to the size of the animal before undergoing body weight loss.
The digestion of pasture plants by sheep. I. Ruminal production of volatile fatty acids by sheep offered diets of ryegrass and forage oats
Authors: Weston RH , Hogan JP
Published: November 2004

The production of volatile fatty acids (VFA) in the rumen of sheep was estimated by isotope dilution techniques. The 12 diets used consisted of dried ryegrass and forage oats and covered a wide range of levels of cell wall constituents (46–40% of the organic matter), crude protein (6–32%), and soluble carbohydrate (5–18%). Each diet was offered at a level equal to approximately 90% of the sheep's ad libitum intake. The production of VFA was correlated with the total amount of organic matter digested in the alimentary tract (r = 0.93–0.95). The mean VFA production per 100 g of organic matter digested in the alimentary tract was equivalent to 56.8 g, 243 kcal, or 0.85 mole. Values for individual diets varied about these means with a coefficient of variation of 6–7%. Rates of VFA production in, and VFA absorption from the rumen were correlated with VFA concentration in rumen liquor (r = 0.67, r = 0.67) and the rumen VFA pool (r = 0.81, r = 0.79). Approximately 76% of the VFA produced in the rumen was absorbed from the rumen, 19% was absorbed from the omasum and abomasum, and 5% passed from the abomasum to the intestines.
The effect of urea on the absorption of volatile fatty acids from the rumen of sheep fed on oat straw
Authors: Faichney GJ
Published: November 2004

The effect of a urea supplement on the utilization of a diet of poor quality oat straw plus minerals, fed to sheep, was investigated. The supplement of urea was responsible for a highly significant (P < 0.01) increase in dry matter and energy intake and a highly significant ( P < 0.01) decrease in body weight loss. There was a significant (P < 0.05) increase in nitrogen balance and in the rate of passage of food residues through the alimentary tract. A tendency for the digestibility of dry matter, energy, crude fibre, and cellulose to be higher when the urea supplement was given was not significant. There was a significant (P < 0.05) increase in the VFA absorbed from the rumen reflecting the increase in intake, but there were no differences between diets in the contributions of acetic, propionic, and butyric acids to VFA absorption. The mean values obtained for the proportion of the digested energy accounted for by the VFA on the straw plus urea diet and the straw diet (with the standard error of the mean) were 31.4 (± 2.5)% and 38.1 (± 5.6)% respectively.
Symbiotic characteristics of subspecies of Trifolium subterraneum L.
Authors: Gibson AH , Brockwell J
Published: November 2004

An examination was made of the ability of lines of Trifolium subterraneum L. subsp. subterraneum, subsp. yanninicum Katzn. et Morley, and subsp. brachycalycinum Katzn. et Morley to nodulate and fix nitrogen with strains of .Rlzizobium trifolii isolated from habitats dominated by each of the subspecies.Host line x bacterial strain specificity was demonstrated at two levels: (a) some strains nodulated one, or two, host lines ineffectively, yet formed an effective symbiosis with the other host lines; (b) among the symbiotic combinations classed as effective, the degree of effectiveness of the strains was dependent on the host lines. It was found that the lines of a subspecies were not more effectively nodulated by the bacterial strains isolated from a habitat in which that subspecies was the predominant subterranean clover, than they were by strains isolated from habitats in which the other subspecies predominated. For example, lines of T. subterraneum subsp. yanninicum fixed nitrogen as well with strains of R. trifolii isolated from habitats of subsp. subterraneum or subsp. brachycalycinum as they did with strains isolated from its own habitat. Similarly, there was little evidence that the strains from the habitat in which a subspecies predominated were more effective in their symbiosis with the lines of that subspecies than they were with the lines of the other subspecies. The only exception to this latter generalization was that the strains isolated from the subsp. brachycalycinum habitat were slightly more effective with subsp. brachycalycinum than with subspp. yanninicum or subterraneum. Groupings of the strains based on their response with the lines of any subspecies, or with the lines of all subspecies combined, bore no relation to groupings based on the origin of the strains. It was concluded that it was not possible to predict the effectiveness of any symbiotic combination from a consideration of the taxonomy of the host or the habitat from which the bacterium was isolated. The feasibility of using a standard host line for the screening of the general effectiveness of all strains of potential value in subterranean clover inoculants is discussed. The commercial inoculant strain, TA1, was not the most effective strain with all lines, and overall, ranked fifth among the strains examined.
Corrigendum - Studies on presowing drought hardening of wheat
Authors: Woodruff DR
Published: November 2004

