bluuebunny/crossref_metadata_2025 huggingface dataset:
Rumen microbial adaptation to long-term feeding of virginiamycin in sheep fed barley and virginiamycin as a supplement
Authors: Godfrey SI , Nagaraja TG , Winslow SW , Rowe JB
Published: November 2004

Profiles of rumen fermentation were examined in sheep supplemented with barley or barley plus virginiamycin for 7 weeks and challenged with 1.7 kg of barley with or without virginiamycin. Twenty-five sheep were housed in individual pens and fed chaff, up to a maximum of 1.4 kg/day. Sheep were allocated to one of three treatments: no grain supplement (n = 5), barley grain 700 g twice weekly (n = 10) or barley with virginiamycin (40 g/t grain; n = 10). After 7 weeks, five animals in each treatment group fed grain received 1.7 kg of barley and five received 1.7 kg of barley plus virginiamycin (40 g/t). Sheep supplemented with barley alone maintained a normal pattern of rumen fermentation in response to 1.7 kg of barley indicating adaptation of rumen microbes to grain feeding. In animals supplemented with barley on its own and then fed barley plus virginiamycin there were higher concentrations of L-lactic acid (P < 0.001) and ammonia (P < 0.01) and a lower rumen pH (P < 0.01) than sheep in other treatments at 9, 12 and 24 h following grain feeding. The number of protozoa was decreased (P < 0.001) 24 h following feeding in sheep supplemented with barley and challenged with barley plus virginiamycin compared to pre-feeding (0 h) counts, but not in other treatment groups. Incubations of rumen fluid with glucose from sheep supplemented with barley and barley plus virginiamycin indicated virginiamycin was still effective in reducing L-lactate production following 9 weeks of supplement feeding. The results indicate virginiamycin may disrupt rumen function in sheep already adapted to grain that has not been treated with virginiamycin.
Resistance to seed transmission of cucumber mosaic virus in narrow-leafed lupins (Lupinus angustifolius)
Authors: Jones RAC , Cowling WA
Published: November 2004

Cucumber mosaic virus (CMV) is seed-transmitted in L. angusti,folius (narrow-leafed lupin) and plants that grow from infected seed are the primary source of inoculum for field epidemics. Resistance to seed transmission of CMV was sought in cultivars, breeding lines and wild types of this species. The field screening method developed was based on spreader rows, where a susceptible cultivar (Wandoo) with high intrinsic seed infection levels was grown on either side of every test row, and CMV spread occurred by natural aphid transmission. Inoculum pressure was so great that spreader and test rows became virtually 100% infected. Harvested seed from each test row was assessed for the level of infection present by testing for the presence of CMV in the radicles of newly germinated seeds or in leaves of seedlings by ELISA. This method was used successfully from 1987 to 1992 to screen lines for relative resistance/susceptibility to CMV seed transmission. Based on their intrinsic CMV seed transmission rates during the experiments test lines were categorized into four groups: moderately resistant (1-6% seed transmission, as in cvv. Danja and Frost), moderately susceptible (6-20% seed transmission, as in cvv. Illyarrie, Yorrel and Gungurru), susceptible (20-35% seed transmission, as in cv. Wandoo), and very susceptible (35-75% seed transmission, as found in some breeding lines and wild types). No lines were highly resistant (<l% seed transmission) or immune (0%). Differences in seed transmission rates between lines were highly significant and stable from year to year. Resistance or susceptibility was not related to alkaloid content or flowering date of lines but appeared to be polygenically controlled. Breeding for low CMV seed transmission rates is recommended for use in L. angustifolius breeding programs. Also, advanced breeding lines with unacceptably high intrinsic seed transmission rates (i.e. >20%) should be culled out.
Effect of sowing time on yield and agronomic characteristics of wheat in south-eastern Australia
Authors: Gomez-Macpherson H , Richards RA
Published: November 2004

The main environmental constraints to the yield of dryland wheat in south-eastern Australia are: a low and erratic rainfall throughout the growing season, the chance of frost at flowering time, and high temperatures during the grain-filling period. The aims of this work were threefold. Firstly, to determine which sowing period minimizes these constraints and results in the highest yields. Secondly, what is the optimum flowering time for a given sowing date so that maximum yield is achieved. The third aim was to determine whether any crop characteristic was associated with high yield or may limit yield in the different sowings. The experiments were conducted at three sites in New South Wales that were representative of dry (Condobolin) and cooler and wetter (Moombooldool, Wagga Wagga) sites in the south-eastern wheatbelt. In this study several sets of isogenic material, involving a total of 23 genotypes, that were similar in all respects except for flowering time, were sown early (mid-April and early May), normal (mid to late May) and late (June to mid July). Characteristics of the highest-yielding lines in each experiment are presented. The average flowering time of the highest yielding lines in all sowings had a range of only 12 days at the driest site, but a range of over 20 days at the coolest and wettest site. The optimum anthesis date (day of year, y) was related to sowing date (day of year, doy) at the cooler sites such that: y = 245+0.32 doy (r2 = 0.86) and at Condobolin, y = 253+0.19 doy (r2 = 0.91). Optimum anthesis date expressed in thermal time (�C days) after sowing (y) was related to sowing time (doy) as follows: y = 2709 -8-3 doy (r2 = 0.84). It is suggested that these relationships are likely to be quite robust and should hold true for similar thermal environments in eastern Australia. There was little variation in grain yield between the earliest sowing in mid-April (108 doy) and sowings throughout May (up to 147 doy). Grain yield declined 1.3% per day that sowing was delayed after late May. Aboveground biomass was substantially higher in early sown crops. However, this did not translate into higher yields. From the evidence presented it is argued that the principal reason that greater yields were not obtained in the early sowings, particularly in the April sowing, was the greater competition for assimilates between the growing spike and the elongating stem. It is suggested that a way of overcoming this competition is to genetically shorten the stems of winter wheats. This should capitalize on the considerable advantages in terms of water use efficiency that early sowing offers and result in greater yields. Barley yellow dwarf virus, although present at the cooler, wettest site in one year, was more frequent in the later sowings than in the early sowing and was not likely to have contributed to the lower than expected yields in the early sowings.
Nitrogen fixation in grazed and ungrazed subterranean clover pasture in south-west Australia assessed by the 15N natural abundance technique
Authors: Sanford P , Pate JS , Unkovich MJ , Thompson AN
Published: November 2004

