bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transport and settlement mechanisms of larval stone flounder, Kareius bicoloratus, into nursery grounds
Authors: YAMASHITA YOH , TSURUTA YOSHINARI , YAMADA HIDEAKI 
Published: October 2007

ABSTRACTThe transport mechanism of stone flounder,Kareius bicoloratus, larvae from the central area of Sendai Bay to inshore areas and their settlement in shallow nursery grounds during winter‐early spring were studied in 1991 and 1992. Stone flounder eggs were abundant in the central area of Sendai Bay at depths of 25–50 m, and their larvae are thought to be transported inshore by warm offshore waters entering into the Bay through its central part. Settling larvae consisted primarily of stages G through I1. These stages correspond to the metamorphosing period and showed behaviour related to selective tidal‐stream transport, occurring on and near the bottom during the daytime and ascending at night, especially on flood tides, enabling migration to inshore and estuarine nursery habitats. This diel vertical migration is also considered to play an important role in avoiding predation by diurnal piscivorous fishes and nocturnal benthic sand shrimp. Settling flounder were abundant in deeper waters in February, and with inshore movement, densities peaked in late March in estuaries. In exposed inshore areas of Sendai Bay with no easily accessible estuaries, settling and settled flounder concentrated in inshore areas at depths of around 10 m. The mechanisms by which selective tidal‐stream transport occurs are discussed.
The Bering Sea Green Belt: shelf‐edge processes and ecosystem production
Authors: SPRINGER ALAN M. , McROY C. PETER , FLINT MIKHAIL V. 
Published: October 2007

ABSTRACTThe concept of a highly productive habitat, or Green Belt, along the edge of the continental shelf in the Bering Sea is based upon compelling but fragmentary and often anecdotal observations of a variety of physical and biological features acquired from many sources over many years. Enhanced production at continental margins is not a novel concept, but in the case of the Bering Sea its importance has been overlooked during studies of the unusually broad continental shelf. The limited data reported from the vicinity of the shelf edge in the Bering Sea indicate that annual primary production can be as high as 175 to 275 g C m˜ year‐, or approximately 60% greater than production in the adjacent outer shelf domain and 270% greater than in the oceanic domain. Estimates of annual secondary production at the eastern shelf edge also average approximately 60% higher than estimates for the outer domain and 260% higher than those for the oceanic domain. Physical processes at the shelf edge, such as intensive tidal mixing and transverse circulation and eddies in the Bering Slope Current, bring nutrients into the euphoric zone and contribute to enhanced primary and secondary production and elevated biomass of phytoplankton and zooplankton. Fishes and squids concentrate in this narrow corridor because of favourable feeding conditions and because of a thermal refuge from cold shelf‐bottom temperatures that can be found at the shelf edge from fall to spring. The abundance of zooplankton, fishes and squids, in turn, attracts large numbers of marine birds and mammals. In aggregate, the observations suggest that sustained primary productivity, intense food web exchange and high transfer efficiency at the shelf edge are important to biomass yield at numerous trophic levels and to ecosystem production of the Bering Sea.
Effects of pheasant management on vegetation and birds in lowland woodlands
Authors: Draycott Roger A. H. , Hoodless Andrew N. , Sage Rufus B. 
Published: October 2007

Summary

Releasing pheasants in woodlands for game shooting is a widespread practice in the British countryside. Apart from changes to ground flora in woodland release pens, the effects of pheasant releasing on woodland biodiversity are poorly understood.
We surveyed 159 lowland broad‐leaved woods in southern and eastern England during spring–summer 2004 to determine the impact of pheasant management on vegetation structure and composition and on bird populations. Eighty‐one of the woods contained pheasant release pens with annual releases of pheasants and associated gamebird management such as supplementary feeding in winter. In the remaining 78 woods there had been no pheasant management for at least 25 years.
We found that the pheasant‐managed woods had a more open structure, with between 2% and 7% less canopy cover and a denser field layer with between 5% and 58% more ground vegetation cover, including grasses and bramble Rubus fruticosus.
We recorded approximately 40% more birds in woods in southern England and between 22% and 32% more birds were observed in pheasant‐managed woods than control woods. Woodpigeons and warblers were more abundant in pheasant‐managed woods.
Synthesis and applications: We conclude that the impacts of pheasant releasing on vegetation structure and bird communities in woodlands are benign or positive. This study demonstrates that some aspects of woodland management for pheasants, including reducing the extent of canopy cover can encourage growth of understorey vegetation which helps create favourable conditions for some woodland bird species.
Cognitive‐behavioural treatment for men with intellectual disabilities and sexually abusive behaviour: a pilot study
Authors: Murphy Glynis , Powell Simon , Guzman Ana‐Maria , Hays Sarah‐Jane 
Published: October 2007