The effects of presowing drought hardening of wheat on subsequent leaf relative water content (RWC) and grain yield were assessed under a number of environmental conditions. In general, the treatment reduced the rate at which critical levels of RWC developed during periods of moisture stress, but not necessarily the final value to which the RWC fell. No differences were found in any of the measured parameters during periods when there were no internal water deficits. Grain yield increases due to the hardening treatment varied "from 0 to 20%" in the different experiments. This variation is explained in terms of both the phenological stage at which RWC differences occurred and the transient effect of the RWC differences. The results are also discussed in relation to both the cause of the observed RWC differences and the potential practical role of the technique in arid zone agriculture.
The transfer of nitrogen from the blood to the rumen in cattle
Authors: Vercoe JE
Published: November 2004

A Brahman x Hereford and a Hereford steer fed on a chaffed tropical pasture hay were infused intravenously and intraruminally with urea at 9–45 g N/day. By comparing the respective increases in rumen ammonia concentration which occurred when urea was infused intravenously and intraruminally, it was possible to estimate the net flow of urea into the rumen resulting from the intravenous administration. In both steers there was a limit to the net amount of urea passing from the blood to the rumen of c. 17–20 g N/day, which was reached at plasma urea concentrations of c. 12 mg N/100 ml. This concentration of plasma urea was achieved in the Brahman x Hereford steer when c. 23 g N/day was infused intravenously but in the Hereford when 32–35 g N/day was infused.
The influence of body weight (fatness) on the energic efficiency of adult sheep
Authors: McC Graham N
Published: November 2004

Energy, carbon, and nitrogen balances were determined in adult wether sheep given a diet of lucerne hay and whole oats at several planes of nutrition between fasting and ad libitum. Four sheep were studied when their weight was c. 30 kg (10% fat) and later when they weighed c. 75 kg (33% fat); another four were studied at c. 70 kg (30% fat) and later at c. 45 kg (16% fat). The most obvious effect of fatness was loss of appetite. Voluntary food intake began to decline when body weight approached 60 kg and was half of the maximal amount when the sheep weighed 70 kg or more; one very fat sheep ate only 100–200 g food/day for several weeks. 1n addition, environmental changes such as transfer from a pen to a cage or respiration chamber often caused temporary inappetence when the sheep were in fat condition but seldom when they were lean. Fasting metabolic rate increased with body weight in accordance with the relationship generally applicable to adult sheep except when the sheep were in the anorectic phase of obesity, at which time their metabolic rate was 30–40% above normal. The digestibility of the diet was not dependent on the fatness of the sheep, nor was the relationship between metabolizable and digestible energy. At each level of feeding, the heaviest sheep produced most heat, but differences were less than at fasting; oxidation of fat, rather than protein, was responsible. When daily heat production and metabolizable energy were both expressed as multiples of the fasting energy loss, all sheep conformed to one relationship; the same held for the relation between energy balance and metabolizable energy. Net efficiency (change of energy balance divided by change of metabolizable energy intake) was 78% for maintenance and 55% for production, irrespective of body condition. Gross efficiency (energy storage divided by gross energy intake) was strongly influenced by body condition. When fed ad libitum, thin sheep achieved an efficiency of c. 26 % and fat sheep reached 21 % whereas anorectic very fat sheep never exceeded 10%. Thin, fat, and very fat sheep required 400, 500 and 650 g dry matter/day respectively for maintenance (zero gross efficiency).
The effect of phosphorus on the growth and chemical composition of some tropical pasture legumes. I. Growth and critical percentages of phosphorus
Authors: Andrew CS , Robins MF
Published: November 2004

Nine tropical and one temperate pasture legume species were grown in pots of soil with varying additions of phosphate. Growth responses and chemical conlposition of the plant tops were recorded, and from the latter, critical percentages of phosphorus were established. These were verified by using data from two soils in the pot culture investigation and a total of six field sites. Glycine javanica and Desmodium intortum were the most responsive species in pots, and Stylosanthes humilis and Lotononis bainesii were the least responsive species. The quantity of phosphorus per pot accumulated in the tops of the plants was greatest for Stylosanthes humilis and Lotononis bainesii at all treatment levels. Critical percentages of phosphorus in the tops of Phaseolus Iathyroides, Phaseolus atropurpureus, Stylosanthes humilis, Centrosema pubescens, Glycine javanica, Lotononis bainesii, Medicago sativa, Desmodium uncinatum, Desmodium intortum, and Vigna luteola sampled at the immediate pre-flowering stage of growth were 0.20, 0.24, 0.17, 0.16, 0.23, 0.17, 0.24, 0.23, 0.22, and 0.25% phosphorus respectively.
Studies of zinc nutrition in sheep. I. The relation of zinc to growth, testicular development, and spermatogenesis in young rams
Authors: Underwood EJ , Somers M
Published: November 2004

