bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence and Analysis of Genomic Segment A and B of Very Virulent Infectious Bursal Disease Virus Isolated from China
Authors: Sun J.‐H. , Lu P. , Yan Y.‐X. , Hua X.‐G. , Jiang J. , Zhao Y. 
Published: October 2010

SummaryA very virulent infectious bursal disease virus (vvIBDV) field strain, named SH95, was identified and characterized from flocks with vaccination failure in Shanghai. The use of random primer and a reverse transcriptase lacking RNase‐H activity produced full‐length cDNA copies of the viral genomic A and B segments of SH95. The 3259 base pairs (bp) of segment A and 2827 bp of segment B were amplified by long and accurate PCR in a single step, then successfully cloned and sequenced. There were five to 27 amino acid substitutions compared with other IBDV strains within the segment A polyprotein (of these, three are unique) and about nine to 38 amino acid substitutions within VP1 (of which, four are unique). The comparison of sequences encoding the polyprotein showed that vvIBDV SH95 was most closely related to Asiatic vvIBDVs, which formed a closely related group clearly distinguishable from other classical strains of IBDV. Phylogenetic analysis suggested that vvIBDV SH95 and some other Asiatic vvIBDVs were derived from similar origin. But the topology tree performed on segment B was quite different from that performed on segment A, indicating that a genetic reassortment had played an important role in the emergence of vvIBDV SH95.
Otitis in Cattle, an Aetiological Review
Authors: Duarte E. R. , Hamdan J. S. 
Published: October 2010

SummaryOtitis externa in cattle has a significant impact in tropical and subtropical regions, and the aetiological agents are predominantly rhabditiform nematodes and mites of the genusRaillietia. Its prevalence is higher in mature and Zebu cattle. In advanced clinical cases there can be irreversible and fatal neural lesions. Ear infection in calves has been associated with concurrent respiratory diseases and mixed infection. The principal reported agents of otitis in calves are bacteria such asActinomycesspp.,Corynebacterium pseudotuberculosis,Escherichia coli,Haemophilus somnus,Pasteurella multocida,Mannheimia haemolytica,Pseudomonasspp.,Streptococcusspp. andMycoplasma bovis. The control and treatment of bovine otitis is not standardized and there is little evidence‐based support for the diverse treatments available in the literature.
Campylobacterspp. in Irish Feedlot Cattle: A Longitudinal Study Involving Pre‐harvest and Harvest Phases of the Food Chain
Authors: Minihan D. , Whyte P. , O'Mahony M. , Fanning S. , McGill K. , Collins J. D. 
Published: October 2010

SummaryThe aim of this study was to investigate faecal shedding and transmission ofCampylobacterspp. in cohorts of cattle within a feedlot, to assess subsequent contamination of carcasses with this pathogen and to identify risk factors associated with faecal shedding ofCampylobacterspp. A cohort of 133 heifers housed in four adjacent pens was examined over a five and a half month period, from entering the feedlot to slaughter. A parallel investigation of individual rectal faecal samples and pen environmental samples were taken at monthly intervals from November to February. The entire outer and inner surfaces of a carcass side of each animal were swabbed immediately following slaughter.Campylobacterspp. were isolated from 322 (54%) of the 600 rectal faecal samples.Campylobacter jejuniandC. coliaccounted for 69 and 29.7% of the isolate recovered, respectively. A total of 159 environmental samples were examined, of theseCampylobacterspp. was isolated from 46 samples (29%).Campylobacter jejuniandC. coliaccounted for 35 and 59% of these isolates, respectively.Campylobacterspp. was not isolated from any of the dressed carcasses. Logistic regression indicated prevalence ofCampylobacterspp. faecal shedding within pens was positively correlated to the pen, the month of sampling and theCampylobacterspp. contamination status of the pen dividing bars and the water trough surface.Campylobacterspp. should be considered as a pathogen shed in the faeces of a substantial proportion of feedlot cattle. However, with good hygienic practice during harvest, a very low level of this pathogen can be achieved on dressed carcasses.
Schoolchildren's abilities to frame, understand and successfully manipulate food label information: enabling consumer choice through education
Authors: Stuart Stephen A. , Schröder Monika J.A. , Bower John A. 
Published: October 2010

