bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel open-system technique to monitor real-time oxygen consumption during early phases of seed germination
Authors: Jacyn Baker C. , Roberts Daniel P. , Mock Norton M. , Blount Vansie L.
Published: May 2008

A novel technique allows long-term monitoring of real-time oxygen consumption during seed germination in an open system. Most current techniques used to detect oxygen consumption by seeds measure the decrease in oxygen concentration in a closed chamber. This is not ideal for long-term experiments because the chamber must be replenished with air periodically, subjecting the seeds to abrupt changes in oxygen concentration. The current technique employs an open system, in which seeds are submerged in a continuously aerated aqueous environment. Oxygen electrodes are used to measure the steady-state concentration of oxygen in the solution, which is a function of both the rate of oxygen consumption by the seed and the rate of aeration from the atmosphere. The rate of aeration is directly dependent on the oxygen concentration of the bathing solution; therefore, previous calibration of the system allows the direct conversion of steady-state oxygen concentrations into oxygen consumption rates. Because oxygen is not limiting, the experimental design described here can monitor the same sample non-intrusively every minute for more than 24 h, allowing for greater precision than hourly readings often reported with current techniques. Multiple treatments and/or replicates can be run simultaneously, allowing sensitive comparison of various seed treatments or seed types. To illustrate its potential application, the technique was used to follow the rehydration and pre-emergence phases of germination of cucumber (Cucumis sativum), pea (Pisum sativum) and mustard (Brassica juncea) seeds, detect the inhibitory effects of surface sterilization techniques on seed respiration of cucumber, and follow the interaction of a bacterial biocontrol agent with germinating cucumber and pea seeds.
Expansin gene expression in Datura ferox L. seeds is regulated by the low-fluence response, but not by the high-irradiance response, of phytochromes
Authors: Mella R. Alejandra , Burgin Maria José , Sánchez Rodolfo A.
Published: May 2008

Expansins are a multi-gene family of proteins involved in changes in cell wall properties. In seeds where the embryo is completely surrounded by the endosperm, dormancy breakage requires weakening of the micropylar endosperm, increased embryo growth potential or both. Cell wall alterations are fundamental components of these processes, and expansins are thought to participate in them. Here, we explore the possible involvement of expansins in the control of germination by phytochrome in Datura ferox L. seeds. Based on the conserved sequences of known expansin genes, corresponding primers were designed to investigate the expression of expansin mRNAs by reverse transcriptase polymerase chain reaction (RT-PCR). One expansin mRNA was detected in micropylar endosperm of D. ferox, while two mRNAs were present in the embryo prior to radicle emergence. Expansin transcript content is promoted by red (R) light, both in the micropylar endosperm and the embryo; these effects of R are far-red light (FR) reversible, displaying a typical low-fluence response (LFR) in a way fully consistent with the photocontrol of germination. On the other hand, when the promotion of germination by the LFR is antagonized by exposing the seeds to continuous FR through a high-irradiance response (HIR) or by ABA, the inhibitory treatments do not affect expansin mRNA abundance. The results support the participation of expansins in the promotion of germination by LFR of phytochromes, and suggest that inhibition of germination by HIR or ABA does not include a reduction in the transcription of expansin genes.
Is ‘NO’ news good news? Nitrogen oxides are not components of smoke that elicits germination in two smoke-stimulated species, Nicotiana attenuata and Emmenanthe penduliflora
Authors: Preston Catherine A. , Becker Romy , Baldwin Ian T.
Published: May 2008

Both the California chaparral species,Emmenanthe pendulifloraBenth. (Hydrophyllaceae), and a tobacco native to the Great Basin Desert of south-western Utah,Nicotiana attenuataTorr. ex Wats. (Solanaceae), germinate in response to component(s) of wood smoke. Nitrogen oxides (NO and NO2), in amounts produced by a fire, have been proposed to be germination signals forE. penduliflora. We examined the germination response of dormant seeds ofE. pendulifloraandN. attenuatato aqueous solutions of smoke adjusted to different pHs, and two NO donors [sodium nitroprusside (SNP) andS-nitroso-N-acetylpenicillamine (SNAP)]. The smoke solutions, at pH 4 or 5, induced the maximum germination response. Aqueous solutions of SNP and SNAP, releasing NOx as high as 42 μM, had no effect on germination. Additionally, NO2–could not be detected in aqueous smoke extracts derived from combusted cellulose or wood. Therefore, unidentified cellulose combustion factors, rather than NOx, are likely to be the ecologically relevant germination signals.
Mechanical and enzymatic separation of ripening rice (Oryza sativa L.) caryopsis tissues
Authors: Hay Jordan O. , Spanswick Roger M.
Published: May 2008

The ripening rice (Oryza sativa L.) caryopsis contains several maternal and embryonic tissues that transport assimilates along the partitioning pathway. Experimental access to transport steps in the pathway is limited by the separability of the tissues. Hence, the extent to which tissues can be mechanically and enzymatically separated was assessed. The caryopsis coat was isolated during mid-ripening, dissected and microscopically characterized. In centripetal order, the pericarp (epidermis, parenchyma-cell layer, cross-cell layer, tube-cell layer), inner integument, nucellar epidermis, aleurone layer and subaleurone layer adhered to each other. There was mechanical separation at the tube-cell layer, but not at the maternal/embryonic interface. Aleurone- and subaleurone-layer cells exposed on the inner surface of isolated caryopsis coats were macerated with Pectolyase Y-23 and manually sheared, which freed the endosperm and exposed the nucellar epidermis. Yield of endosperm cells increased linearly with the number of coats and reached a maximum after 1 h. The proportion of cells that were viable was approximately 10%. Subaleurone-layer cells contributed less than 25% to the yield. These results suggest that pectin polymers are necessary for adherence between the nucellar epidermis and the aleurone layer, and that enzymatic maceration is useful for separating the tissues at the maternal/embryonic interface.
Inheritance of deep seed dormancy and stratification-mediated dormancy alleviation in Amaranthus tuberculatus
Authors: Leon Ramon G. , Bassham Diane C. , Owen Micheal D.K.
Published: May 2008