Ram lambs fed on a diet containing 2.4 p.p.m. zinc made poor growth, developed clinical signs of severe zinc deficiency, showed impaired testicular growth, and showed a complete cessation of spermatogenesis within a period of 20–24 weeks. Lambs fed on the same diet supplemented with zinc sulphate to provide total zinc levels of 17.4 and 32.4 p.p.m. had a higher feed intake, made significantly greater liveweight gains, and showed no signs of zinc deficiency. Testicular growth and sperm production were markedly improved by both the zinc supplements. No differences in liveweight gains or feed consumption between the two supplemented groups were observed but testicular growth and sperm production were highly significantly greater in the lambs receiving the larger zinc supplement. It was concluded that a dietary zinc intake of 17.4 p.p.m. is adequate for growth of ram lambs but is inadequate for normal testicular development and function. Lambs in which consumption of the diet containing 32.4 p.p.m. zinc was restricted to that of the zinc-deficient group showed no significant improvement in liveweight gains, but testicular development and sperm production were significantly greater than in the zinc-deficient lambs. Complete remission of all signs of zinc deficiency and full recovery of testicular size, structure, and function were achieved in a zinc repletion period lasting 20 weeks.
Potential for biological denitrification of fertilizer nitrogen in sugarcane soils
Authors: Weier KL , McEwan CW , Vallis I , Catchpoole VR , Myers RJ
Published: November 2004

Nitrogen (N) fertilizer is being lost from sugarcane soils following application to the crop. This study was conducted to estimate the quantity of N being lost from the soil through biological denitrification and to determine the proportion of gaseous N being emitted either as N2O or as N2. Field studies were conducted on four different soils (humic gley, alluvial massive earth, red earth and gleyed podzolic), and on different crop management systems, by installing plastic (PVC) cylinders (23.5 cm diam., 25 cm long) in the soil to a depth of 20 cm beside the plant row in a ratoon sugarcane crop. 15N-labelled KNO3 was applied as a band across each cylinder to a depth of 2.5 cm at a rate of 160 kg N/ha. After rainfall or irrigation, the cylinders were capped for 3 h intervals and gas in the headspace sampled in the morning and afternoon, for up to 4 days. Denitrification losses from the humic gley ranged from 247 g N/ha.day for cultivated plots to 1673 g N/ha.day for no-till plots. Over the sampling period, this was equivalent to 3.2% and 19.7% of the N applied, respectively. Nitrous oxide accounted for 46% to 78% of the total N lost. For the alluvial, massive earth and the red earth and gleyed podzolic, losses over the sampling period ranged from 25 to 117 g N/h.day and represented <1% of the N applied. Recovery of 15N in the soil ranged from 67% at the first sampling on the red earth soil to 4.9% at the third sampling on the alluvial, massive earth soil. In a glasshouse study, intact soil cores (23.5 cm diam., 20 cm long), taken from the humic gley and the alluvial, massive earth, were waterlogged after band application of 15N-labelled KNO3 at a rate of 160 kg N/ha. Gas samples from the headspace were taken after 3 h, and then morning and afternoon for the next 14 days. Denitrification losses ranged from 13.2 to 38.6% of N applied with the majority of gaseous N loss occurring as N2. Total recoveries after 14 days, including the evolved gases, ranged from 68.7 to 88.2%. We conclude that denitrification is a major cause of fertilizer N loss from fine-textured soils, with nitrous oxide the major gaseous N product when soil nitrate concentrations are high.
Nitrogen metabolism by ruminal microorganisms: current understanding and future perspectives
Authors: Morrison M , Mackie RI
Published: November 2004

This review presents an outline of our current understanding of ruminal nitrogen metabolism from three perspectives: proteolytic microorganisms and their enzymes, intraruminal recycling of microbial protein, and enzymes of ammonia assimilation. Some of the pending advances and future research opportunities in these areas are also discussed. The 'smugglin' concept appears to offer the potential to inhibit peptide-utilizing bacteria selectively in the rumen, as demonstrated by initial studies with Prevotella ruminicola. The relative contributions of protozoa-, bacteriophage-, and self-mediated lysis of bacteria to intraruminal recycling of microbial protein are not yet quantified, and further efforts to understand the biology and dynamics of ruminal bacteriophage and protozoa populations are warranted. In Ruminococcus flavefaciens and Prevotella ruminicola, glutamate dehydrogenase (GDH) appears to be the predominant route of ammonia assimilation irrespective of ammonia concentration, and peptides modulate GDH activity in P. ruminicola. The physiological basis behind the difference between optimal ammonia concentrations for ruminal fibre digestion and microbial protein synthesis remains unclear. Molecular biology techniques extend beyond their application in pursuit of the 'superbug' concept, by offering new and exciting opportunities to understand better microbial physiology, diversity, and ecology. Fundamental research in these areas must be continued if further advances in feed utilization and nutrient retention are to be realized.
Options for manipulating nutrition if feed supply is immutable
Authors: Hogan JP
Published: November 2004

