bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viruses in freshwater ecosystems: an introduction to the exploration of viruses in new aquatic habitats
Authors: MIDDELBOE MATHIAS , JACQUET STÉPHAN , WEINBAUER MARKUS 
Published: May 2008

Summary1. Viruses have become widely recognized as the most abundant biological entities and important players in aquatic environments, and this realization has profoundly changed our conceptual understanding of the functioning and regulation of aquatic ecosystems in the last two decades. However, most of this research has focussed on marine viruses, especially in pelagic environments.2. Here we introduce a special issue of Freshwater Biology dealing with viruses in freshwater ecosystems. It represents the first attempt to summarize progress in freshwater viral ecology made by diverse research groups and to direct attention of viral ecologists towards fresh waters.3. Six review‐type articles and ten original research papers cover a wide range of aspects of freshwater viral ecology. This includes reports on the distribution of freshwater viral communities in contrasting habitats (e.g. sediments, wetlands, littoral zone, open waters), on different roles of viruses in freshwater ecosystems (e.g. mortality rates of bacteria and phytoplankton, transduction, influence on bacterial diversity and organic matter), and on different types of viruses (bacteriophages, cyanophages, algal viruses, and a fish‐pathogenic virus).4. Collectively the series of papers presented in this special issue indicates that freshwater environments cover great habitat diversity and that the significance of some of the mechanisms controlling viral dynamics and impacts may differ between freshwater and marine habitats.
Stereotomography assisted by migration of attributes
Authors: Nguyen Sylvain , Baina Reda , Alerini Mathias , Lambaré Gilles , Devaux Vincent , Noble Mark 
Published: May 2008

ABSTRACTDepth velocity model building remains a difficult step within the seismic depth imaging sequence. Stereotomography provides an efficient solution to this problem but was limited until now to a picking of seismic data in the prestack time un‐migrated domain. We propose here a method for stereotomographic data picking in the depth migrated domain. Picking in the depth migrated domain exhibits the advantage of a better signal‐to‐noise ratio and of a more regular distribution of picked events in the model, leading to a better constrained tomographic inverse problem. Moreover, any improvement on the velocity model will improve the migrated results, again leading to improved picking. Our strategy for obtaining a stereotomographic dataset from a prestack depth migration is based on migration of attributes (and not on a kinematic demigration approach!). For any locally coherent event in the migrated image, migration of attributes allows one to compute ray parameter attributes corresponding to the specular reflection angle and dip. For application to stereotomography, the necessary attributes are the source/receiver locations, the traveltime and the data slopes. For the data slope, when the migration velocity model is erroneous, some additional corrections have to be applied to the result of migration of the attributes. Applying these corrections, our picking method is theoretically valid whatever the quality of the migration velocity model. We first present the theoretical aspects of the method and then validate it on 2D synthetic and real seismic reflection data sets.
Seismic scale saturation relations in turbidite reservoirs undergoing waterflood
Authors: MacBeth Colin , Stephen Karl 
Published: May 2008

ABSTRACTEstimates of the effective fluid modulus from seismic cannot be directly converted to the true pore‐volume weighted mean saturation determined from fluid flow principles by using the saturation laws currently in use. One of the reasons is that seismic waves sample the reservoir geology and production induced saturation heterogeneity in a different way from the fluids. This mismatch prevents accurate quantitative evaluation of saturation changes from 4D seismic analysis. To tackle this problem, a reservoir‐related saturation law is developed for a turbidite reservoir – this geology being chosen because the architecture for a single sand package can be modelled as a stack of horizontal beds. An effective medium and perturbation theory are applied to the determination of the seismic properties of this model. This calculation provides a relationship that connects the true saturation to the effective fluid modulus from seismic via statistical measures of the vertical spread of the porosity and saturation variations in the reservoir. These statistics can be extracted from the simulation model and if known, enable the new saturation law to deliver a significant improvement in accuracy when estimating compared to other well‐known laws. The relationship that has been developed also captures the effect of inter‐bedded shales and can therefore be used to estimate true saturation in regions of the reservoir with moderate to low net‐to‐gross, provided the fraction of the shale component is known. In practice, the final choice of saturation law depends upon the reservoir information available, the assumptions that can be tolerated and the accuracy required in any particular reservoir characterization study.
Gpr83 expression is not required for the maintenance of intestinal immune homeostasis and regulation of T‐cell‐dependent colitis
Authors: Toms Christy , Jessup Heidi , Thompson Claire , Baban Dilair , Davies Kay , Powrie Fiona 
Published: May 2008