At a time when the major dialogue in food labelling is directed towards the volume and type of information presented, it is important to understand whether adolescents leaving education have the abilities to comprehend and use the current label as they represent the next generation of consumers.Legislation has been created to protect consumers and to enable them to make informed food choices. Food labels carry a significant volume of mandatory and voluntary information, designed to fulfil a variety of commercial and consumer functions. For these laws to be effective at an individual level, it is important that information is framed correctly, and that people can manipulate the data in an accurate and meaningful manner.In order to optimise food label information consumers require some competence across three different conceptual dimensions: maths, English comprehension, and health and nutrition. Most individuals acquire such skills at school.The pilot research that this paper describes investigates changes in   the   abilities   to   frame,   comprehend   and   manipulate label information, of 19 schoolchildren at one secondary school in Scotland. The main research, to be conducted in 2003, will include over a thousand children from another seven Scottish schools.Statistical analysis indicates that there is a significant improvement in the dimensions of both maths and English comprehension between levels S1 and S5, whilst the health and nutrition dimension does not show such significance.Each dimension has been measured against attitudes towards the use of labels in shopping and cooking to determine if the differences between those who use labels and those who do not are significantThe research also proposes a new method of presenting nutrition information to make it more meaningful to individuals across a wide spectrum of competence by reducing the number of conceptual components required to comprehend it.
Determination of isoprene and α‐/β‐pinene oxidation products in boreal forest aerosols from Hyytiälä, Finland: diel variations and possible link with particle formation events
Authors: Kourtchev I. , Ruuskanen T. M. , Keronen P. , Sogacheva L. , Dal Maso M. , Reissell A. , Chi X. , Vermeylen R. , Kulmala M. , Maenhaut W. , Claeys M. 
Published: October 2010

AbstractBiogenic volatile organic compounds (VOCs), such as isoprene and α‐/β‐pinene, are photo‐oxidized in the atmosphere to non‐volatile species resulting in secondary organic aerosol (SOA). The goal of this study was to examine time trends and diel variations of oxidation products of isoprene and α‐/β‐pinene in order to investigate whether they are linked with meteorological parameters or trace gases. Separate day‐night aerosol samples (PM1) were collected in a Scots pine dominated forest in southern Finland during 28 July–11 August 2005 and analyzed with gas chromatography/mass spectrometry (GC/MS). In addition, inorganic trace gases (SO2, CO, NOx, and O3), meteorological parameters, and the particle number concentration were monitored. The median total concentration of terpenoic acids (i.e., pinic acid, norpinic acid, and two novel compounds, 3‐hydroxyglutaric acid and 2‐hydroxy‐4‐isopropyladipic acid) was 65 ng m−3, while that of isoprene oxidation products (i.e., 2‐methyltetrols and C5 alkene triols) was 17.2 ng m−3. The 2‐methyltetrols exhibited day/night variations with maxima during day‐time, while α‐/β‐pinene oxidation products did not show any diel variation. The sampling period was marked by a relatively high condensation sink, caused by pre‐existing aerosol particles, and no nucleation events. In general, the concentration trends of the SOA compounds reflected those of the inorganic trace gases, meteorological parameters, and condensation sink. Both the isoprene and α‐/β‐pinene SOA products were strongly influenced by SO2, which is consistent with earlier reports that acidity plays a role in SOA formation. The results support previous proposals that oxygenated VOCs contribute to particle growth processes above boreal forest.
Why plant volatile analysis needs bioinformatics – detecting signal from noise in increasingly complex profiles
Authors: Van Dam N. M. , Poppy G. M. 
Published: October 2010