AbstractBackground  Cognitive‐behaviour therapy (CBT) seems to be becoming the treatment of choice for non‐disabled sex offenders. Nevertheless, there have been relatively few evaluations of such treatment for men with intellectual disabilities (ID) and sexually abusive behaviour.Method  A pilot study providing CBT for two groups of men with ID is described. Measures of change in sexual knowledge, victim empathy and cognitive distortions were collected, together with a log of further sexually abusive behaviour.Results  Fifteen men were offered treatment but some dropped out and some declined to take part in the research. The results for the eight men who consented to the research and completed treatment showed significant positive changes in sexual knowledge and victim empathy (two men completed both groups, making 10 sets of data in all). Cognitive distortions showed significant change on only one of the two measures. Some men showed further sexually abusive behaviour either during or after the treatment group (all had been previously diagnosed as on the autistic spectrum).Conclusion  There is a need for a larger multi‐site trial of treatment with a broad set of measures and the ability to analyse who benefits from such treatments and who does not.
Dual‐mode reflectance and fluorescence near‐video‐rate confocal microscope for architectural, morphological and molecular imaging of tissue
Authors: CARLSON ALICIA L. , COGHLAN LEZLEE G. , GILLENWATER ANN M. , RICHARDS‐KORTUM REBECCA R. 
Published: October 2007

SummaryWe have developed a near‐video‐rate dual‐mode reflectance and fluorescence confocal microscope for the purpose of imaging ex vivo human specimens and in vivo animal models. The dual‐mode confocal microscope (DCM) has light sources at 488, 664 and 784 nm, a frame rate of 15 frames per second, a maximum field of view of 300 × 250 μm and a resolution limit of 0.31 μm laterally and 1.37 μm axially. The DCM can image tissue architecture and cellular morphology, as well as molecular properties of tissue, using reflective and fluorescent molecular‐specific optical contrast agents.Images acquired with the DCM demonstrate that the system has the sub‐cellular resolution needed to visualize the morphological and molecular changes associated with cancer progression and has the capability to image animal models of disease in vivo. In the hamster cheek pouch model of oral carcinogenesis, the DCM was used to image the epithelium and stroma of the cheek pouch; blood flow was visible and areas of dysplasia could be distinguished from normal epithelium using 6% acetic acid contrast. In human oral cavity tissue slices, DCM reflectance images showed an increase in the nuclear‐to‐cytoplasmic ratio and density of nuclei in neoplastic tissues as compared to normal tissue. After labelling tissue slices with fluorescent contrast agents targeting the epidermal growth factor receptor, an increase in epidermal growth factor receptor expression was detected in cancerous tissue as compared to normal tissue. The combination of reflectance and fluorescence imaging in a single system allowed imaging of two different parameters involved in neoplastic progression, providing information about both the morphological and molecular expression changes that occur with cancer progression.The dual‐mode imaging capabilities of the DCM allow investigation of both morphological changes as well as molecular changes that occur in disease processes. Analyzing both factors simultaneously may be advantageous when trying to detect and diagnose disease. The DCM's high resolution and near‐video‐rate image acquisition and the growing inventory of molecular‐specific contrast agents and disease‐specific molecular markers holds significant promise for in vivo studies of disease processes such as carcinogenesis.
Quantitative STEM mass measurement of biological macromolecules in a 300 kV TEM
Authors: SOUSA ALIOSCKA A. , LEAPMAN RICHARD D. 
Published: October 2007