Amaranthus tuberculatusis a weed species that has shifted emergence patterns over the past few years, presumably due to changes in seed dormancy in response to selection in agricultural fields. Although it is recognized that the seed dormancy phenotype is greatly affected by the environment, it is also acknowledged that the genotype plays a significant role. However, the importance of the genotype in determining intra-population seed dormancy variability, and the effect on emergence patterns, is not well understood. The objective of the present study was to determine the importance of the genotype on deep dormancy and the stratification-mediated dormancy alleviation inA. tuberculatus. Wild populations differing in seed dormancy were crossed and F2families were generated. These families were used to determine narrow sense heritability of dormancy and stratification-mediated dormancy alleviation at the individual (hi2) and family (hf2) levels.hi2ranged from 0.13 to 0.4 and 0.04 to 0.06 for the dormancy and stratification response, respectively. In the case ofhf2, the values ranged from 0.76 to 0.91 for deep dormancy and from 0.33 to 0.58 for the stratification response. The genetic correlation between these two traits was below 0.075, indicating that different genes control them. High temperature strengthened the dormancy of deeply dormant seeds, making them less sensitive to stratification. However, high temperature promoted the germination of non-deeply dormant seeds. It is proposed that delayed weed emergence can be generated by selecting genes that control stratification response, and not necessarily only the genes that are directly responsible for deep dormancy.
Seed remains of common millet from the 4th (Mongolia) and 15th (Hungary) centuries: AFLP, SSR and mtDNA sequence recoveries
Authors: Gyulai G. , Humphreys M. , Lagler R. , Szabo Z. , Toth Z. , Bittsanszky A. , Gyulai F. , Heszky L.
Published: May 2008

Seed remains of common millet (Panicum miliaceumL.) were excavated from sites of ad 4th-century Darhan (Mongolia), and ad 15th-century Budapest (Hungary). Because the 15th-century medieval grains looked so intact, a germination test was carried out under aseptic conditions, which resulted in swelling of the grains but no cell proliferation or germination. Ancient DNA (aDNA) was extracted from the aseptic grains; analysed for amplified fragment length polymorphisms (AFLP), simple sequence repeats (SSR) and mitochondrial DNA (mtDNA); and compared with the modern millet cultivar ‘Topaz’. AFLP analysis revealed that extensive DNA degradation had occurred in the 4th-century ancient millet, resulting in only 2 (1.2%) AFLP fragments (98.8% degradation) amplified byMseCAA–EcoAGT, compared to the 15th-century medieval millet, with 158 (40%) fragments (60% degradation), and modern millet cultivar ‘Topaz’ with 264 fragments (100%).EcoAGT–MseCAA was found to be the most effective selective-primer combination for the analysis of medieval and modern millet. Eight AFLP fragments were sequenced after re-amplification and cloning. Microsatellite (SSR) analysis at the nucleargln4,sh1,rps28 andrps15 loci revealed one SNP (single nucleotide polymorphism) at the 29th position (A→G) ofrps28 locus, compared to modern millet. An mtDNA fragment (MboI), amplified at the 18S–5S ribosomal DNA (rDNA) locus in the medieval millet, showed no molecular changes compared to modern millet. The results underline the significance of aDNA extraction and analysis of excavated seeds for comparative analysis and molecular reconstruction of ancient and extinct plant genotypes.
Osmotin-regulated reserve accumulation and germination in genetically transformed tea somatic embryos: a step towards regulation of stress tolerance and seed recalcitrance1
Authors: Bhattacharya Amita , Saini Uksha , Sharma Preeti , Nagar P.K. , Ahuja Paramvir Singh
Published: May 2008

The osmotin gene was introduced into tea [Camellia sinensis(L.) O. Kuntze] somatic embryos at the globular stage of development via microprojectile bombardment, to determine the effects of this stress-tolerance-related gene on the accumulation of storage reserves and acquisition of desiccation tolerance during embryo maturation. Changes in total soluble sugars, starch and proteins in response to osmotin were estimated in the stably transformed embryos, using standard biochemical and histochemical methods, after the globular embryos had matured to the heart stage of development. These changes also were compared with two types of controls, comprising (1) untransformed embryos and (2) embryos that were bombarded without osmotin DNA. The control embryos showed poor reserve accumulation and negligible germination but, in contrast, the embryos bombarded with the osmotin gene showed a several-fold increase in storage reserves, normal maturation and 57–63% germination. When these transformed embryos were desiccated to 15.5% moisture content, only 40% germinated, although a further increase in the accumulation of storage reserves occurred. In contrast, the control embryos became necrotic and failed to germinate. This study demonstrates the use of somatic embryogenesis as a tool for understanding seed recalcitrance in tea, and suggests that transformation with stress-tolerance genes can overcome the developmental problems associated with recalcitrant seeds.
Molecular and Genetic Analysis of Condensin Function in Vertebrate Cells
Authors: Hudson Damien F. , Ohta Shinya , Freisinger Tina , MacIsaac Fiona , Sennels Lau , Alves Flavia , Lai Fan , Kerr Alastair , Rappsilber Juri , Earnshaw William C.
Published: May 2008