AbstractPlant volatile analysis may be the oldest form of what now is called plant “metabolomic” analysis. A wide array of volatile organic compounds (VOCs), such as alkanes, alcohols, isoprenoids, and esters, can be collected simultaneously from the plant headspace, either within the laboratory or in the field. Increasingly faster and more sensitive analysis techniques allow detection of an ever‐growing number of compounds in decreasing concentrations. However, the myriads of data becoming available from such experiments do not automatically increase our ecological and evolutionary understanding of the roles these VOCs play in plant‐insect interactions. Herbivores and parasitoids responding to changes in VOC emissions are able to perceive minute changes within a complex VOC background. Plants modified in genes involved in VOC synthesis may be valuable for the evaluation of changes in plant‐animal interactions compared to tests with synthetic compounds, as they allow changes to be made within the context of a more complex profile. We argue that bioinformatics is an essential tool to integrate statistical analysis of plant VOC profiles with insect behavioural data. The implementation of statistical techniques such as multivariate analysis (MVA) and meta‐analysis is of the utmost importance to interpreting changes in plant VOC mixtures. MVA focuses on differences in volatile patterns rather than in single compounds. Therefore, it more closely resembles the information processing in insects that base their behavioural decisions on differences in VOC profiles between plants. Meta‐analysis of different datasets will reveal general patterns pertaining to the ecological role of VOC in plant‐insect interactions. Successful implementation of bioinformatics in VOC research also includes the development of MVA that integrate time‐resolved chemical and behavioural analyses, as well as databases that link plant VOCs to their effects on insects.
Modeling volatile isoprenoid emissions – a story with split ends
Authors: Grote R. , Niinemets Ü. 
Published: October 2010

AbstractAccurate prediction of plant‐generated volatile isoprenoid fluxes is necessary for reliable estimation of atmospheric ozone and aerosol formation potentials. In recent years, significant progress has been made in understanding the environmental and physiological controls on isoprenoid emission and in scaling these emissions to canopy and landscape levels. We summarize recent developments and compare different approaches for simulating volatile isoprenoid emission and scaling up to whole forest canopies with complex architecture. We show that the current developments in modeling volatile isoprenoid emissions are “split‐ended” with simultaneous but separated efforts in fine‐tuning the empirical emission algorithms and in constructing process‐based models. In modeling volatile isoprenoid emissions, simplified leaf‐level emission algorithms (Guenther algorithms) are highly successful, particularly after scaling these models up to whole regions, where the influences of different ecosystem types, ontogenetic stages, and variations in environmental conditions on emission rates and dynamics partly cancel out. However, recent experimental evidence indicates important environmental effects yet unconsidered and emphasize, the importance of a highly dynamic plant acclimation in space and time. This suggests that current parameterizations are unlikely to hold in a globally changing and dynamic environment. Therefore, long‐term predictions using empirical algorithms are not necessarily reliable. We show that process‐based models have large potential to capture the influence of changing environmental conditions, in particular if the leaf models are linked with physiologically based whole‐plant models. This combination is also promising in considering the possible feedback impacts of emissions on plant physiological status such as mitigation of thermal and oxidative stresses by volatile isoprenoids. It might be further worth while to incorporate main features of these approaches in regional empirically‐based emission estimations thereby merging the “split ends”.
Foliar limonene uptake scales positively with leaf lipid content: “non‐emitting” species absorb and release monoterpenes
Authors: Noe S. M. , Copolovici L. , Niinemets Ü. , Vaino E. 
Published: October 2010