SummaryFor almost four decades, the scanning transmission electron microscope (STEM) has made significant contributions to structural biology by providing accurate determinations of the molecular masses of large protein assemblies that have arbitrary shapes and sizes. Nevertheless, STEM mass mapping has been implemented in very few laboratories, most of which have employed cold field‐emission gun (FEG) electron sources operating at acceleration voltages of 100 kV and lower. Here we show that a 300 kV commercial transmission electron microscope (TEM) equipped with a thermally assisted Shottky FEG can also provide accurate STEM mass measurements. Using the recently published database of elastic‐scattering cross sections from the National Institute of Standards and Technology, we show that the measured absolute mass values for tobacco mosaic virus and limpet hemocyanin didecamers agree with the known values to within better than 10%. Applying the established approach, whereby tobacco mosaic virus is added to a specimen as a calibration standard, we find that the measured molecular weight of the hemocyanin assemblies agrees with the known value to within 3%. This accuracy is achievable although only a very small fraction (∼0.002) of the incident probe current of 300 kV electrons is scattered onto the annular dark‐field STEM detector. FEG TEMs operating at intermediate voltages (200–400 kV) are becoming common tools for determining the structure of frozen hydrated protein assemblies. The ability to perform mass determination with the same instrument can provide important complementary information about the numbers of subunits comprising the protein assemblies whose structure is being studied.
Improved correction of axial geometrical distortion in index‐mismatched fluorescent confocal microscopic images using high‐aperture objective lenses
Authors: VAN ELBURG H.J. , KUYPERS L.C. , DECRAEMER W.F. , DIRCKX J.J.J. 
Published: October 2007

SummaryExtracting quantitative data from microscopic volume images is straightforward when the refractive indices of the immersion medium and the mounting medium are equal. The readings of the position of the specimen stage can be directly used to measure depth and width. Imperfectly matched immersion and mounting media result in axial geometrical distortion. Linear correction of the axial distortion using the paraxial estimate of the axial scaling factor yields results that may differ as much as 4% from the actual values. From calculations based on a theoretical expression of the 3‐D point‐spread function in the focal region of a high‐aperture microscope focussing into a mismatched mounting medium, we derived axial scaling factors that result in quantitative results accurate to better than 1%. From a non‐linear correction procedure, an improved formula for the paraxial estimate of the axial scaling factor is derived.
Quantitative investigation of murine cytomegalovirus nucleocapsid interaction
Authors: BUSER CHRISTOPHER , FLEISCHER FRANK , MERTENS THOMAS , MICHEL DETLEF , SCHMIDT VOLKER , WALTHER PAUL 
Published: October 2007

SummaryIn this study, we quantitatively investigate the role of the M97 protein for viral morphogenesis in murine cytomegalovirus (MCMV)‐infected fibroblast cells. For this purpose, a statistical analysis is performed for the spatial distribution of nuclear B‐capsids (devoid of DNA, containing the scaffold) and C‐capsids (filled with DNA). Cell nuclei infected with either wild‐type or an M97 deletion mutant were compared. Univariate and multivariate point process characteristics (like Ripley's K‐function, the L‐function and the nearest neighbour distance distribution function) are investigated in order to describe and quantify the effects that the deletion of M97 causes to the process of DNA packaging into nucleocapsids. The estimation of the function L(r) −r reveals that with respect to the wild type there is an increased frequency of point pairs at a very short distance (less than approximately 100 nm) for both the B‐capsids as well as for the C‐capsids. For the M97 deletion mutant type this is no longer true. Here only the C‐capsids show such a clustering behaviour, whereas for B‐capsids it is almost nonexistant. Estimations of functionals such as the nearest neighbour distance distribution function confirmed these results. Thereby, a quantification is provided for the effect that the deletion of M97 leads to a loss of typical nucleocapsid clustering in MCMV‐infected nuclei.
Regulation of fatty acid metabolism in bacteria
Authors: Fujita Yasutaro , Matsuoka Hiroshi , Hirooka Kazutake 
Published: October 2007