The Australian pastoral industries depend almost entirely on the nutrients derived from the available pasture and browse. This is particularly true for the northern cattle industry, where the production of pasture, and hence animal productivity, depend on the length of time that sufficient soil moisture is available during and after the wet season to sustain pasture growth. Animal nutrition is further affected by the relatively low digestibility of tropical grasses even at early stages of maturity. Hence animal production is marked by relatively low annual weight gain and poor reproductive performance. Research to date has demonstrated that lack of nitrogen both as ammonia for rumen microbes and as amino acids for the animal's tissues is the major nutritional deficit, which causes a depression in feed intake and hence exacerbates an already existing energy deficit. In many areas, too, deficiencies of P, Na, S and trace elements have been identified. Broadly speaking, the technology has been developed to overcome these nutritional deficiencies and to investigate remaining problems of undernutrition and low productivity. It is probable that new tropical legumes suited for areas with less than 750 mm annual rainfall will also be developed. However, despite these efforts, animal production will tend to be low, because for much of the year the high fibre low protein forage is eaten in only restricted amounts, and because only 40% or so of the energy in the forage becomes available to the animal. There is, therefore, need to develop rumen microbes capable of more rapid and more extensive breakdown of plant fibre and to achieve new methods to improve the conversion of amino acids into animal protein.
Resistance to barley scald (Rhynchosporium secalis) in wild barley grass (Hordeum glaucum and Hordeum leporinum) populations in south-eastern Australia
Authors: Jarosz AM , Burdon JJ
Published: November 2004

Plants from 22 wild barley grass populations, 10 Hordeum glaucum, 11 Hordeum leporinum, and one mixed population, were inoculated with seven isolates of Rhynchosporium secalis originally collected from H. leporinum plants. There was substantial variability for resistance within and among populations from both Hordeurn species, but H. glaucum was: on average more resistant than H. leporlnum. Individual populations often responded differentially to the R. secalis isolates, being resistant to some isolates and susceptible to others. Differential responses were more pronounced among H. glaucum populations. No consistent geographic correlations between level of resistance within a population and geographic location were found, indicating that large scale trends for resistance do not exist in either H. gluucum or H. leporinwm. The existence of widespread resistance variation in both wild barley grasses may create substantial selection pressures favouring the emergence of variability for pathogenicity in R. secalis, which would complicate efforts to breed for R. secalis resistance in cultivated barley.
Gestational exposure of
Ahr
and
Arnt
hypomorphs to dioxin rescues vascular development
Authors: Walisser Jacqueline A. , Bunger Maureen K. , Glover Edward , Bradfield Christopher A.
Published: November 2004

The aryl hydrocarbon receptor (AHR) is commonly known for its role in the adaptive metabolism of xenobiotics and in the toxic events that follow exposure to 2,3,7,8-tetrachlorodibenzo-
p
-dioxin (dioxin). Previously, we have demonstrated that the AHR and its heterodimeric partner, the AHR nuclear translocator (ARNT), play a role in the developmental closure of a hepatic vascular shunt known as the ductus venosus (DV). To investigate the mechanism of DV closure, we generated hypomorphic alleles of the
Ahr
and
Arnt
loci. Using these models, we then asked whether this vascular defect could be rescued by receptor activation during late development. By manipulating gestational exposure, the patent DV in AHR or ARNT hypomorphs could be efficiently closed by dioxin exposure as early as embryonic day 12.5 and as late as embryonic day 18.5. These findings define the temporal regulation of receptor activation during normal ontogeny and provide evidence to support the idea that receptor activation and AHR–ARNT heterodimerization are essential for normal vascular development. Taken in the broader context, these data demonstrate that similar AHR signaling steps govern all major aspects of AHR biology.
Medicinal chemistry applied to a synthetic protein: Development of highly potent HIV entry inhibitors
Authors: Hartley Oliver , Gaertner Hubert , Wilken Jill , Thompson Darren , Fish Richard , Ramos Alejandra , Pastore Cristina , Dufour Brigitte , Cerini Fabrice , Melotti Astrid , Heveker Nikolaus , Picard Laurent , Alizon Marc , Mosier Donald , Kent Stephen , Offord Robin
Published: November 2004