AbstractMonoterpenes synthesized and released by emitting vegetation can be taken up by neighboring non‐emitting plants, but the uptake capacity of non‐emitting species has not been studied extensively. We investigated the foliar uptake potential of the hydrophobic monoterpene limonene in 13 species of contrasting leaf structure and lipid content to determine the structural and chemical controls of monoterpene uptake. Leaf dry mass per unit area (MA,D) varied 6.5‐fold, dry to fresh mass ratio (DF) 2.7‐fold, lipid content per dry mass (LM) 2.5‐fold and per unit area (LA) 4.6‐fold across the studied species. Average foliar limonene uptake rate (UA) from air at saturating limonene partial pressures varied from 0.9 to 6 nmol m−2 s−1, and limonene leaf to air partition coefficient (KFA, ratio of limonene content per dry mass to limonene partial pressure) from 0.7 to 6.8 μmol kg−1 Pa−1. UA and KFA scaled positively with leaf lipid content, and were independent of DF, indicating that variation in leaf lipid content was the primary determinant of species differences in monoterpene uptake rate and KFA. Mass‐based limonene uptake rates further suggested that thinner leaves with greater surface area per unit dry mass have higher uptake rates. In addition, limonene lipid to air partition coefficient (KLA = KFA/LM) varied 19‐fold, indicating large differences in limonene uptake capacity at common leaf lipid content. We suggest that the significant uptake of hydrophobic monoterpenes when monoterpene ambient air concentration is high and release when the concentration is low should be included in large‐scale monoterpene emission models.
Fluid dynamical niches of phytoplankton types
Authors: d’Ovidio Francesco , De Monte Silvia , Alvain Séverine , Dandonneau Yves , Lévy Marina 
Published: October 2010

The biogeochemical role of phytoplanktonic organisms strongly varies from one plankton type to another, and their relative abundance and distribution have fundamental consequences at the global and climatological scales. In situ observations find dominant types often associated to specific physical and chemical water properties. However, the mechanisms and spatiotemporal scales by which marine ecosystems are organized are largely not known. Here we investigate the spatiotemporal organization of phytoplankton communities by combining multisatellite data, notably high-resolution ocean-color maps of dominant types and altimetry-derived Lagrangian diagnostics of the surface transport. We find that the phytoplanktonic landscape is organized in (sub-)mesoscale patches (10–100 km) of dominant types separated by physical fronts induced by horizontal stirring. These physical fronts delimit niches supported by water masses of similar history and whose lifetimes are comparable with the timescale of the bloom onset (few weeks). The resonance between biological activity and physical processes suggest that the spatiotemporal (sub-)mesoscales associated to stirring are determinant in the observation and modeling of marine ecosystems.
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome
Authors: Armache Jean-Paul , Jarasch Alexander , Anger Andreas M. , Villa Elizabeth , Becker Thomas , Bhushan Shashi , Jossinet Fabrice , Habeck Michael , Dindar Gülcin , Franckenberg Sibylle , Marquez Viter , Mielke Thorsten , Thomm Michael , Berninghausen Otto , Beatrix Birgitta , Söding Johannes , Westhof Eric , Wilson Daniel N. , Beckmann Roland 
Published: October 2010

Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than their bacterial counterparts due in part to the presence of 80 r proteins rather than 54 in bacteria. Using cryoelectron microscopy reconstructions of a translating plant (
Triticum aestivum
) 80S ribosome at 5.5-Å resolution, together with a 6.1-Å map of a translating
Saccharomyces cerevisiae
80S ribosome, we have localized and modeled 74/80 (92.5%) of the ribosomal proteins, encompassing 12 archaeal/eukaryote-specific small subunit proteins as well as the complete complement of the ribosomal proteins of the eukaryotic large subunit. Near-complete atomic models of the 80S ribosome provide insights into the structure, function, and evolution of the eukaryotic translational apparatus.
Crystal structure of prethrombin-1
Authors: Chen Zhiwei , Pelc Leslie A. , Di Cera Enrico 
Published: October 2010

Prothrombin is the zymogen precursor of the clotting enzyme thrombin, which is generated by two sequential cleavages at R271 and R320 by the prothrombinase complex. The structure of prothrombin is currently unknown. Prethrombin-1 differs from prothrombin for the absence of 155 residues in the N-terminal domain and is composed of a single polypeptide chain containing fragment 2 (residues 156–271), A chain (residues 272–320), and B chain (residues 321–579). The X-ray crystal structure of prethrombin-1 solved at 2.2-Å resolution shows an overall conformation significantly different (rmsd = 3.6
Å
) from that of its active form meizothrombin desF1 carrying a cleavage at R320. Fragment 2 is rotated around the
y
axis by 29° and makes only few contacts with the B chain. In the B chain, the oxyanion hole is disrupted due to absence of the I16-D194 ion pair and the Na
+
binding site and adjacent primary specificity pocket are highly perturbed. A remarkable feature of the structure is that the autolysis loop assumes a helical conformation enabling W148 and W215, located 17 Å apart in meizothrombin desF1, to come within 3.3 Å of each other and completely occlude access to the active site. These findings suggest that the zymogen form of thrombin possesses conformational plasticity comparable to that of the mature enzyme and have significant implications for the mechanism of prothrombin activation and the zymogen → protease conversion in trypsin-like proteases.
Reassessing the Role of N-Hydroxytryptamine in Auxin Biosynthesis
Authors: Tivendale Nathan D. , Davies Noel W. , Molesworth Peter P. , Davidson Sandra E. , Smith Jason A. , Lowe Edwin K. , Reid James B. , Ross John J. 
Published: October 2010