SummaryRegulatory T (TR) cells are integral to the maintenance of intestinal homeostasis, where an intricate balance between tolerance and immunity must be maintained. Recently, studies have focused on the identification of molecules involved in the function and/or development of TR cells. One such molecule, the G‐protein coupled receptor Gpr83, has been identified through gene expression analysis as being overexpressed within thymic and peripheral naturally arising regulatory T (nTR) cell populations. The aim of this study was to further define the characteristics of Gpr83 expression and to investigate the role of Gpr83 in TR‐cell development and function through the generation and analysis of Gpr83‐deficient mice. Following activation, naïve CD4+ T cells induce Gpr83 expression in a transforming growth factor (TGF)‐β dependent manner. Rather than being a general marker of activation, Gpr83 expression could only be detected in cells also expressing forkhead/winged helix transcription factor (Foxp3), further supporting the association of Gpr83 with the regulatory cell phenotype. Mice deficient in Gpr83 expression developed normally and did not display signs of inflammatory disease. Thymic nTR‐cell development was unaffected by a lack of Gpr83 expression and peripheral nTR‐cell homeostasis was normal when compared with that of wild‐type mice. Gpr83 expression was dispensable for the regulatory activity of nTR cells as Gpr83‐deficient nTR cells could suppress the development of disease in a T‐cell transfer model of colitis. These results suggest a redundant role for Gpr83 in the function of TR cells in this model of disease. Further studies are required to determine the role of Gpr83 in TR‐cell biology.
Environmental stresses induce the expression of putative glycine‐rich insect cuticular protein genes in adult Leptinotarsa decemlineata (Say)
Authors: Zhang J. , Goyer C. , Pelletier Y. 
Published: May 2008

AbstractThe deposition of cuticular proteins in insects usually occurs during the moulting process. Three putative glycine‐rich insect cuticular proteins, Ld‐GRP1 to 3, were identified and characterized from the Colorado potato beetle, Leptinotarsa decemlineata. The Ld‐GRPs contained conserved GXGX and/or GGXG sequence repeats. Ld‐GRP1 also contained a conserved AAPA/V motif commonly found in cuticular proteins. The transcripts of Ld‐GRP1 and Ld‐GRP2 were detected in the epidermal cell layer by in situ hybridization, making them putative insect cuticular proteins. The putative cuticular protein genes were highly induced by the insecticide azinphosmethyl (organophosphorous) 2–3 weeks after adult moulting. Putative cuticular protein gene expression level was higher in azinphosmethyl‐resistant beetles than in susceptible beetles. Furthermore, two of the putative cuticular protein genes were highly induced by dry environmental conditions. These results suggest that the insect might increase cuticular component deposition in the adult stage in response to environmental stresses. This ability may allow the insect to adapt to new or changing environments.
Molecular cloning, partial genomic structure and functional characterization of succinic semialdehyde dehydrogenase genes from the parasitic insectsLucilia cuprinaandCtenocephalides felis
Authors: Rothacker B. , Werr M. , Ilg T. 
Published: May 2008

AbstractThe enzyme succinic semialdehyde dehydrogenase (SSADH; EC1.2.1.24) is a component of the γ‐aminobutyric acid degradation pathway in mammals and is essential for development and function of the nervous system. Here we report the identification, cDNA cloning and functional expression of SSADH from the parasitic insectsLucilia cuprinaandCtenocephalides felis. The recombinant proteins possess potent NAD+‐dependent SSADH activity, while their catalytic efficiency for other aldehyde substrates is lower. A genomic copy of theL. cuprinaSSADH gene contains two introns, while a genomic gene version ofC. felisis devoid of introns. In contrast to the single copy SSADH genes inDrosophila melanogasterand mammals, inL. cuprinaandC. felis, multiple SSADH gene copies are present in the genome.
Global and comparative protein profiles of the pronotum of the southern pine beetle, Dendroctonus frontalis
Authors: Pechanova O. , Stone W. D. , Monroe W. , Nebeker T. E. , Klepzig K. D. , Yuceer C. 
Published: May 2008