We engineered mutants into residues of SMC2 to dissect the role of ATPase function in the condensin complex. These residues are predicted to be involved in ATP binding or hydrolysis and in the Q-loop, which is thought to act as a mediator of conformational changes induced by substrate binding. All the engineered ATPase mutations resulted in lethality when introduced into SMC2 null cells. We found that ATP binding, but not hydrolysis, is essential to allow stable condensin association with chromosomes. How SMC proteins bind and interact with DNA is still a major question. Cohesin may form a ring structure that topologically encircles DNA. We examined whether condensin behaves in an analogous way to its cohesin counterpart, and we have generated a cleavable form of biologically active condensin with PreScission protease sites engineered into the SMC2 protein. This has allowed us to demonstrate that topological integrity of the SMC2-SMC4 heterodimer is not necessary for the stability of the condensin complex in vitro or for its stable association with mitotic chromosomes. Thus, despite their similar molecular organization, condensin and cohesin exhibit fundamental differences in their structure and function.
An overview of the wcd EST clustering tool
Authors: Hazelhurst Scott , Hide Winston , Lipták Zsuzsanna , Nogueira Ramon , Starfield Richard
Published: May 2008

Summary: The wcd system is an open source tool for clustering expressed sequence tags (EST) and other DNA and RNA sequences. wcd allows efficient all-versus-all comparison of ESTs using either the d2 distance function or edit distance, improving existing implementations of d2. It supports merging, refinement and reclustering of clusters. It is ‘drop in’ compatible with the StackPack clustering package. wcd supports parallelization under both shared memory and cluster architectures. It is distributed with an EMBOSS wrapper allowing wcd to be installed as part of an EMBOSS installation (and so provided by a web server).

Availability: wcd is distributed under a GPL licence and is available from http://code.google.com/p/wcdest

Contact:  scott.hazelhurst@wits.ac.za

Supplementary information: Additional experimental results. The wcd manual, a companion paper describing underlying algorithms, and all datasets used for experimentation can also be found at www.bioinf.wits.ac.za/~scott/wcdsupp.html
Sleeping outside the box: electroencephalographic measures of sleep in sloths inhabiting a rainforest
Authors: Rattenborg Niels C , Voirin Bryson , Vyssotski Alexei L , Kays Roland W , Spoelstra Kamiel , Kuemmeth Franz , Heidrich Wolfgang , Wikelski Martin
Published: May 2008

The functions of sleep remain an unresolved question in biology. One approach to revealing sleep's purpose is to identify traits that explain why some species sleep more than others. Recent comparative studies of sleep have identified relationships between various physiological, neuroanatomical and ecological traits, and the time mammals spend in rapid eye movement (REM) and non-REM sleep. However, owing to technological constraints, these studies were based exclusively on animals in captivity. Consequently, it is unclear to what extent the unnatural laboratory environment affected time spent sleeping, and thereby the identification and interpretation of informative clues to the functions of sleep. We performed the first electroencephalogram (EEG) recordings of sleep on unrestricted animals in the wild using a recently developed miniaturized EEG recorder, and found that brown-throated three-toed sloths (
Bradypus variegatus
) inhabiting the canopy of a tropical rainforest only sleep 9.63 h d
−1
, over 6 h less than previously reported in captivity. Although the influence of factors such as the age of the animals studied cannot be ruled out, our results suggest that sleep in the wild may be markedly different from that in captivity. Additional studies of various species are thus needed to determine whether the relationships between sleep duration and various traits identified in captivity are fundamentally different in the wild. Our initial study of sloths demonstrates the feasibility of this endeavour, and thereby opens the door to comparative studies of sleep occurring within the ecological context within which it evolved.
Conformational variability of molecules in different crystal environments: a database study
Authors: Weng Ze F. , Motherwell W. D. Sam , Allen Frank H. , Cole Jacqueline M.
Published: May 2008

A methodology is described for analysing the Cambridge Structural Database (CSD) in terms of molecular conformations. Molecular species that have more than a single occurrence across the complete CSD are identified, either as the sole crystal component or co-crystallized with other components. Cluster analysis, based on a root-mean-square fit of coordinates and chemical connectivity, is performed to identify conformational variance for each molecule. Results are analysed in terms of the number of discrete conformations observed versus the number of crystal environments and number of acyclic torsion angles in the molecule. Special subsets of environments are also analysed, namely polymorphs, co-crystals and solvates. In general, conformational diversity increases with an increasing number of different crystal environments and with an increasing number of flexible torsion angles. Overall, molecules with one or more acyclic flexible torsion angle are observed to exist in more than one conformation in ca 40% of cases. There is evidence that solvated molecules exhibit more conformational flexibility on average, compared with polymorphs and co-crystals.
Hydrogen-bonding properties of galanthamine: an investigation through crystallographic database observations and computational chemistry
Authors: Koné Soleymane , Galland Nicolas , Bamba El-Hadji Sawaliho , Le Questel Jean-Yves
Published: May 2008