We have used total chemical synthesis to perform high-resolution dissection of the pharmacophore of a potent anti-HIV protein, the aminooxypentane oxime of [glyoxylyl
1
]RANTES(2-68), known as AOP–RANTES, of which we designed and made 37 analogs. All involved incorporation of one or more rationally chosen nonnatural noncoded structures, for which we found a clear comparative advantage over coded ones. We investigated structure–activity relationships in the pharmacophore by screening the analogs for their ability to block the HIV entry process and produced a derivative, PSC-RANTES {
N
-nonanoyl, des-Ser
1
[
l
-thioproline
2
,
l
-cyclohexylglycine
3
]-RANTES(2–68)}, which is 50 times more potent than AOP–RANTES. This promising group of compounds might be optimized yet further as potential prophylactic and therapeutic anti-HIV agents. The remarkable potency of our RANTES analogs probably involves the unusual mechanism of intracellular sequestration of CC-chemokine receptor 5 (CCR5), and it has been suggested that this arises from enhanced affinity for the receptor. We found that inhibitory potency and capacity to induce CCR5 down-modulation do appear to be correlated, but that unexpectedly, inhibitory potency and affinity for CCR5 do not. We believe this study represents the proof of principle for the use of a medicinal chemistry approach, above all one showing the advantage of noncoded structures, to the optimization of the pharmacological properties of a protein. Medicinal chemistry of small molecules is the foundation of modern pharmaceutical practice, and we believe we have shown that techniques have now reached the point at which the approach could also be applied to the many macromolecular drugs now in common use.
Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription
Authors: Alter Orly , Golub Gene H.
Published: November 2004

We describe an integrative data-driven mathematical framework that formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the “basis” set. By using pseudoinverse projection, the molecular biological profiles of the data samples are least-squares-approximated as superpositions of the basis profiles. Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis and gives a global picture of the correlations and possibly also causal coordination of these two sets of states. We illustrate this framework with an integration of yeast genome-scale proteins' DNA-binding data with cell cycle mRNA expression time course data. Novel correlation between DNA replication initiation and RNA transcription during the yeast cell cycle, which might be due to a previously unknown mechanism of regulation, is predicted.
Structure and function of the phenazine biosynthetic protein PhzF from
Pseudomonas fluorescens
Authors: Blankenfeldt Wulf , Kuzin Alexandre P. , Skarina Tatiana , Korniyenko Yuriy , Tong Liang , Bayer Peter , Janning Petra , Thomashow Linda S. , Mavrodi Dmitri V.
Published: November 2004

Phenazines produced by
Pseudomonas
and
Streptomyces
spp. are heterocyclic nitrogen-containing metabolites with antibiotic, antitumor, and antiparasitic activity. The antibiotic properties of pyocyanin, produced by
Pseudomonas aeruginosa
, were recognized in the 1890s, although this blue phenazine is now known to be a virulence factor in human disease. Despite their biological significance, the biosynthesis of phenazines is not fully understood. Here we present structural and functional studies of PhzF, an enzyme essential for phenazine synthesis in
Pseudomonas
spp. PhzF shares topology with diaminopimelate epimerase DapF but lacks the same catalytic residues. The structure of PhzF in complex with its substrate,
trans
-2,3-dihydro-3-hydroxyanthranilic acid, suggests that it is an isomerase using the conserved glutamate E45 to abstract a proton from C3 of the substrate. The proton is returned to C1 of the substrate after rearrangement of the double-bond system, yielding an enol that converts to the corresponding ketone. PhzF is a dimer that may be bifunctional, providing a shielded cavity for ketone dimerization via double Schiff-base formation to produce the phenazine scaffold. Our proposed mechanism is supported by mass and NMR spectroscopy. The results are discussed in the context of related structures and protein sequences of unknown biochemical function.
A genetic screen to isolate type III effectors translocated into pepper cells during
Xanthomonas
infection
Authors: Roden Julie Anne , Belt Brandis , Ross Jason Barzel , Tachibana Thomas , Vargas Joe , Mudgett Mary Beth
Published: November 2004