The progress of N2 fixation by subterranean clover (Trifolium subterraneum L.) was followed throughout a growing season in adjacent grazed and ungrazed portions of a pasture at Mount Barker, W.A. Proportions of plant nitrogen derived from the atmosphere (%Ndfa) were determined at a sequence of sampling times using the 15N natural abundance technique with capeweed (Arctotheca calendula L.) as non-fixing reference species. Cumulative yields of fixed N by above ground biomass of clover were determined from %Ndfa values, concurrent estimates of dry matter (DM) yields, and percentage nitrogen in clover shoot DM. Seasonal DM yields of clover, capeweed and mixed grasses were in the approximate ratio 60 : 20: 20. Total herbage yields were 11.8 and 7.8 t ha-1 for the grazed and ungrazed swards respectively. Poorer performance of the latter was attributed to shading by taller grasses late in the season. Starting from a low value of 58%, Ndfa of the ungrazed sward became uniformly high (73-88%) for the rest of the season. Clover of the more productive grazed sward behaved similarly except for a significant mid winter depression to 55%Ndfa, probably caused by excessive defoliation through overgrazing. Fixed N recovered from clover shoot biomass was 103 and 188 kg N ha-1 for ungrazed and grazed pasture respectively. Mineral N under the grazed sward first consisted mostly of nitrate, and then predominantly of ammonium. Soil-derived N was utilized roughly equally by clover, grasses and capeweed and a field study of %Ndfa of subterranean clover grown in varying proportion with either the main pasture grass (Lolium rigidum Gaudin) or capeweed indicated the grass to be the more effective competitor for soil N against the clover. The data suggested that reliable estimates of seasonal accumulation of fixed N by pastures would be obtained from assessments of cumulative biomass yield of clover N with a single determination of %Ndfa at peak productivity in mid to late spring.
A feral goat rumen fluid inoculum improves nitrogen retention in sheep consuming a mulga (Acacia aneura) diet
Authors: Miller SM , Brooker JD , Blackall LL
Published: November 2004

Rumen micro-organisms which are resistant to high levels of condensed tannins (CT) may constitute a unique response by feral goats to the nutritive depressing effects of mulga (Acacia aneura) CT. Transferring these micro-organisms to domestic livestock lacking this response may be beneficial when CT-rich mulga diets are consumed. Three experiments were conducted in which sheep consuming a mulga diet were given a ruminal inoculation of feral goat rumen fluid (FGRF). Feed intake and nitrogen (N) retention were significantly greater (P < 0.05) in both sheep and domestic goats following inoculation and in inoculated compared with uninoculated sheep. Inoculation also improved N digestibility and reduced the rate of liveweight loss in sheep and domestic goats. These improvements were of similar magnitude to those attributable to the traditional N, phosphorus and sulfur mineral supplement for mulga fed sheep. FGRF inoculated sheep also grew as much wool as uninoculated sheep receiving a production enhancing mineral supplement. The results from these experiments suggest that FGRF is readily transferable to sheep and improves N metabolism in these animals. Using micro-organisms from FGRF as an inoculum for sheep consuming a mulga diet has the potential to be an alternative to mineral supplements.
The effect of dietary lysine and methionine concentrations on the growth characteristics and breast meat yields of Australian broiler chickens
Authors: Gorman I , Balnave D
Published: November 2004

Two experiments were conducted with an Australian broiler strain to determine the optimum dietary lysine and methionine concentrations for growth and breast meat yield. In the first experiment, supplementing lysine to 14.1 and 13.0 g/kg in combination with methionine supplemented to 6.2 and 5.3 g/kg in starter and finisher diets respectively, resulted in significant improvements in breast meat yield with no effect on growth rate. Increasing the crude protein concentration by increasing the concentrations of all indispensable amino acids to balance the additional lysine and methionine supplements improved weight gain but gave no further improvement in breast meat yield. In the second experiment, dietary concentrations of 13.1 and 12.5 g lysine/kg and 6.5 and 5.1 g methionine/kg in starter and finisher diets respectively, were found to support optimum liveweight gain when supplemented individually. A further study was conducted to confirm that the ranges in age and bodyweight at which breast meat yield was measured had no significant effect on breast meat yield. The optimum dietary concentrations of lysine and methionine observed in these studies are higher than those recommended by the Standing Committee on Agriculture (1987) for broilers in Australia.
Sulfur amino acid metabolism and protein synthesis in young sheep fed ryegrass pasture and two Lotus cultivars containing condensed tannin
Authors: Lee J , Harris PM , Sinclair BR , Treloar BP
Published: November 2004