Abstract
The tryptamine pathway is one of five proposed pathways for the biosynthesis of indole-3-acetic acid (IAA), the primary auxin in plants. The enzymes AtYUC1 (Arabidopsis thaliana), FZY (Solanum lycopersicum), and ZmYUC (Zea mays) are reported to catalyze the conversion of tryptamine to N-hydroxytryptamine, putatively a rate-limiting step of the tryptamine pathway for IAA biosynthesis. This conclusion was based on in vitro assays followed by mass spectrometry or HPLC analyses. However, there are major inconsistencies between the mass spectra reported for the reaction products. Here, we present mass spectral data for authentic N-hydroxytryptamine, 5-hydroxytryptamine (serotonin), and tryptamine to demonstrate that at least some of the published mass spectral data for the YUC in vitro product are not consistent with N-hydroxytryptamine. We also show that tryptamine is not metabolized to IAA in pea (Pisum sativum) seeds, even though a PsYUC-like gene is strongly expressed in these organs. Combining these findings, we propose that at present there is insufficient evidence to consider N-hydroxytryptamine an intermediate for IAA biosynthesis.
C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism
Authors: de Oliveira Dal’Molin Cristiana Gomes , Quek Lake-Ee , Palfreyman Robin William , Brumbley Stevens Michael , Nielsen Lars Keld 
Published: October 2010

AbstractLeaves of C4 grasses (such as maize [Zea mays], sugarcane [Saccharum officinarum], and sorghum [Sorghum bicolor]) form a classical Kranz leaf anatomy. Unlike C3 plants, where photosynthetic CO2 fixation proceeds in the mesophyll (M), the fixation process in C4 plants is distributed between two cell types, the M cell and the bundle sheath (BS) cell. Here, we develop a C4 genome-scale model (C4GEM) for the investigation of flux distribution in M and BS cells during C4 photosynthesis. C4GEM, to our knowledge, is the first large-scale metabolic model that encapsulates metabolic interactions between two different cell types. C4GEM is based on the Arabidopsis (Arabidopsis thaliana) model (AraGEM) but has been extended by adding reactions and transporters responsible to represent three different C4 subtypes (NADP-ME [for malic enzyme], NAD-ME, and phosphoenolpyruvate carboxykinase). C4GEM has been validated for its ability to synthesize 47 biomass components and consists of 1,588 unique reactions, 1,755 metabolites, 83 interorganelle transporters, and 29 external transporters (including transport through plasmodesmata). Reactions in the common C4 model have been associated with well-annotated C4 species (NADP-ME subtypes): 3,557 genes in sorghum, 11,623 genes in maize, and 3,881 genes in sugarcane. The number of essential reactions not assigned to genes is 131, 135, and 156 in sorghum, maize, and sugarcane, respectively. Flux balance analysis was used to assess the metabolic activity in M and BS cells during C4 photosynthesis. Our simulations were consistent with chloroplast proteomic studies, and C4GEM predicted the classical C4 photosynthesis pathway and its major effect in organelle function in M and BS. The model also highlights differences in metabolic activities around photosystem I and photosystem II for three different C4 subtypes. Effects of CO2 leakage were also explored. C4GEM is a viable framework for in silico analysis of cell cooperation between M and BS cells during photosynthesis and can be used to explore C4 plant metabolism.