The bacterial pathogen
Xanthomonas campestris
pv.
vesicatoria
(
Xcv
) uses a type III secretion system (TTSS) to translocate effector proteins into host plant cells. The TTSS is required for
Xcv
colonization, yet the identity of many proteins translocated through this apparatus is not known. We used a genetic screen to functionally identify
Xcv
TTSS effectors. A transposon 5 (Tn
5
)-based transposon construct including the coding sequence for the
Xcv
AvrBs2 effector devoid of its TTSS signal was randomly inserted into the
Xcv
genome. Insertion of the
avrBs2
reporter gene into
Xcv
genes coding for proteins containing a functional TTSS signal peptide resulted in the creation of chimeric TTSS effector::AvrBs2 fusion proteins.
Xcv
strains containing these fusions translocated the AvrBs2 reporter in a TTSS-dependent manner into resistant
BS2
pepper cells during infection, activating the
avrBs2
-dependent hypersensitive response (HR). We isolated seven chimeric fusion proteins and designated the identified TTSS effectors as
Xanthomonas
outer proteins (Xops). Translocation of each Xop was confirmed by using the calmodulin-dependent adenylate cydase reporter assay. Three
xop
genes are
Xanthomonas
spp.-specific, whereas homologs for the rest are found in other phytopathogenic bacteria. XopF1 and XopF2 define an effector gene family in
Xcv
. XopN contains a eukaryotic protein fold repeat and is required for full
Xcv
pathogenicity in pepper and tomato. The translocated effectors identified in this work expand our knowledge of the diversity of proteins that
Xcv
uses to manipulate its hosts.
The role of the glycocalyx in reorganization of the actin cytoskeleton under fluid shear stress: A “bumper-car” model
Authors: Thi Mia M. , Tarbell John M. , Weinbaum Sheldon , Spray David C.
Published: November 2004

We propose a conceptual model for the cytoskeletal organization of endothelial cells (ECs) based on a major dichotomy in structure and function at basal and apical aspects of the cells. Intracellular distributions of filamentous actin (F-actin), vinculin, paxillin, ZO-1, and Cx43 were analyzed from confocal micrographs of rat fat-pad ECs after 5 h of shear stress. With intact glycocalyx, there was severe disruption of the dense peripheral actin bands (DPABs) and migration of vinculin to cell borders under a uniform shear stress (10.5 dyne/cm2; 1 dyne = 10 μN). This behavior was augmented in corner flow regions of the flow chamber where high shear stress gradients were present. In striking contrast, no such reorganization was observed if the glycocalyx was compromised. These results are explained in terms of a “bumper-car” model, in which the actin cortical web and DPAB are only loosely connected to basal attachment sites, allowing for two distinct cellular signaling pathways in response to fluid shear stress, one transmitted by glycocalyx core proteins as a torque that acts on the actin cortical web (ACW) and DPAB, and the other emanating from focal adhesions and stress fibers at the basal and apical membranes of the cell.
Dietary patterns in middle-aged Irish men and women defined by cluster analysis
Authors: Villegas R , Salim A , Collins MM , Flynn A , Perry IJ
Published: November 2004

Objectives:

To identify and characterise dietary patterns in a middle-aged Irish population sample and study associations between these patterns, sociodemographic and anthropometric variables and major risk factors for cardiovascular disease.

Design:

A cross-sectional study.

Subjects and methods:

A group of 1473 men and women were sampled from 17 general practice lists in the South of Ireland. A total of 1018 attended for screening, with a response rate of 69%. Participants completed a detailed health and lifestyle questionnaire and provided a fasting blood sample for glucose, lipids and homocysteine. Dietary intake was assessed using a standard food-frequency questionnaire adapted for use in the Irish population. The food-frequency questionnaire was a modification of that used in the UK arm of the European Prospective Investigation into Cancer study, which was based on that used in the US Nurses' Health Study. Dietary patterns were assessed primarily by K-means cluster analysis, following initial principal components analysis to identify the seeds.

Results:

Three dietary patterns were identified. These clusters corresponded to a traditional Irish diet, a prudent diet and a diet characterised by high consumption of alcoholic drinks and convenience foods. Cluster 1 (Traditional Diet) had the highest intakes of saturated fat (SFA), monounsaturated fat (MUFA) and percentage of total energy from fat, and the lowest polyunsaturated fat (PUFA) intake and ratio of polyunsaturated to saturated fat (P:S). Cluster 2 (Prudent Diet) was characterised by significantly higher intakes of fibre, PUFA, P:S ratio and antioxidant vitamins (vitamins C and E), and lower intakes of total fat, MUFA, SFA and cholesterol. Cluster 3 (Alcohol & Convenience Foods) had the highest intakes of alcohol, protein, cholesterol, vitamin B12, vitamin B6, folate, iron, phosphorus, selenium and zinc, and the lowest intakes of PUFA, vitamin A and antioxidant vitamins (vitamins C and E). There were significant differences between clusters in gender distribution, smoking status, physical activity, body mass index, waist circumference and serum homocysteine concentrations.