Groups of sheep were fed either fresh ryegrass pasture, a low condensed tannin (CT) diet (Lotus corniculatus; or a medium CT diet (L. pedunculatus) to compare the effects of these feeds on methionine and cysteine metabolism, because of their significance in wool production, and on phenylalanine as an indicator of general protein metabolism. Dry matter intake (DMI) among groups, ryegrass pasture, Lotus corniculatus, L. pedunculatus, were significantly different, therefore the treatment means for metabolic measurements and wool growth were adjusted by covariate analysis using DMI. Neither diet nor DM1 had any overall effect on phenylalanine concentrations in whole blood or phenylalanine irrevirible loss rate (IRL). However there were significant (P < 0.001) diet effects on cysteine blood concentrations. Methionine effects paralleled those of cysteine, with higher concentrations in sheep fed L. pedunculatus relative to pasture fed animals. Sheep fed L. pedunculatus had much higher cysteine and methionine ILRs compared with either the pasture or L. corniculatus groups. Sheep fed the highest level of condensed tannin in their diet (l. pedunculatus) had significantly greater rates of transsulfuration, cysteine and methionine oxidation. Overall the results show that CT in L. pedunculatus gives a greater degree of 'protection' during digestion for cysteine, methionine and phenylalanine, while L. corniculatus resulted in very little advantage. Condensed tannin effects on wool production are marginal and secondary to whole body metabolic influences.
Differences among bread wheat genotypes for tissue nitrogen content and their relationship to grain yield and protein content
Authors: Rostami MA , O'Brien L
Published: November 2004

This study was conducted to examine genotypic differences in tissue nitrogen content of wheat and establish the extent to which they were related to variation in grain yield and protein content. Thirty-six genotypes consisting of cultivars and advanced breeding lines were grown at four rates of applied nitrogen: 0, 50, 100 and 200 kg N/ha, for 3 years. Above-ground plant matter was harvested at approximately Zadoks growth stage 31 (commencement of stem elongation), microwaved for 4 min, then oven-dried at 60�C. Tissue nitrogen content of the hammermill-ground sample and grain protein content were determined by Near Infrared Reflectance Spectrometry. Genotypic differences in tissue nitrogen content, grain yield and protein content were established in each year. Maxima for tissue nitrogen and grain protein were obtained at the highest nitrogen rate, whereas the minima were at the zero rate. Yield responses to nitrogen application varied between years. Tissue nitrogen content was positively correlated with grain protein content in 8 of 12 within individual nitrogen rate comparisons. Over all nitrogen rates, the two variables were significantly positively correlated (ranging from r = 0.453 to r = 0.771). Tissue nitrogen content and protein content generally exhibited high heritability estimates within and over years, whereas grain yield had a high within year but a low over years heritability value. The use of tissue nitrogen content provides a possible basis for a screening test to select for yield and protein content in wheat breeding programs.
Detection of phytoplasmas in dieback, yellow crinkle, and mosaic diseases of papaya using polymerase chain reaction techniques
Authors: Liu B , White DT , Walsh KB , Scott PT
Published: November 2004

Oligonucleotide primers complementary to regions specific to plant-pathogenic mycoplasma-like organisms (phytoplasmas) were used in polymerase chain reactions on tissue samples from dieback, yellow crinkle, and mosaic affected papaya plants. The primer pair P068/P069, which hybridise to internal regions of the 16s rRNA gene, amplified an approximately 560 bp product in dieback, yellow crinkle and mosaic affected papaya. The primer pair P3/P7, which hybridise to the spacer region between the 16s and 23s rRNA genes, amplified an approximately 300 bp fragment in yellow crinkle and mosaic affected papaya, with no product from dieback affected plants. No PCR product was obtained with either set of primers from healthy plants. An identical Alu I restriction enzyme profile was obtained with all three 560 bp products. This study provides the first evidence for the association of phytoplasmas with papaya mosaic and Australian papaya dieback.
Comparative growth of wheat, barley, and annual ryegrass (Lolium rigidum) in monoculture and mixture
Authors: Cousens RD
Published: November 2004

The growth and development of wheat, barley, and annual ryegrass (Lolium rigidum Gaud.) were studied in monoculture and in additive mixtures at two sites of contrasting climate and soil type in New South Wales. Although smaller, annual ryegrass paralleled the behaviour of the two cereals in monoculture in all respects. The phenological development of all three species was more rapid at the wheatbelt site (Forbes) than on the coastal plain (Camden); yield loss was also greater at Forbes. The early growth rate of barley was greater than that of wheat or ryegrass at both sites. As a result, barley was more able to suppress ryegrass in mixtures and to maintain its yield than wheat. Sensitivity analysis of a growth simulation model suggested that the early rate of leaf production was likely to be influential in determining the magnitude of biomass reduction at anthesis; relative phenological development and height growth dynamics appeared to have little effect.
Predictions of food intake in ruminants from analyses of food composition
Authors: Poppi DP
Published: November 2004