The hydrogen-bonding properties of galanthamine have been investigated experimentally from a thorough analysis of crystallographic data retrieved from the Protein Data Bank and Cambridge Structural Database databases and theoretically through ab initio [MP2/6-311++G(2d,p)] and density functional theory [MPWB1K/6-31++G(d,p)] calculations. The main hydrogen-bond acceptor (HBA) interaction sites of the molecule are the O atoms and their spatial proximity allows multi-centered hydrogen-bond (HB) motifs. The hydrogen-bond donor (HBD) sites of the molecule are the NH+ and OH groups as well as several CH donors. Among them, the preferred ones are those directly linked to the ammonium nitrogen, followed by aromatic CH and finally the methyl group of the methoxy substituent. All these observations are in fairly good agreement with the computed positions of the molecular electrostatic potential (MEP) minima and maxima of various galanthamine species. The galanthamine HBD and HBA properties, investigated through the MEP analysis, appear sensitive to the degree of neutralization of the ammonium NH+ positive charge.
Structure and electron density of oxysulfide Sm2Ti2S2O4.9, a visible-light-responsive photocatalyst
Authors: Yashima Masatomo , Ogisu Kiyonori , Domen Kazunari
Published: May 2008

We report the crystal structure and electron density of samarium titanium oxysulfide, Sm2Ti2S2O4.9, photocatalyst obtained through the Rietveld analysis, maximum-entropy method (MEM) and MEM-based pattern fitting of the high-resolution synchrotron powder diffraction data taken at 298.7 K. The Sm2Ti2S2O4.9 has a tetragonal structure with the space group I4/mmm. Refined occupancy factors at the `equatorial' O1 and `apical' O2 sites were 0.994 (3) and 0.944 (12), respectively, which strongly suggest oxygen deficiency at the O2 site. Electron-density analyses based on the synchrotron diffraction data of Sm2Ti2S2O4.9 in combination with density-functional theory (DFT) calculations of stoichiometric Sm2Ti2S2O5 reveal covalent bonds between Ti and O atoms, while the Sm and S atoms are more ionic. The presence of S 3p and O 2p orbitals results in increased dispersion of the valence band, raising the top of the valence band and making the material active at visible wavelengths. The present DFT calculations of stoichiometric Sm2Ti2S2O5 indicate the possibility of overall splitting of water, although Sm2Ti2S2O4.9 works as a visible-light-responsive photocatalyst in aqueous solutions only in the presence of sacrificial electron donors or acceptors. The oxygen deficiency and cocatalyst seem to be factors affecting the catalytic activity.
Disorder and pseudo-symmetry in octakis(trivinylsilyl)octasilicate
Authors: Slebodnick Carla , Angel Ross J. , Hanson Brian E. , Agaskar Pradyot A. , Soler Tatiana , Falvello Larry R.
Published: May 2008

Octakis(trivinylsilyl)octasilicate was prepared by capping octaspherosilicate cubes, [Si8O20]8−, with trivinylsilyl groups in methanol solution. Crystals grown from CCl4 crystallize in the tetragonal space group I41. Systematic absences are consistent with the space group I41/amd, although the R
int values clearly indicate 4/m rather than 4/mmm Laue symmetry. Structure solution and refinement show that the pseudo a-glide results from the approximate m\bar 3m symmetry of the core (Si8O12)O_8^{8-} unit. The positions of the molecules conform to a {110} d-glide that is broken by the small rotations of all the molecules in the same direction about [001]. Crystals grown from toluene give a diffraction pattern consisting of sharp peaks that can be indexed on the same ca 7200 Å3 unit cell, but with h + k even, and l even only. The l = odd layers contain no Bragg spots, but instead exhibit diffuse sheets of intensity. Within the sheets of diffuse scattering are streaks parallel to r* = 〈110〉* that cross at the h + k odd Bragg positions. This diffuse scattering pattern arises from well ordered rods of molecules parallel to c with frequent faults in the stacking sequence of molecules parallel to 〈110〉, with displacement vectors of [00½].
Dipolar C[triple-bond]N...C[triple-bond]N interactions in organic crystal structures: database analysis and calculation of interaction energies
Authors: Wood Peter A. , Borwick Simon J. , Watkin David J. , Motherwell W. D. Samuel , Allen Frank H.
Published: May 2008

The Cambridge Structural Database (CSD) has been used to study nonbonded interactions between dipolar cyano groups. The analysis shows that C[triple-bond]N...C[triple-bond]N interactions form in an analogous manner to those involving carbonyl groups, and with the same interaction motifs: a dominant antiparallel dimer (57.5%) together with smaller populations of perpendicular (19.4%) and sheared parallel (23.0%) motifs. Ab initio calculations using intermolecular perturbation theory (IMPT) show an attractive C[triple-bond]N...C[triple-bond]N interaction in the dominant antiparallel dimer, with E
t = −20.0 kJ mol−1 at d(C...N) = 3.30 Å and with the motif having a shear angle close to 102°. The antiparallel C[triple-bond]N...C[triple-bond]N interaction is therefore slightly weaker than the analogous C=O...C=O dimer (−23.5 kJ mol−1), but both interactions have attractive energies similar to that of a medium-strength hydrogen bond and, where sterically favoured, they are important in the stabilization of extended crystal structures.
Approaches to the treatment of early rheumatoid arthritis with disease‐modifying antirheumatic drugs
Authors: Sizova Lyudmila
Published: May 2008