SummaryIn Escherichia coli, the main player in transcription regulation of fatty acid metabolism is the FadR protein, which is involved in negative regulation of fatty acid degradation and in positive and negative regulation of the cellular processes related to it, as well as in positive regulation of the biosynthesis of unsaturated fatty acids in a concerted manner with negative regulation of FabR. On the other hand, Bacillus subtilis possesses two global transcriptional regulators, FadR (YsiA) and FapR. B. subtilis FadR represses fatty acid degradation, whereas FapR represses almost all the processes in the biosynthesis of saturated fatty acids and phospholipids. Furthermore, Streptococcus pneumoniae FabT represses the genes of fatty acid biosynthesis that are clustered in its genome. Long‐chain acyl‐CoAs appear to be metabolic signals for fatty acid degradation by bacteria in general, and antagonize the FadR protein from either E. coli or B. subtilis. However, malonyl‐CoA is a metabolic signal for fatty acid and phospholipid biosynthesis by Gram‐positive low‐GC bacteria, and it antagonizes FapR. These would be the primary aspects for understanding the elaborate and complex regulation of fatty acid metabolism in bacteria to maintain membrane lipid homeostasis.
Glucosylceramide synthase is essential for alfalfa defensin‐mediated growth inhibition but not for pathogenicity of Fusarium graminearum
Authors: Ramamoorthy Vellaisamy , Cahoon Edgar B. , Li Jia , Thokala Mercy , Minto Robert E. , Shah Dilip M. 
Published: October 2007

SummaryAntifungal defensins, MsDef1 and MtDef4, from Medicago spp., inhibit the growth of a fungal pathogen, Fusarium graminearum, at micromolar concentrations. However, molecular mechanisms by which they inhibit the growth of this fungus are not known. We have characterized a functional role of the fungal sphingolipid glucosylceramide in regulating sensitivity of the fungus to MsDef1 and MtDef4. A null mutation of the FgGCS1 gene encoding glucosylceramide synthase results in a mutant lacking glucosylceramide. The ΔFggcs1‐null mutant becomes resistant to MsDef1, but not to MtDef4. It shows a significant change in the conidial morphology and displays dramatic polar growth defect, and its mycelia are resistant to cell wall degrading enzymes. Contrary to its essential role in the pathogenicity of a human fungal pathogen, Cryptococcus neoformans, GCS1 is not required for the pathogenicity of F. graminearum. The ΔFggcs1 mutant successfully colonizes wheat heads and corn silk, but its ability to spread in these tissues is significantly reduced as compared with the wild‐type PH‐1 strain. In contrast, it retains full virulence on tomato fruits and Arabidopsis thaliana floral and foliar tissues. Based on our findings, we conclude that glucosylceramide is essential for MsDef1‐mediated growth inhibition of F. graminearum, but its role in fungal pathogenesis is host‐dependent.
Function of heterologous and truncated RNase P proteins in Bacillus subtilis
Authors: Gößringer Markus , Hartmann Roland K. 
Published: October 2007

SummaryBacterial RNase P is composed of an RNA subunit and a single protein (encoded by the rnpB and rnpA genes respectively). The Bacillus subtilis rnpA knockdown strain d7 was used to screen for functional conservation among bacterial RNase P proteins from a representative spectrum of bacterial subphyla. We demonstrate conserved function of bacterial RNase P (RnpA) proteins despite low sequence conservation. Even rnpA genes from psychrophilic and thermophilic bacteria rescued growth of B. subtilis d7 bacteria; likewise, terminal extensions and insertions between β strands 2 and 3, in the so‐called metal binding loop, were compatible with RnpA function in B. subtilis. A deletion analysis of B. subtilis RnpA defined the structural elements essential for bacterial RNase P function in vivo. We further extended our complementation analysis in B. subtilis strain d7 to the four individual RNase P protein subunits from three different Archaea, as well as to human Rpp21 and Rpp29 as representatives of eukaryal RNase P. None of these non‐bacterial RNase P proteins showed any evidence of being able to replace the B. subtilis RNase P protein in vivo, supporting the notion that archaeal/eukaryal RNase P proteins are evolutionary unrelated to the bacterial RnpA protein.
Deformation in the Neoproterozoic Smalfjord Formation, northern Norway: an indicator of glacial depositional conditions?
Authors: ARNAUD EMMANUELLE 
Published: October 2007