Equations used to predict intake by cattle from some chemical or physical characteristic of food were examined. The equations are empirical or mechanistic in nature. Mechanistic equations are not used widely, usually only in a research context. The input to mechanistic models requires too much time to quantify to be used routinely. Empirical relationships form the basis of most feeding standards and are based on a wide variety of prescribed characteristics (digestibility, chemical composition, etc.), but the underlying principle is a relationship between intake and digestibility. Equations are modified to take account of feed types, animal weight and physiological state, rumen modifiers, hormone implants, environmental conditions, and whether grazing or hand fed. Quite significant differences exist between the equations in the intakes they predict in response to variation in weight, breed type, and feed digestibility. Equations can be very precise in their prediction when used with feed types and breed types on which they are based. Near infrared reflectance (NIR) offers the most potential for long-term development of equations. At present, NIR is used largely to determine chemical composition because of speed of operation, but long-term storage of data is simple, allowing further associative relationships to be developed readily. More sophisticated statistical procedures being employed to improve the precision of the relationships between intake and prescribed characteristics of food and NIR will be vitally important as they enable extra parameters to be incorporated at no extra cost or time for analysis.
Changes in feed intake and digestibility in sheep given virginiamycin
Authors: Thorniley GR , Boyce MD , Rowe JB
Published: November 2004

An experiment was conducted to investigate why virginiamycin reduces feed intake when it is first included in diets fed to sheep and cattle. Sheep were dosed daily with various amounts of virginiamycin, and measurements were made of both in vitro and in vivo dry matter digestibility and of blood gastrin concentrations. Virginiamycin decreased feed intake and there was some evidence that the effect was dose related. Dry matter digestibility was reduced by doses of virginiamycin >80 mg/day. Although highly correlated with feed intake, digestibility did not seem to be the sole factor influencing feed intake. Blood gastrin concentration was not significantly affected by virginiamycin and was not correlated with feed intake.
Fusarium wilt of banana in Australia: a review
Authors: Pegg KG , Moore NY , Bentley S
Published: November 2004

The history of Fusarium wilt of bananas (caused by F. oxysporum f.sp. cubense) and the research conducted on the disease in Australia is summarised in this review. Subjects covered include the classification of banana cultivars, the cultivars in production in the Australian banana industry, the distribution and diversity of the pathogen in Australia and pathogenicity and control of the disease.
Influence of phenology on grain yield variation among barley cultivars grown under terminal drought
Authors: Mitchell JH , Fukai S , Cooper M
Published: November 2004

We investigated the influence of sowing time and genotypic variation for phenology on grain yield of barley in south-eastern Queensland. Over 3 seasons, 8 trials with 10 cultivars and 1 trial with 4 cultivars were conducted under either irrigated or terminal drought conditions at 2 locations. Rainout shelters ensured the development of severe terminal water stress. Trials were either sown on a common date, as conducted in traditional multi-environment trials, or over 3 weeks to synchronise anthesis among cultivars of different phenologies. Within the common sowing date trials, variation (P < 0.01) existed among cultivars for grain yield. From the 6 common sowing trials there was a negative correlation (P < 0.05) between grain yield and days to anthesis; that is, the shorter duration cultivars expressed the highest grain yield. Variation in days to anthesis accounted for 48-72% of the variation for grain yield. In the staggered sowing trials, where anthesis of all cultivars occurred within 4 or 2 days of the mean anthesis date, variation for grain yield was small or non-significant, and there was no association between grain yield and days to anthesis. The staggered sowing experiment with 10 cultivars indicated that duration of the vegetative phase was important in determining total dry matter production at maturity when cultivars were grown under terminal drought. Long-duration cultivars sown earlier had greater total dry matter at maturity than short-duration cultivars. This was associated with a greater water extraction by the long-duration cultivars, especially at depth, which remained inaccessible to later sown, short-duration cultivars. However, due to the low harvest index of the long-duration cultivars, grain yield of long- and short-duration cultivars was comparable when anthesis of cultivars was synchronised. When sown at the same time, a short-duration cultivar is advantageous because of a high chance of escaping water stress that develops during the critical development stage of anthesis. The results from the staggered sowing date experiments, however, indicated that the long-duration cultivars, when sown earlier in the season, had no yield disadvantage in comparison with the short-duration cultivars sown later in the season. Therefore, there is scope to develop barley cultivars of later phenology than is currently available to provide Queensland farmers with the option of utilising early rainfall events which are sometimes the only planting opportunity.
The influence of grazing frequency and intensity on the vigour of Lolium perenne L. under subtropical conditions
Authors: McKenzie FR
Published: November 2004

Lolium perenne L. (perennial ryegrass) exhibits poor persistence in subtropical environments. Grazing management may enhance the vigour and hence persistence of this species. Perennial ryegrass was subjected to various grazing treatments, and its vigour, indexed by etiolated growth, was evaluated over 2 years. Pasture and individual tiller vigour were monitored under 5 combinations of grazing frequency and intensity, applied rotationally, and 1 treatment of continuous grazing. The vigour of infrequently grazed plots was greater than that of frequently or continuously grazed plots; however, grazing intensity did not influence vigour. Seasonally, vigour declined during mid (December and .January) to late (February and March) summer of the establishment year and from early summer (October) to autumn (May) during the second year. Poor vigour in frequently grazed plots was associated with low growth reserves rather than a lack of active tiller growth points. Towards the end of the second year, however, a lack of active tiller growth points also limited vigour in frequently grazed plots. Tillers from infrequently grazed plots (regardless of grazing intensity) had greater vigour than tillers from the frequently grazed plots. To enhance the vigour of perennial ryegrass in subtropical environments, the frequency of grazing should be reduced, particularly in summer.
Development and use of a barley crop simulation model to evaluate production management strategies in north-eastern Australia
Authors: Goyne PJ , Meinke H , Milroy SP , Hammer GL , Hare JM
Published: November 2004