This paper reviews recent approaches to treatment of early rheumatoid arthritis (RA) with disease‐modifying antirheumatic drugs (DMARDs). The literature on treatment the early RA published between 1995 and 2007 was accessed through the PubMed database from the National Library of Medicine. Keywords were ‘early rheumatoid arthritis’, ‘disease‐modifying antirheumatic drugs’, ‘biologic agents’ and ‘combination therapy’. Only results of trials on human subjects that directly measured the effects of DMARDs or biological agents on clinical, laboratory parameters and radiological progression of early RA were selected. Combination therapy suppresses RA activity and radiological progression more effectively than monotherapy. If better control of RA is evident after 3–6 months of treatment with the combination of DMARDs, one must still decide whether to stop the first DMARD, stop the second, or continue with the combination. Combination therapy biological agents (infliximab, adalimumab) with methotrexate and etanercept therapy alone may induce remission in many patients with early RA. It is a method of choice in patients with an adverse prognosis. The main indications for combination therapy ‘standard’ DMARDs or combination 1 DMARDs with a biological agent are such variables as detection of a shared epitope, increase of concentration of anticyclic citrullinated peptide antibodies, rheumatoid factor, C‐reactive protein, 28‐joint disease activity score, Sharp score and presence of erosion in joints. The majority of rheumatologists believe that patients with RA should be treated with DMARDs earlier rather than later in the disease process. Further trials should establish the optimal approaches to early RA therapy.
Effect of supplementation with grain, hay or straw on the performance of weaner Merino sheep grazing old man (Atriplex nummularia) or river (Atriplex amnicola) saltbush
Authors: Norman H. C. , Masters D. G. , Wilmot M. G. , Rintoul A. J.
Published: May 2008

Old man saltbush (Atriplex nummularia) and river saltbush (A. amnicola) are widely used in commercial grazing systems on saline land in south‐western Australia. Three hypotheses were tested during a 3‐year study aimed at understanding the performance of weaner Merino sheep grazing saltbush‐based pastures. The first hypothesis, that young Merino sheep grazing river saltbush would be better able to maintain live weight, body condition and would grow more wool than sheep grazing old man saltbush, was not supported by the data. Across the 3 years of the study, sheep grazing old man saltbush lost significantly less live weight and grew more wool (proportionately 0·06) than sheep grazing river saltbush. Differences in animal performance were considered to be associated with differences between the plant species in in vitro digestibility, concentrations of fibre, sulphur and crude protein in the herbage and the architecture of the Atriplex plants. The second and third hypotheses concerned supplementation strategies for sheep grazing saltbush. Three supplements were offered, namely barley grain, cereal straw or cereal hay, at a rate that approximated to one‐third of the daily metabolizable energy requirements for maintenance of live weight. The performance of the sheep was higher when the grain supplement was offered but there was no effect of feeding roughage supplements compared to no supplementation. The findings suggested that the practice of feeding saltbush with adjacent crop stubbles is unlikely to be beneficial once any fallen grain has been consumed.
Age of regrowth as a factor affecting the nutritive value of hay of kikuyu grass (Pennisetum clandestinum) offered to lambs
Authors: Ruggia Chiesa A. P. , Kozloski G. V. , Bonnecarrère Sanchez L. M. , Lima L. D. , Oliveira L. , Härter C. J. , Fiorentini G. , Cadorin Jr R. L.
Published: May 2008

The changes in chemical composition of hay of kikuyu grass (Pennisetum clandestinum) harvested at 50, 70 and 90 d of regrowth, and its effect on intake, digestibility, fermentation and microbial protein synthesis in the rumen (Experiment 1) and oxygen uptake by portal‐drained viscera (PDV) (Experiment 2) were evaluated. The experiments were carried out with Polwarth × Texel crossbreed lambs with a mean live weight (s.e.m.) of 35(3·0) kg housed in metabolic cages. Organic matter (OM), neutral‐detergent fibre (NDF) and nitrogen (N) intake, as well as rumen ammonia‐N concentration, decreased linearly with age of regrowth (P < 0·05). Acid‐detergent fibre (ADF) and indigestible NDF intakes were similar for all treatments. Apparent digestibility of organic matter (OM), NDF and N, as well as true digestibility of OM, microbial protein synthesis in the rumen, N retention, pH of rumen fluid and sugars, amino acids and peptide concentrations in rumen fluid were similar for all treatments. Age of regrowth also did not affect the kinetics of passage of the particulate phase through the digestive tract nor oxygen uptake by PDV. Heat production by PDV represented an average of 0·039 of digestible energy (DE) intake. Increasing the age of regrowth of kikuyu grass from 50 to 90 d did not affect digestibility nor the efficiency of DE use by PDV tissues of lambs but it reduced the nutritive value of the hay due to a lower intake of OM. Intake of hay appeared to be most limited by the ADF and indigestible NDF concentrations of the hay.
Factors influencing tissue turnover during winter in perennial ryegrass‐dominated swards
Authors: Hennessy D. , O’Donovan M. , French P. , Laidlaw A. S.
Published: May 2008