AbstractThe southern pine beetle (Dendroctonus frontalis Zimmermann) kills all pines within its range and is among the most important forest pest species in the US. Using a specialized mycangium surrounded by gland cells in the pronotum, adult females culture, transport, and inoculate two fungi into beetle galleries during oviposition. These fungal symbionts, to varying degrees, exclude antagonistic fungi and provide nutrients to larvae. However, the mechanisms (e.g. secreted antibiotic chemicals or nutrients, proteins or pathways) by which this relationship is maintained are not known. Here we present the first global and differential proteome profile of the southern pine beetle pronotum. Two‐dimensional polyacrylamide electrophoresis, tandem mass spectrometry, and database searches revealed that the majority of pronotal proteins were related to energy‐yielding metabolism, contractile apparati, cell structure, and defence. The identified proteins provide important insights into the molecular and biochemical processes of, and candidates for functional genomics to understand mycangia and pronotum functions in, the southern pine beetle.
The constituents of Microctonus sp. parasitoid venoms
Authors: Crawford A. M. , Brauning R. , Smolenski G. , Ferguson C. , Barton D. , Wheeler T. T. , Mcculloch A. 
Published: May 2008

AbstractPurified RNA transcripts from venom glands dissected from the parasitoid wasp Microctonus hyperodae were copied, cloned and sequenced using traditional dideoxy sequencing methods. Using mass spectrometry analysis of the trypsinised PAGE gel protein bands we identified the RNA transcripts for the 3 most abundant proteins found in the venom and hence obtained their full protein sequence. Other abundant transcripts were also further sequenced. To reduce the effort required to obtain transcript information we dissected venom glands from a second parasitoid, Microctonus aethiopoides (Morocco biotype). The RNA transcripts were purified and reverse transcribed but instead of cloning the cDNA it was directly sequenced using Roche GS20 pyrosequencing. Results from a single GS20 sequencing run provided data similar to that obtained by the traditional methods used in analysing transcripts from M. hyperodae in a fraction of the time and cost. Comparing the transcripts between the two species showed that a similar range of genes are expressed with the putative orthologs of seven of the eight full length genes characterised from M. hyperodae being found in M. aethiopoides. Pyrosequencing should provide a valuable new method for rapidly sampling transcripts from a wide range of specialised insect tissues.
Characterization of the antimicrobial peptide attacin loci from Glossina morsitans
Authors: Wang J. , Hu C. , Wu Y. , Stuart A. , Amemiya C. , Berriman M. , Toyoda A. , Hattori M. , Aksoy S. 
Published: May 2008

AbstractThe antimicrobial peptide Attacin is an immune effector molecule that can inhibit the growth of gram‐negative bacteria. In Glossina morsitans morsitans, which serves as the sole vectors of African trypanosomes, Attacins also play a role in trypanosome resistance, and in maintaining parasite numbers at homeostatic levels in infected individuals. We characterized the attacin encoding loci from a Bacterial Artificial Chromosome (BAC) library. The attacin genes are organized into three clusters. Cluster 1 contains two attacin (attA) genes located in head‐to‐head orientation, cluster 2 contains two closely related genes (attA and attB) located in a similar transcriptional orientation, and cluster 3 contains a single attacin gene (attD). Coding and transcription regulatory sequences of attA and attB are nearly identical, but differ significantly from attD. Putative AttA and AttB have signal peptide sequences, but lack the pro domain typically present in insect Attacins. Putative AttD lacks both domains. Analysis of attacin cDNA sequences shows polymorphisms that could arise either from allelic variations or from the presence of additional attacin genomic loci. Real time‐PCR analysis reveals that attA and attB expression is induced in the fat body of flies per os challenged with Escherichia coli and parasitized with trypanosomes. In the midgut, expression of these attacins is similarly induced following microbial challenge, but reduced in response to parasite infections. Transcription of AttD is significantly less relative to the other two genes, and is preferentially induced in the fat body of parasitized flies. These results indicate that the different attacin genes may be differentially regulated.
Structure and physicochemical properties of defatted and pin‐milled oat bran concentrate fractions separated by air‐classification4
Authors: Stevenson David G. , Eller Fred J. , Jane Jay‐lin , Inglett George E. 
Published: May 2008