A study was undertaken to identify improved management strategies for barley (Hordeum vulgare L.), particularly in relation to time of planting, location, and frost risk in the variable climate of north-eastern Australia. To achieve this objective, a crop growth simulation model (QBAR) was constructed to integrate the understanding, gained from field experiments, of the dynamics of crop growth as influenced by soil moisture and environmental variables. QBAR simulates the growth and yield potential of barley grown under optimal nutrient supply, in the absence of pests, diseases, and weeds. Genotypic variables have been determined for 4 cultivars commonly grown in the northern cereal production areas. Simulations were conducted using long-term weather data to generate the probabilistic yield outcome of cv. Grimmet for a range of times of planting at 10 locations in the north-eastern Australian grain belt. The study indicated that the common planting times used by growers could be too late under certain circumstances to gain full yield potential. Further applications of QBAR to generating information suitable for crop management decision support packages and crop yield forecasting are discussed.
Estimates of lupin below-ground biomass nitrogen, dry matter, and nitrogen turnover to wheat
Authors: Russell CA , Fillery IRP
Published: November 2004

The amount of lupin below-ground biomass (BGB), BGB nitrogen (N) content, and utilization of BGB-N by subsequent wheat was estimated from lupins grown in soil columns. Lupin plants were enriched in situ with 15N-labelled urea through a cotton wick inserted through the stem. Of the applied 15N. 92% was recovered in the lupin plant-soil system at maturity: 87% of this 15N was in lupin aboveground biomass and 13% in the soil columns. Total mature lupin dry matter (DM) approximated 11 t/ha, with 3.0 t/ha (27%) of this DM below ground. Total mature lupin N approximated 321 kg/ha, of which 91 kg/ha (28%) resided below ground. In terms of N and DM, BGB was the largest lupin residue component even though only 35% of this was recoverable as root material. About 13% of the BGB-N was in inorganic form at maturity. The net mineralisation of lupin BGB-N after 2 consecutive years of wheat growth was 27%. and wheat assimilated about 74% of this N (i.e. 20% of BGB-N), with equal quantities assimilated in each year. The contribution of lupin BGB-N to the N in wheat tops ranged from 40% for soil columns receiving no fertiliser N to 15-20% for soil columns fertilised with 30 kg N/ha. The net mineralisation of BGB-N and the assimilation of BGB-N by wheat were unaffected by the application of fertiliser N.
Genetic parameters for cow weight and condition score in Angus, Hereford, and Poll Hereford cattle
Authors: Johnston DJ , Chandler H , Graser HU
Published: November 2004

Heritabilities and genetic correlations for cow weight and body condition score were estimated from field data for 3 beef breeds in Australia. In all, 8177 cows of mixed ages were weighed and scored for body condition at calf weaning time in seedstock herds as part of a large research project. The average weaning age was 212, 221, and 218 days for Angus, Hereford, and Poll Hereford, respectively. Cow weights and condition scores were analysed separately for each breed and estimates of genetic parameters were obtained by Restricted Maximum Likelihood (REML). Cow weight and condition score were moderately heritable: h2 = 0.43 and 0.21 for Angus, 0.39 and 0.14 for Hereford, and 0.48 and 0.17 for Poll Hereford. The genetic correlation between CW and CS was 0.49, 0.65, and 0.58 for Angus, Hereford, and Poll Hereford, respectively. There is potential for providing a genetic evaluation for cow weight using field data in Australian beef cattle. Its modelling for inclusion in a multiple trait genetic evaluation system such as BREEDPLAN is discussed.
On the mechanism and biology of cytochrome oxidase inhibition by nitric oxide
Authors: Antunes Fernando , Boveris Alberto , Cadenas Enrique
Published: November 2004

The detailed molecular mechanism for the reversible inhibition of mitochondrial respiration by NO has puzzled investigators: The rate constants for the binding of NO and O
2
to the reduced binuclear center Cu
B
/a
3
of cytochrome oxidase (COX) are similar, and NO is able to dissociate slowly from this center whereas O
2
is kinetically trapped, which altogether seems to favor the complex of COX with O
2
over the complex of COX with NO. Paradoxically, the inhibition of COX by NO is observed at high ratios of O
2
to NO (in the 40–500 range) and is very fast (seconds or faster). In this work, we used simple mathematical models to investigate this paradox and other important biological questions concerning the inhibition of COX by NO. The results showed that all known features of the inhibition of COX by NO can be accounted for by a direct competition between NO and O
2
for the reduced binuclear center Cu
B
/a
3
of COX. Besides conciliating apparently contradictory data, this work provided an explanation for the so-called excess capacity of COX by showing that the COX activity found in tissues actually is optimized to avoid an excessive inhibition of mitochondrial respiration by NO, allowing a moderate, but not excessive, overlap between the roles of NO in COX inhibition and in cellular signaling. In pathological situations such as COX-deficiency diseases and chronic inflammation, an excessive inhibition of the mitochondrial respiration is predicted.
Neural synchrony indexes disordered perception and cognition in schizophrenia
Authors: Spencer Kevin M. , Nestor Paul G. , Perlmutter Ruth , Niznikiewicz Margaret A. , Klump Meredith C. , Frumin Melissa , Shenton Martha E. , McCarley Robert W.
Published: November 2004