Despite low net grass growth rates in Ireland between mid‐November and February, tissue continuously turns over as new leaves are produced and older leaves senesce. The effects of closing swards from grazing on three dates in autumn (1 September, 20 September and 10 October) on tissue turnover in a perennial ryegrass sward during the winter were examined at two sites in the north‐east and south of Ireland. Leaf extension and senescence rates were greater in the south than in the north‐east, and were greatest on the earliest closing date at both sites. Leaf appearance and extension rates at both sites were closely correlated with accumulated daily air temperature above 6°C and mean soil temperature. Site‐specific factors also influenced tissue flux, possibly including grazing intensity at closing and density of tillers of perennial ryegrass. Swards in the autumn with high herbage masses [>2000 kg dry matter (DM) ha−1 approximately] and high leaf area index (LAI; about 2·5 and above) had the greatest leaf senescence rates and the greatest declines in herbage mass during the winter. Leaf senescence rates per tiller in high LAI swards were correlated positively with amount of leaf per tiller and also the proportion of green leaf in the second youngest expanding leaf lost to senescence. As potentially a complex of interactive factors influences tissue flux in winter, it is proposed that the data from this study be used in conjunction with other data to construct a dynamic model to predict more reliably optimum closing date in autumn for herbage utilization in winter.
Effects of harvest date of timothy (Phleum pratense) on its nutritive value, and on the voluntary silage intake and liveweight gain of lambs
Authors: Bernes G. , Hetta M. , Martinsson K.
Published: May 2008

The effects of harvest date of timothy on the chemical composition of herbage and silage, and on the voluntary intake, liveweight gain and feed conversion efficiency by finishing lambs, were evaluated. The herbage was harvested and ensiled on three dates: 16 June (before heading), 20 June and 26 June. The silages were analysed for chemical composition and degradation characteristics by an in vitro gas production (GP) technique with end‐point measurements (72 h) of degradability of organic matter (OM) and neutral‐detergent fibre (NDF). There were clear effects of later dates of harvest increasing the concentration of NDF, and reducing the degradability of OM and NDF, and the rate of GP, of silages made from this herbage. The silages were fed ad libitum to lambs in a feeding experiment using a Latin square design. Later harvest dates decreased the voluntary intake of silage, liveweight gain and feed conversion efficiency. Lambs fed the early‐cut silage had a liveweight gain of 152 g d−1 and those fed the silage harvested 10 d later had a liveweight gain of 76 g d−1. Changes in the chemical composition of herbage and silage and in in vitro degradation characteristics of silages with later harvests were associated, to a large extent, with the reduction in voluntary intake and liveweight gain of lambs.
Establishment and production of common sainfoin (Onobrychis viciifolia Scop.) in the UK. 1. Effects of sowing date and autumn management on establishment and yield
Authors: Liu Z. , Lane G. P. F. , Davies W. P.
Published: May 2008

The effects of sowing date and autumn management of sainfoin (Onobrychis viciifolia Scop.) were investigated over 3 years in the UK. Replicated plots were sown between April and September in 2003 and 2004. Autumn management treatments were early and late cutting carried out in the establishment year and in subsequent years. Dry matter (DM) yields were measured over 3 years. One harvest was taken from April to July sowings in the establishment year and three harvests in each of the following years. DM yields from sowings in April and May were 2·8 and 3·3 t DM ha−1, respectively, in the establishment year, which were higher (P < 0·001) than from sowings in June and July. Sowings from April to July yielded 10·9–12·5 t DM ha−1 in the first full‐harvest year, and 9·5–11·5 t DM ha−1 in the following year. Sowings in August and September only gave 5 t DM ha−1 year−1. Early‐autumn cutting of an established sward reduced yields of sainfoin at the second harvest in the first and second full‐harvest years. Sowing in May had the lowest proportion of weed species (0·06) in the establishment year, and sowing in July had the highest (0·53). Crude protein concentration increased as the seasons progressed from 149·8 to 230·1 g kg−1 DM.
Establishment and production of common sainfoin (Onobrychis viciifolia Scop.) in the UK. 2. Effects of direct sowing and undersowing in spring barley on sainfoin and sainfoin‐grass mixtures
Authors: Liu Z. , Lane G. P. F. , Davies W. P.
Published: May 2008

The dry matter (DM) yield and herbage quality of swards of sainfoin (Onobrychis viciifolia), meadow fescue (Festuca pratensis,) and tetraploid perennial ryegrass (Lolium perenne) grown in monocultures and in four sainfoin:grass mixtures (0·33 sainfoin:0·66 meadow fescue, 0·66 sainfoin:0·33 meadow fescue, 0·33 sainfoin:0·66 perennial ryegrass and 0·66 sainfoin:0·33 perennial ryegrass), established by direct sowing or undersowing in spring barley, were investigated over 3 years in a field experiment in the UK. Direct sowing produced a mean yield across all species and mixtures of 1·8 t DM ha−1 in the establishment year, whereas undersowing produced no measurable yield except for that of the spring barley. Undersowing reduced the yields of sainfoin and sainfoin‐grass mixtures in the first full‐harvest year but not in the second. The annual yield of a monoculture of sainfoin was 7·53 t DM ha−1 and that of sainfoin‐grass mixtures was 8·33 t DM ha−1 averaged over 3 years. Both sainfoin and the sainfoin‐grass mixtures had higher annual DM yields than the grass monocultures. The mixture of 0·66 sainfoin:0·33 meadow fescue gave the highest mean annual yield (9·07 t DM ha−1) over the 3 years. There was a higher proportion of sainfoin maintained in mixtures with perennial ryegrass than with meadow fescue. The proportion of sainfoin in sainfoin–meadow fescue mixtures declined from 0·62 in the first year to 0·32 in the third year, whereas the proportion in sainfoin–perennial ryegrass increased from 0·48 in the first year to 0·67 in the second year and remained stable in the third year.
Effect of altering the grazing interval on growth and utilization of grass herbage and performance of dairy cows under rotational grazing
Authors: Dale A. J. , Mayne C. S. , Laidlaw A. S. , Ferris C. P.
Published: May 2008