SummaryOat bran concentrate (OBC) was defatted by supercritical carbon dioxide, pin‐milled and air‐classified into five fractions (<15, 15–18, 18–24, 24–30 and > 30 μm). β‐glucan content (% dry weight) of defatted OBC, its subsequent pin‐milling and the air‐classified fractions in ascending particle size was 14.3, 17.0, 4.3, 5.8, 12.6, 14.7 and 22.4, respectively. High‐performance size‐exclusion chromatography equipped with multi‐angle laser‐light scattering and refractive index detectors showed that amylopectin was the predominant molecule present in all OBC powders but was present in greater concentration in fractions collected that were < 24 μm. Fractions >24 μm, which had the highest β‐glucan contents had higher starch gelatinisation temperatures (measured using differential scanning calorimeter), and had substantially higher peak, breakdown, final and setback paste viscosity (measured using Rapid Visco Analyser, Foss North America, Eden Prairie, MN, USA) compared with the other lower‐β‐glucan containing fractions. No differences in water retention of 25% (w/w) oat powders in water (measured using thermogravimetric analyser) were observed among defatted OBC, its subsequent pin‐milling and the five fractions separated by air‐classification. In particular, differences in pasting properties show that defatted, pin‐milled OBC that is fractionated by air‐classification will have different food applications depending on particle size collected.
Technological effect of red grape antioxidant dietary fibre added to minced fish muscle
Authors: Sánchez‐Alonso Isabel , Borderías Antonio Javier 
Published: May 2008

SummaryThe aim was to study the effect, over 6 months in frozen storage, of addition of grape antioxidant dietary fibre (GADF) to horse mackerel (Trachurus trachurus) minced muscle (MFM) as a technological ingredient. Concentrations of 0, 2 and 4% GADF were added to MFM samples. Protein solubility, water retention, colour, mechanical properties, lipid oxidation and sensory analyses were carried out immediately after preparation of samples and during and after storage at −20° C. Bound water after thawing and cooking minced samples was proportional to the amount of GADF used. Mechanical properties indicated softness and loss of cohesiveness depending on the amount of GADF. There was inhibition of lipid oxidation during frozen storage when GADF was added. Chemical, physical and sensory analyses suggest that GADF is a highly active technological ingredient in frozen dark minced fish.
Production of black rice cake using ground black rice and medium‐grain brown rice
Authors: Lee Jin‐Cheol , Kim Jong‐Dae , Hsieh Fu‐hung , Eun Jong‐Bang 
Published: May 2008

SummaryPuffed rice cakes were produced from a blend of ground black rice (GBR) and medium‐grain brown rice (GMBR) by using a rice cake machine. Effects of moisture content, heating temperature and heating time on quality of the black rice cake were investigated. The specific volume of black rice cakes showed an increasing trend with increasing tempering moisture, heating temperature and heating time. The hardness of puffed black rice cake decreased as tempering moisture and heating time increased, and was influenced more by GMBR content than heating temperature. In general, the black rice cake lightness and yellowness decreased steadily with increasing GBR content, while tempering moisture, heating temperature and heating time did not significantly affect the colours of black rice cake. On the contrary, the redness increased with increasing GBR contents. The weight loss during tumbling was not found at all puffing conditions.
Detection and quantification of palm mid‐fraction in a chocolate model system
Authors: Moazami Farahany Elham , Selamat Jinap , Che Man Yakoob Bin , Idris Nor Aini 
Published: May 2008

SummaryThe tocopherol and tocotrienol compositions of the genuine cocoa butter (CB) and palm mid‐fraction (PMF) were investigated to introduce a more reliable indicator in detecting PMF in CB. The results suggested that the α‐tocotrienol data presented could be utilised for the detection of the PMF admixture to CB. The PMF was added to CB at different levels. HPLC was used to detect the presence of PMF admixture to CB using α‐tocotrienol as an indicator. The results derived from the model system indicated that increasing the PMF amount at 0–15% to CB resulted in an increase in the concentration of the α‐tocotrienol significantly (P < 0.05). The addition of PMF amount more than 15% did not have any effect on the α‐tocotrienol concentration. A linear plot with a high correlation of 0.9967 was obtained with SE of 1.527. The high correlation obtained indicated good accuracy, reflecting a close relationship between experimental and theoretical predicted value.
Chemical and microbial quality indexes of Norwegian lobsters (Nephrops norvegicus) dusted with sulphites
Authors: Martínez‐Álvarez Óscar , Gómez‐Guillén María del Carmen , Montero Pilar 
Published: May 2008