Current views of schizophrenia suggest that it results from abnormalities in neural circuitry, but empirical evidence in the millisecond range of neural activity has been difficult to obtain. In pursuit of relevant evidence, we previously demonstrated that schizophrenia is associated with abnormal patterns of stimulus-evoked phaselocking of the electroencephalogram in the γ band (30–100 Hz). These patterns may reflect impairments in neural assemblies, which have been proposed to use γ-band oscillations as a mechanism for synchronization. Here, we report the unique finding that, in both healthy controls and schizophrenia patients, visual Gestalt stimuli elicit a γ-band oscillation that is phase-locked to reaction time and hence may reflect processes leading to conscious perception of the stimuli. However, the frequency of this oscillation is lower in schizophrenics than in healthy individuals. This finding suggests that, although synchronization must occur for perception of the Gestalt, it occurs at a lower frequency because of a reduced capability of neural networks to support high-frequency synchronization in the brain of schizophrenics. Furthermore, the degree of phase locking of this oscillation is correlated with visual hallucinations, thought disorder, and disorganization in the schizophrenia patients. These data provide support for linking dysfunctional neural circuitry and the core symptoms of schizophrenia.
Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry
Authors: Chu Feixia , Shan Shu-ou , Moustakas Demetri T. , Alber Frank , Egea Pascal F. , Stroud Robert M. , Walter Peter , Burlingame Alma L.
Published: November 2004

Among the methods used to unravel protein interaction surfaces, chemical cross-linking followed by identification of the cross-linked peptides by mass spectrometry has proven especially useful in dynamic and complex systems. During the signal recognition particle (SRP)-dependent targeting of proteins to the bacterial plasma membrane, the specific interaction between Ffh (the protein component of SRP) and FtsY (the SRP receptor) is known to be essential for the efficiency and fidelity of this process. In this work, we studied theEscherichia coliandThermus aquaticusFfh·FtsY complexes by using chemical cross-linking and tandem mass spectrometry to identify nine intermolecular cross-linked peptides. This information was used in conjunction with a previously undescribed model-building approach that combines geometric restraint optimization with macromolecular docking. The resulting model of the Ffh·FtsY complex is in good agreement with the crystal structure solved shortly thereafter. Intriguingly, four of the cross-linked pairs involve the M domain of Ffh, which is absent from the crystal structure, providing previously undocumented experimental evidence that the M domain is positioned in close proximity to the Ffh·FtsY interface in the complex.
Interspecies communication in
Streptococcus gordonii–Veillonella atypica
biofilms: Signaling in flow conditions requires juxtaposition
Authors: Egland Paul G. , Palmer Robert J. , Kolenbrander Paul E.
Published: November 2004

During the development of human oral biofilm communities, the spatial arrangement of the bacteria is thought to be driven by metabolic interactions between them.
Streptococcus gordonii
and
Veillonella atypica
, two early colonizing members of the dental plaque biofilm, have been postulated to participate in metabolic communication;
S. gordonii
ferments carbohydrates to form lactic acid, which is a preferred fermentation substrate for
V. atypica
. We found that, during agar-plate coculture of these organisms, a signaling event occurs that results in increased expression of the
S. gordonii
α-amylase-encoding gene
amyB
. Confocal scanning laser microscopy of coculture flowcell-grown biofilms using human saliva as the sole nutrient showed that
V. atypica
caused
S. gordonii
to increase expression of a
PamyB
-′
gfp
transcriptional fusion in a spatially resolved fashion. In this open system, only those streptococci in mixed-species microcolonies containing
V. atypica
expressed GFP; nearby
S. gordonii
colonies that lacked
V. atypica
did not express GFP. In a closed system containing
S. gordonii
and
V. atypica
, flow cytometric analysis showed that
S. gordonii
containing the
PamyB
-′
gfp
reporter plasmid exhibited mean fluorescence levels 20-fold higher than did
S. gordonii
that had not been incubated with
V. atypica
. Thus, in a closed system where a diffusible signal can accumulate above a required threshold, interspecies signaling mediates a change in gene expression. We provide evidence that, in open systems like those that predominate in natural biofilms, diffusible signals between species are designed to function over short distances, on the order of 1 μm.
BRAGI: linking and visualization of database information in a 3D viewer and modeling tool
Authors: Reichelt Joachim , Dieterich Guido , Kvesic Marsel , Schomburg Dietmar , Heinz Dirk W.
Published: November 2004

Summary: BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules. A new version of BRAGI has been developed that is supported on Windows, Linux and SGI. The user interface has been rewritten to give the standard ‘look and feel’ of the chosen operating system and to provide a more intuitive, easier usage. A large number of new features have been added. Information from public databases such as SWISS-PROT, InterPro, DALI and OMIM can be displayed in the 3D viewer. Structures can be searched for homologous sequences using the NCBI BLAST server.