The effects of short grazing intervals in the early part of the grazing season on the growth and utilization of grass herbage, and the performance of grazing dairy cows, in a rotational grazing system were examined. Seventy‐six cows were allocated to two grazing treatments: a normal rotation treatment (20‐d rotations for the first 60 d) and a short rotation treatment (12‐, 8‐, 8‐, 8‐, 12‐ and 12‐day rotations). Thereafter, both treatments had the same grazing interval and over the season as a whole both treatments received the same amount of nitrogen fertilizer and were stocked at the same rate. The short rotation treatment significantly reduced pre‐ and post‐grazing sward heights and pre‐grazing herbage mass in May and June. Total herbage production was significantly lower on the short than the normal rotation treatment as a result of a significant reduction in the growth rate of herbage in May and June. The short rotation treatment had a significantly lower milk output per cow. Grazing shorter swards, as a result of shorter rotations, significantly reduced herbage intake, reflecting reductions in intake per bite, grazing time and total bites per day. Treatment had no significant effect on herbage quality or pre‐ and post‐grazing sward height in August and September, despite the increased grazing severity in May and June with the short rotations. The severity of rotation length in this instance had a detrimental impact on animal performance, whereas a more modest reduction in grazing interval may control herbage production, without reducing animal performance.
Endoscopy in Barrett’s oesophagus: adherence to standards and neoplasia detection in the community practice versus hospital setting
Authors: Pohl H. , Aschenbeck J. , Drossel R. , Schröder A. , Mayr M. , Koch M. , Rothe K. , Anders M. , Voderholzer W. , Hoffmann J. , Schulz H.‐J. , Liehr R.‐M. , Gottschalk U. , Wiedenmann B. , Rösch T.
Published: May 2008

Objective.  Potential process differences between hospital and community‐based endoscopy for Barrett’s oesophagus have not been examined. We aimed at comparing adherence to guidelines and neoplasia detection rates in medical centres (MC) and community practices (CP).

Design.  Retrospective analysis.

Setting.  All histologically confirmed Barrett cases seen over a 3‐year period in six MC and 19 CP covering a third of all upper gastrointestinal endoscopies (n = 126 000) performed annually in Berlin, Germany.

Main outcome measure.  Rate of relevant neoplasia (high‐grade intraepithelial neoplasia or more) in both settings in relation to adherence to standards.

Results.  Of 1317 Barrett cases, 66% were seen in CP. CP patients had a shorter mean Barrett length (2.6 cm vs. 3.8 cm; P < 0.001) with fewer biopsies taken during an examination (2.5 vs. 4.1 for Barrett length ≤2 cm; P < 0.001). CPs also provided fewer complete esophagogastroduodenoscopy documentation (25.1% vs. 57.8%, P < 0.001). Neoplasias were found more commonly in MCs compared to CPs (9.2% vs. 0.8%; P < 0.001). However, on exclusion of all referred patients with known neoplasia (65%) or those examined for other reasons (27.5%), the detection rate at MCs decreased to 1.3%, not different from the one seen at CPs (0.8%, P = 0.43). Only 13% were found during surveillance, but 57% were diagnosed at an early stage.

Conclusions.  Referral bias and not better adherence to guidelines could explain the higher neoplasia prevalence in Barrett’s oesophagus at hospital centres. Despite a generally poor adherence to guidelines, most neoplasias found were at an early and potentially curable stage.
Pharmacokinetics and physiological effects of intravenous hydromorphone in conscious dogs
Authors: GUEDES A. G. P. , PAPICH M. G. , RUDE E. P. , RIDER M. A.
Published: May 2008

This study evaluated the pharmacokinetics, the sedative and anti‐nociceptive effects of intravenous hydromorphone in dogs. Five adult dogs were administered hydromorphone (0.1 mg/kg and 0.2 mg/kg) and morphine (0.5 mg/kg and 1 mg/kg) at weekly intervals. Blood samples were drawn before and at 1, 2, 5, 15, 30, 60 and 120 min after drug administration. Plasma hydromorphone only was measured by high pressure liquid chromatography (HPLC) with electrochemical detection and pharmacokinetic parameters calculated. Anti‐nociceptive and sedation scores were submitted to Kruskal‐Wallis one‐way anova on ranks and post‐hoc Bonferroni test with 5% significance level. The data fitted a two‐compartment model with a fast distribution (<1 min for both doses) and slower elimination rate. Mean elimination half‐life was 80 ± 52.7 and 57.7 ± 30.4 min for the high and low dose, respectively. The apparent mean volumes of distribution at steady‐state were 7.2 ± 3 and 4.5 ± 2.4 L/kg, while the clearance was 74.7 ± 19 and 68.1 ± 20 mL/kg/min for the high and low doses, respectively. Compared to saline, hydromorphone and morphine produced significant anti‐nociception and sedation of similar magnitude for 120 min. In conclusion, intravenous hydromorphone has a large volume of distribution, and high clearance rate that exceeds hepatic blood flow. In dogs, it produced mechanical anti‐nociception and sedation of a magnitude similar to morphine.
Pegylated interferons for chronic hepatitis C virus infection: an indirect analysis of randomized trials
Authors: Chou R. , Carson S. , Chan B. K. S.
Published: May 2008