SummaryThe effect of dusting with a commercial sulphite‐based anti‐melanosis formulation on several chemical quality indexes of Norwegian lobsters (Nephrops norvegicus) was evaluated and compared with a control batch during chilled storage. Dusting with 6% of the commercial product did not exceed the SO2 residual levels permitted by the EU Directive and by the Food and Drug Administration. The additive retarded successfully the occurrence of black spots on the crustacean surface for at least 7 days and also bleached the samples. The prior addition of the sulphite‐based compound did not affect either muscle pH or total volatile basic nitrogen content during storage, although it did produce increased lipid oxidation. The protease activity decreased, and differences in the pool composition of proteases were observed, so serine and cysteine protease activities showing an increase. Finally, the sulphite‐based compound delayed agmatine production and exerted an antimicrobial effect on H2S producers and Enterobacteriaceae.
A basic/hydrophobic cleft of the T4 activator MotA interacts with the C‐terminus of E. coli	σ70 to activate middle gene transcription
Authors: Bonocora Richard P. , Caignan Gregori , Woodrell Christopher , Werner Milton H. , Hinton Deborah M. 
Published: May 2008

SummaryTranscriptional activation often employs a direct interaction between an activator and RNA polymerase. For activation of its middle genes, bacteriophage T4 appropriates Escherichia coli RNA polymerase through the action of two phage‐encoded proteins, MotA and AsiA. Alone, AsiA inhibits transcription from a large class of host promoters by structurally remodelling region 4 of σ70, the primary specificity subunit of E. coli RNA polymerase. MotA interacts both with σ70 region 4 and with a DNA element present in T4 middle promoters. AsiA‐induced remodelling is proposed to make the far C‐terminus of σ70 region 4 accessible for MotA binding. Here, NMR chemical shift analysis indicates that MotA uses a ‘basic/hydrophobic’ cleft to interact with the C‐terminus of AsiA‐remodelled σ70, but MotA does not interact with AsiA itself. Mutations within this cleft, at residues K3, K28 and Q76, both impair the interaction of MotA with σ70 region 4 and MotA‐dependent activation. Furthermore, mutations at these residues greatly decrease phage viability. Most previously described activators that target σ70 directly use acidic residues to engage a basic surface of region 4. Our work supports accumulated evidence indicating that ‘σ appropriation’ by MotA and AsiA uses a fundamentally different mechanism to activate transcription.
In vitro characterization of a carotenoid cleavage dioxygenase from Nostoc sp. PCC 7120 reveals a novel cleavage pattern, cytosolic localization and induction by highlight
Authors: Scherzinger Daniel , Al‐Babili Salim 
Published: May 2008

SummaryCarotenoid oxygenases catalyse the cleavage of C‐C double bonds forming apocarotenoids, a diverse group of compounds, including retinoids and the precursors of some phytohormones. Some apocarotenoids, like β‐ionone (C13), are ecologically important volatiles released by plants and cyanobacteria. In this work, we elucidated the activity of the Nostoccarotenoid cleavage dioxygenase (NosCCD, previously named NSC1) using synthetic and cyanobacterial substrates. NosCCD converted bicyclic and monocyclic xanthophylls, including myxoxanthophylls, glycosylated carotenoids that are essential for thylakoid and cell wall structure. The products identified revealed two different cleavage patterns. The first is observed with bicyclic xanthophylls and is identical with that of plant orthologues, while the second is novel and occurs upon cleavage of monocyclic substrates at the C9‐C10 and C7′‐C8′ double bonds. These properties enable the enzyme to produce a plenitude of different C10 and C13 apocarotenoids. Expression analyses indicated a role of NosCCD in response to highlight stress. Western blot analyses of Nostoc cells revealed NosCCD as a soluble enzyme in the cytosol, which also accomodates NosCCD substrates. Incubation of the corresponding fraction with synthetic substrates revealed the activity of the native enzyme and confirmed its induction by highlight.