Availability: Freeware, licensed: http://bragi.gbf.de/

Contact:  Reichelt@gbf.de

Supplementary Information:  http://bragi.gbf.de/gallery
Multiple sequence alignment with user-defined constraints at GOBICS
Authors: Morgenstern Burkhard , Werner Nadine , Prohaska Sonja J. , Steinkamp Rasmus , Schneider Isabelle , Subramanian Amarendran R. , Stadler Peter F. , Weyer-Menkhoff Jan
Published: November 2004

Summary: Most multi-alignment methods are fully automated, i.e. they are based on a fixed set of mathematical rules. For various reasons, such methods may fail to produce biologically meaningful alignments. Herein, we describe a semi-automatic approach to multiple sequence alignment where biological expert knowledge can be used to influence the alignment procedure. The user can specify parts of the sequences that are biologically related to each other; our software program uses these sites as anchor points and creates a multiple alignment respecting these user-defined constraints. By using known functionally, structurally or evolutionarily related positions of the input sequences as anchor points, our method can produce alignments that reflect the true biological relationships among the input sequences more accurately than fully automated procedures can do.

Availability: Our software is available online at GÖttingen BIoinformatics Compute Server (GOBICS), http://dialign.gobics.de/anchor/index.php

Contact:  burkhard@gobics.de
CyDAS: a cytogenetic data analysis system
Authors: Hiller Bernhard , Bradtke Jutta , Balz Harald , Rieder Harald
Published: November 2004

For statistical analyses in cancer cytogenetics, the genomic changes encoded by the karyotype must be translated into numerical codes. We developed a program, which extracts chromosomal gains and losses as well as breakpoints from the karyotype. The changes are compiled in tables according to the chromosome bands involved and/or depicted in projection to the respective chromosome ideogram. The data are ready to be integrated into further statistical analyses. The program may be run as desktop or Internet application.

Availability:  http://www.cydas.org/

Contact:  info@cydas.org
Suzanne MacKenzie Memorial LectureConceptually unclad: feminist geography and Aboriginal peoples*
Authors: Peters Evelyn J.
Published: November 2004

This paper argues that feminist geography can provide some useful lessons in an attempt to increase Aboriginal peoples' representation in geography. It asks the question: How can we use the example of feminist geography to think about a geography that is more inclusive of Aboriginal people? The paper focuses on the issues of content in teaching, drawing on examples from urban and social geography, and on methodological challenges, especially the issue of reflexivity. Feminist geographer Suzanne Mackenzie argued that an emerging feminist geography left the discipline ‘conceptually unclad’, challenging scholars to consider new theoretical frameworks and new perspectives. I argue that emphasising the geographies of Aboriginal people also enriches geography, including feminist geography.
A Deleuzian critique of resource‐use management politics in Industria
Authors: Hipwell William T.
Published: November 2004

In an era of increasingly well‐attended and violent protests around the world against globalisation, this commentary seeks to answer the crucial question: The globalisation of what? The answer proposed is that what is globalising is ‘Industria’, a multiplicitous, global system of power/knowledge, a vast ‘machinic assemblage’ recently accreted from diverse, competing world systems. After describing some of the most serious challenges facing human communities and the rest of the biosphere, the commentary enlists the aid of the philosopher Gilles Deleuze and his colleague Félix Guattari to expose the cognitive errors underlying political and environmental problems. Applying Deleuze's philosophy of difference to geopolitics and resource‐use management, it is shown that representational epistemologies and a negative ontology of identity obscure the myriad interconnections among human and non‐human beings, leading to conflict and ecological degradation. From there, the ‘Industria’ hypothesis is presented as a conceptual response to Deleuze and Guattari's critique of the ‘Urstaat’ and as a framework for scholars grappling with the need to achieve socioeconomic and ecological sustainability. Finally, the commentary briefly explores the potential of a differential, bioregional geopolitics as a civilised alternative to the predations of Industria.
Reimagining sustainable cultures: constitutions, land and art
Authors: Doubleday Nancy , Mackenzie A. Fiona D. , Dalby Simon
Published: November 2004

Globalisation is about the interconnection of peoples and places in accelerated ways, but it is also about resistance and adaptation in the face of change. Discussions of sustainability now incorporate both dynamic understandings of culture and the recognition that place matters because the practices that are in need of sustaining, as well as those that pose threats, happen in particular communities and in specific geographic contexts. Culture is codified not only in property rights and legislation, but also in the public artistic expressions of peoples and places. Case studies from Nunavut and Scotland show the interrelationships of sovereignty and claims to identity and community. Art, as a result of creative action in the case of Cape Dorset Inuit printmakers and carvers on Baffin Island, and a millennium tapestry telling the stories of the Isle of Harris, complement matters of property rights. Both discussions show that identity is about material culture and property relations in respect of land. Serious discussions of sustainability, in contrast to the technical practices frequently invoked using the term sustainable development, require considerations of the dynamics of complex cultural arrangements in particular places, rather than assumptions of stability of either peoples or their ecological contexts.
Constraints in the ligament ontogeny and evolution of pteriomorphian Bivalvia
Authors: Malchus N.
Published: November 2004