Conclusion:

In this general population sample, cluster analysis methods yielded two major dietary patterns: prudent and traditional. The prudent dietary pattern is associated with other health-seeking behaviours. Study of dietary patterns will help elucidate links between diet and disease and contribute to the development of healthy eating guidelines for health promotion.
Performance of a short tool to assess dietary intakes of fruits and vegetables, percentage energy from fat and fibre
Authors: Thompson Frances E , Midthune Douglas , Subar Amy F , Kahle Lisa L , Schatzkin Arthur , Kipnis Victor
Published: November 2004

Objectives:

We describe the methods used to develop and score a 17-item ‘screener’ designed to estimate intake of fruit and vegetables, percentage energy from fat and fibre. The ability of this screener and a food-frequency questionnaire (FFQ) to measure these exposures is evaluated.

Design:

Using US national food consumption data, stepwise multiple regression was used to identify the foods to be included on the instrument; multiple regression analysis was used to develop scoring algorithms. The performance of the screener was evaluated in three different studies. Estimates of intakes measured by the screener and the FFQ were compared with true usual intake based on a measurement error model.

Setting:

US adult population.

Subjects:

For development of instrument,n= 9323 adults. For testing of instrument, adult men and women in three studies completing multiple 24-hour dietary recalls, FFQ and screeners,n= 484, 462 and 416, respectively.

Results:

Median recalled intakes for examined exposures were generally estimated closely by the screener. In the various validation studies, the correlations between screener estimates and estimated true intake were 0.5–0.8. In general, the performances of the screener and the full FFQ were similar; estimates of attenuation were lower for screeners than for full FFQs.

Conclusions:

When coupled with appropriate reference data, the screener approach described may yield useful estimates of intake, for both surveillance and epidemiological purposes.
The cost of infant feeding in Liverpool, England
Authors: Berridge K , Hackett AF , Abayomi J , Maxwell SM
Published: November 2004

Objective:

To investigate feeding practices in infants under the age of 4 months in Liverpool, England with particular reference to the cost of infant feeding.

Design:

A cross–sectional survey consisting of self–completion questionnaires and interviews.

Setting:

Subjects' homes within Central and South Liverpool Primary Care Trust areas.

Subjects:

One hundred and forty–nine women (aged 18 to 43 years) and their infants (mean age 13 weeks).

Results:

The average weekly cost of breast–feeding was £11.58 compared with £9.60 for formula–feeding. Many breast– and formula–feeding women spent money however on items that were not needed or used only once or twice. This was especially true of first–time mothers. Characteristics significantly associated with higher spending were: feeding method – mothers that had or were partially breast–feeding (P=0.001), education – those educated to degree level (P=0.028), socio–economic status – those in social classes I and II (P=0.002) and age – those aged 30 years and over (P=0.003).

Conclusions:

This study demonstrates that while breast–feeding is often promoted as being free, this is not the case. Better information needs to be given to parents to avoid wasting money on items that are unnecessary, or where cheaper alternatives are available.
Eating at fast-food restaurants is associated with dietary intake, demographic, psychosocial and behavioural factors among African Americans in North Carolina
Authors: Satia Jessie A , Galanko Joseph A , Siega-Riz Anna Maria
Published: November 2004

Objective:

To examine associations of the frequency of eating at fast-food restaurants with demographic, behavioural and psychosocial factors and dietary intake in African American adults.

Methods:

Self-reported data from a population-based cross-sectional survey of 658 African Americans, aged 20–70 years, in North Carolina. An 11-page questionnaire assessed eating at fast-food restaurants, demographic, behavioural and diet-related psychosocial factors, and dietary intake (fruit, vegetable, total fat and saturated fat intakes, and fat-related dietary behaviours).

Results:

The participants were aged 43.9±11.6 years (mean±standard deviation), 41% were male, 37% were college graduates and 75% were overweight or obese. Seventy-six per cent reported eating at fast-food restaurants during the previous 3 months: 4% usually, 22% often and 50% sometimes. Frequency of eating at fast-food restaurants was positively associated with total fat and saturated fat intakes and fat-related dietary behaviours (P< 0.0001) and inversely associated with vegetable intake (P< 0.05). For example, mean daily fat intake was 39.0 g for usually/often respondents and 28.3 g for those reporting rare/never eating at fast-food restaurants. Participants who reported usual/often eating at fast-food restaurants were younger, never married, obese, physically inactive and multivitamin non-users (allP< 0.01). Frequency of eating at fast-food restaurants was positively associated with fair/poor self-rated health, weak belief in a diet–cancer relationship, low self-efficacy for healthy eating, weight dissatisfaction, and perceived difficulties of preparing healthy meals and ordering healthy foods in restaurants (allP< 0.05). Frequency of eating at fast-food restaurants did not differ significantly by sex, education, smoking, ability to purchase healthy foods or knowledge of the Food Guide Pyramid.