Summary. Dual therapy with pegylated interferon and ribavirin is recommended for patients with chronic hepatitis C virus infection who meet criteria for treatment, but it is unclear whether pegylated interferon alfa‐2a or pegylated interferon alfa‐2b is more effective or associated with fewer adverse events. Because data from head‐to‐head trials of pegylated interferon regimens are sparse, we performed adjusted indirect analysis using trials comparing dual therapy with pegylated interferon alfa‐2a or pegylated interferon alfa‐2bvsdual therapy with non‐pegylated interferon. We searched for potentially relevant randomized controlled trials using electronic databases and reference lists. A total of 16 trials met inclusion criteria. Adjusted indirect comparisons found no statistically significant differences between dual therapy with pegylated interferon alfa‐2a and dual therapy with pegylated interferon alfa‐2b on the outcomes sustained virologic response [relative risk (RR) = 1.59, 95% CI: 0.56–4.46], withdrawal due to adverse events (RR = 0.86, 95% CI: 0.29–2.55), anaemia (RR = 1.67, 95% CI: 0.32–8.84), depression (RR = 1.09, 95% CI: 0.41–2.90) or flu‐like symptoms (RR = 1.10, 95% CI: 0.53–2.29). Adjusting for potential publication bias and stratifying analyses by indicators of methodological quality, human immunodeficiency virus infection status, hepatitis C virus genotype, dose of ribavirin or dose of pegylated interferon did not change conclusions. There is insufficient evidence to support conclusions that dual therapy with one pegylated interferon is superior to the other. However, because estimates are imprecise, our results also do not rule out a clinically significant difference. Head‐to‐head trials are needed to verify the results of indirect analyses and provide additional guidance on optimal treatment choices.
A predatory mechanism dramatically increases the efficiency of lateral gene transfer in Streptococcus pneumoniae and related commensal species
Authors: Johnsborg Ola , Eldholm Vegard , Bjørnstad Martha Langedok , Håvarstein Leiv Sigve
Published: May 2008

Bacteria that are competent for natural genetic transformation, such as pneumococci and their commensal relatives Streptococcus mitis and Streptococcus oralis, take up exogenous DNA and incorporate it into their genomes by homologous recombination. Traditionally, it has been assumed that genetic material leaking from dead bacteria constitutes the sole source of external DNA for competent streptococci. Here we describe a mechanism for active acquisition of homologous DNA that dramatically increases the efficiency of gene exchange between and within the streptococcal species mentioned above. This mechanism gives competent streptococci access to a common gene pool that is significantly larger than their own genomes, a property representing a considerable advantage when these bacteria are subjected to external selection pressures, such as vaccination and treatment with antibiotics.
Crystal structure of Spa40, the specificity switch for the Shigella flexneri type III secretion system
Authors: Deane Janet E. , Graham Stephen C. , Mitchell Edward P. , Flot David , Johnson Steven , Lea Susan M.
Published: May 2008

The pathogenic bacterium Shigella flexneri uses a type III secretion system to inject virulence factors from the bacterial cytosol directly into host cells. The machinery that identifies secretion substrates and controls the export of extracellular components and effector proteins consists of several inner‐membrane and cytoplasmic proteins. One of the inner membrane components, Spa40, belongs to a family of proteins proposed to regulate the switching of substrate specificity of the export apparatus. We show that Spa40 is cleaved within the strictly conserved amino acid sequence NPTH and substitution of the proposed autocatalytic residue abolishes cleavage. Here we also report the crystal structure of the cytoplasmic complex Spa40C and compare it with the recent structures of the homologues from Escherichia coli and Salmonella typhimurium. These structures reveal the tight association of the cleaved fragments and show that the conserved NPTH sequence lies on a loop which, when cleaved, swings away from the catalytic N257 residue, resulting in different surface features in this region. This structural rearrangement suggests a mechanism by which non‐cleaving forms of these proteins interfere with correct substrate switching of the apparatus.
5‐Hydroxytryptamine selectively activates the vagal nodose C‐fibre subtype in the guinea‐pig oesophagus
Authors: Yu S. , Ru F. , Ouyang A. , Kollarik M.
Published: May 2008

Abstract  The afferent neurons innervating the oesophagus originate from two embryonic sources: neurons located in vagal nodose ganglia originate from embryonic placodes and neurons located in vagal jugular and spinal dorsal root ganglia (DRG) originate from the neural crest. Here, we address the hypothesis that 5‐hydroxytryptamine (5‐HT) differentially stimulates afferent nerve subtypes in the oesophagus. Extracellular recordings of single unit activity originating from nerve terminals were made in the isolated innervated guinea‐pig oesophagus. Whole cell patch clamp recordings (35 °C) were made from the primary afferent neurons retrogradely labelled from the oesophagus. 5‐Hydroxytryptamine (10 μmol L−1) activated vagal nodose C‐fibres (70%) in the oesophagus but failed to activate overtly vagal jugular nerve fibres and oesophagus‐specific spinal DRG neurons. The response to 5‐HT in nodose C‐fibre nerve terminals was mimicked by the selective 5‐HT3 receptor agonist 2‐methyl‐5‐HT (10 μmol L−1) and nearly abolished by the 5‐HT3 receptor antagonists ondansetron (10 μmol L−1) and Y‐25130 (10 μmol L−1). In patch clamp studies, 2‐methyl‐5‐HT (10 μmol L−1) activated a proportion of isolated oesophagus‐specific nodose capsaicin‐sensitive neurons (putative cell bodies of nodose C‐fibres). We conclude that the responsiveness to 5‐HT discriminates placode‐derived (vagal nodose) C‐fibres from the neural crest‐derived (vagal jugular and spinal DRG) afferent nerves in the oesophagus. The response to 5‐HT in nodose C‐fibres is mediated by the 5‐HT3 receptor in their neuronal membrane.