A study of ligaments of larval, postlarval and adult shells of fossil and recent pteriomorphian bivalves leads to the following observations and hypotheses: (1) Ligament growth passively follows the general growth pattern of the mantle margin. No independent genetic information fixes the anterior, ventral, or posterior growth direction of the ligament. Further growth constraints relate to physical availability of space on the ligament area and to heterochronic processes. (2) The disjunct ligament and the repetition of fibrous or lamellar sublayers are phenotypic aspects of the same derived ligament Bauplan 1. All Pteriomorphia possess the ability to produce repetitive ligaments. This ability and space reductions of the ligament area in independent phylogenetic lineages are responsible for the iterative evolution of ligament grades. (3) Spondylidae and Plicatulidae are duplivincular, and the Ostreoidea are plesiomorphically multivincular. (4) Larval anterior‐helical growth of the soft tissue produces opisthogyrate shells and possibly caused the evolution of the alivincular‐multivincular grade. Duplivincular‐alivincular and multivincular‐alivincular grades can be distinguished if larval shell characters are known. (5) The taxonomic distribution of ligament grades as amended in this paper is largely consistent with modern phylogeny hypotheses based on genetic or morphologic or combined character sets. However, the resolution of early phylogenetic nodes requires more data on larval shells of Lower Palaeozoic taxa.
The origin of chalicotheres (Perissodactyla, Mammalia)
Authors: Hooker J. J. , Dashzeveg D.
Published: November 2004

Description of a new genus of perissodactyl, Protomoropus, for the species ‘Hyracotherium’gabuniai Dashzeveg and its inclusion with a diversity of other primitive perissodactyls in a cladistic analysis results in the following higher order changes to our knowledge of perissodactyl phylogeny. Protomoropus is sister taxon to the Chalicotheriidae plus Lophiodontidae, which themselves are confirmed as sister groups. The previously monofamilial superfamily Chalicotherioidea is extended to include all three taxa. Paleomoropus and Lophiaspis are shown to be primitive lophiodontids. Various genera of the Isectolophidae are shown to be stem members of a clade that includes chalicotheres and lophiodonts. The infraorder Ancylopoda is extended to include them. Inclusion of isectolophids in the Ancylopoda rather than as stem tapiromorphs results in the break up of the clade Tapiromorpha. Instead, the modern perissodactyl groups, comprising the horse superfamily Equoidea and that of the rhinos and tapirs, the Ceratomorpha (here reduced in rank to parvorder), form a new clade which is here named infraorder Euperissodactyla nov. The Brontotheriidae form the sister group to Ancylopoda plus Euperissodactyla. The clade comprising Ancylopoda plus Euperissodactyla is named suborder Lophodontomorpha nov. The Chalicotherioidea and Chalicotheriidae evolved in Asia. The Lophiodontidae arose following dispersal from Asia to North America. Dispersal continued to Europe, where the family radiated.
Ctenodactylids from the Lower and Middle Miocene of Saudi Arabia
Authors: Antoñanzas Raquel López , Sen Sevket
Published: November 2004

The ctenodactylids from the Lower and Middle Miocene of Saudi Arabia are represented by two species: Sayimys intermedius (Sen and Thomas, 1979) and Sayimys assarrarensis sp. nov. This new taxon differs from the other species of Sayimys by its larger size together with an association of characters such as the presence of a metalophulid II in d4 and the strength of the anteroloph and posteroloph in P4. A cladistic analysis involving Prosayimys flynni, Sayimys obliquidens, S. assarrarensis sp. nov., S. intermedius, S. sivalensis, S. baskini, and Metasayimys curvidens is provided. Sayimys assarrarensis sp. nov. nests between Sayimys obliquidens and Metasayimys curvidens as a relatively primitive taxon.
Maastrichtian cephalopods from Cerralvo, north‐eastern Mexico
Authors: Ifrim Christina , Stinnesbeck Wolfgang , López‐Oliva José Guadalupe
Published: November 2004

Sediments of the Méndez Formation near Cerralvo, north‐eastern Mexico, yield an abundant and diverse Maastrichtian ammonite assemblage. A total of 23 species referred to 18 genera are described, in addition to the possible coleoid Naefia neogaeia. The assemblage is considered to be of early Maastrichtian age on the basis of ammonite occurrences and has been dated to the lower Maastrichtian biozone CF 7 by planktic foraminifera. None of the ammonite species has been reported previously from the Méndez Formation and most species are recorded from Mexico for the first time. In addition to faunal elements known from other Gulf of Mexico localities [Baculites ovatus, Nostoceras (N.) alternatum, N. (N.) colubriformis, N. (N.) rugosum, Solenoceras reesidei] the assemblage is characterized by cosmopolitan (e.g. Anagaudryceras politissimum, Desmophyllites diphylloides, Diplomoceras cylindraceum, Gaudryceras kayei, Phyllopachyceras forbesianum, and Pseudophyllites indra) and Tethyan elements [e.g. Brahmaites (Anabrahmaites) vishnu, Fresvillia constricta, Hauericeras rembda, Solenoceras texanum, Tetragonites superstes]. Some ammonite species have been known from the Indopacific region a [e.g. Fresvillia aff. F. teres, Neophylloceras (Hypophylloceras) hetonaiense, Zelandites varuna] and are clearly cold‐water species. The composition of the assemblage contrasts with other Gulf of Mexico faunas which is related to bathymetry.