Conclusions:

Eating at fast-food restaurants is associated with higher fat and lower vegetable intakes in African Americans. Interventions to reduce fast-food consumption and obesity in African Americans should consider demographic and behavioural characteristics and address attitudes about diet–disease relationships and convenience barriers to healthy eating.
Arachidonic Acid Inhibits Epithelial Na Channel Via Cytochrome P450 (CYP) Epoxygenase-dependent Metabolic Pathways
Authors: Wei Yuan , Lin Dao-Hong , Kemp Rowena , Yaddanapudi Ganesh S.S. , Nasjletti Alberto , Falck John R. , Wang Wen-Hui
Published: November 2004

We used the patch-clamp technique to study the effect of arachidonic acid (AA) on epithelial Na channels (ENaC) in the rat cortical collecting duct (CCD). Application of 10 μM AA decreased the ENaC activity defined by NPo from 1.0 to 0.1. The dose–response curve of the AA effect on ENaC shows that 2 μM AA inhibited the ENaC activity by 50%. The effect of AA on ENaC is specific because neither 5,8,11,14-eicosatetraynoic acid (ETYA), a nonmetabolized analogue of AA, nor 11,14,17-eicosatrienoic acid mimicked the inhibitory effect of AA on ENaC. Moreover, inhibition of either cyclooxygenase (COX) with indomethacin or cytochrome P450 (CYP) ω-hydroxylation with N-methylsulfonyl-12,12-dibromododec-11-enamide (DDMS) failed to abolish the effect of AA on ENaC. In contrast, the inhibitory effect of AA on ENaC was absent in the presence of N-methylsulfonyl-6-(propargyloxyphenyl)hexanamide (MS-PPOH), an agent that inhibits CYP-epoxygenase activity. The notion that the inhibitory effect of AA is mediated by CYP-epoxygenase–dependent metabolites is also supported by the observation that application of 200 nM 11,12-epoxyeicosatrienoic acid (EET) inhibited ENaC in the CCD. In contrast, addition of 5,6-, 8,9-, or 14,15-EET failed to decrease ENaC activity. Also, application of 11,12-EET can still reduce ENaC activity in the presence of MS-PPOH, suggesting that 11,12-EET is a mediator for the AA-induced inhibition of ENaC. Furthermore, gas chromatography mass spectrometry analysis detected the presence of 11,12-EET in the CCD and CYP2C23 is expressed in the principal cells of the CCD. We conclude that AA inhibits ENaC activity in the CCD and that the effect of AA is mediated by a CYP-epoxygenase–dependent metabolite, 11,12-EET.
Grain size dependence of optical properties and positron annihilation parameters in Bi2O3powder
Authors: Chakrabarti Mahuya , Dutta Sreetama , Chattapadhyay S , Sarkar A , Sanyal D , Chakrabarti A
Published: November 2004

Nanocrystalline Bi2O3has been prepared by a ball milling process. The particle size of the ball-milled Bi2O3powder has been determined by the x-ray powder diffraction method and transmission electron microscopy. The absorption spectra, in the spectral range 300–1300 nm, indicate an increase of the optical bandgap for both the direct and indirect transitions due to the reduction of grain size. The defects introduced in Bi2O3during grinding have been investigated by the positron annihilation technique. Positron annihilation results indicate an increase of defects due to ball milling.
Paraffin surfaces for culture-based detection of mycobacteria in environmental samples
Authors: Jing Gaoshan , Eluru Hima B , Polaczyk Amy , Kinkle Brian , Oerther Daniel B , Papautsky Ian
Published: November 2004

In this paper, we describe the development of paraffin surfaces for culture-based detection of mycobacteria in environmental samples. The surfaces use the well-described paraffinophilic nature of mycobacteria to rapidly and selectively differentiate them from non-target microorganisms. New methods of depositing and patterning paraffin were developed, including using butanol or a heat gun to generate molten paraffin that was subsequently deposited by spin coating and patterned by wet and dry etching techniques. Using these techniques, 18 mm glass wafers with paraffin films of 10–70 µm were fabricated and subsequently etched to form different patterns. Prototype paraffin surfaces were experimentally tested to demonstrate the concept of rapid and selective detection of mycobacteria in environmental samples collected from a municipal sewage treatment plant. Our successful demonstration of the culture-based detection on paraffin substrates presents an alternative approach for tracking microorganisms in complex environmental samples.