AbstractRecent studies on Neoproterozoic climate change have prompted renewed interest in Neoproterozoic glacial deposits and renewed debate over the criteria used to identify the nature of glacial influence on sedimentation. Analyses of soft sediment deformation structures have provided important clues to distinguish between competing palaeoenvironmental interpretations of Quaternary glacial deposits; a similar approach is presented here in the analysis of Neoproterozoic glacial deposits of the Smalfjord Formation, northern Norway. A detailed sedimentological and structural analysis at several sites in the Varangerfjorden area reveals complex soft sediment deformation at various scales in conglomerate, sandstone and diamictite. Deformation is predominantly ductile and includes anticlinal and synclinal folding, flow noses, flame structures, recumbent folding and shear structures. The deformed sediments are associated predominantly with conglomerate and sandstone, which record glaciofluvial and deltaic depositional conditions. Some deformations can be attributed to rapid deposition and slumping, whereas others appear to record shear stress associated with overriding ice. The scale, style and range of deformation, together with the coarse‐grained nature of the deformed sediments and facies associations, suggest that these were unfrozen outwash sediments that were overridden by ice and resedimented in a dynamic ice‐proximal setting. Whereas recent studies of diamictite‐bearing strata of the Smalfjord Formation had revealed no clear evidence of glacial influence on deposition, deformation structures documented here suggest that glacial conditions prevailed on the basin margin during deposition of Smalfjord Formation sediments, with sedimentary facies and deformation structures typical of temperate ice‐proximal settings.
The Arabidopsis TALE homeobox gene ATH1 controls floral competency through positive regulation of FLC
Authors: Proveniers Marcel , Rutjens Bas , Brand Marco , Smeekens Sjef 
Published: October 2007

SummaryFloral induction is controlled by a plethora of genes acting in different pathways that either repress or promote floral transition at the shoot apical meristem (SAM). During vegetative development high levels of floral repressors maintain the Arabidopsis SAM as incompetent to respond to promoting factors. Among these repressors, FLOWERING LOCUS C (FLC) is the most prominent. The processes underlying downregulation of FLC in response to environmental and developmental signals have been elucidated in considerable detail. However, the basal induction of FLC and its upregulation by FRIGIDA (FRI) are still poorly understood. Here we report the functional characterization of the ARABIDOPSIS THALIANA HOMEOBOX 1 (ATH1) gene. A function of ATH1 in floral repression is suggested by a gradual downregulation of ATH1 in the SAM prior to floral transition. Further evidence for such a function of ATH1 is provided by the vernalization‐sensitive late flowering of plants that constitutively express ATH1. Analysis of lines that differ in FRI and/or FLC allele strength show that this late flowering is caused by upregulation of FLC as a result of synergism between ATH1 overexpression and FRI. Lack of ATH1, however, results in attenuated FLC levels independently of FRI, suggesting that ATH1 acts as a general activator of FLC expression. This is further corroborated by a reduction of FLC‐mediated late flowering in fca‐1 and fve‐1 autonomous pathway backgrounds when combined with ath1. Since other floral repressors of the FLC clade are not significantly affected by ATH1, we conclude that ATH1 controls floral competency as a specific activator of FLC expression.
Overexpression of Arabidopsis MAP kinase kinase 7 leads to activation of plant basal and systemic acquired resistance
Authors: Zhang Xudong , Dai Ya , Xiong Yuqing , DeFraia Christopher , Li Jiayang , Dong Xinnian , Mou Zhonglin 
Published: October 2007

SummaryThere is a growing body of evidence indicating that mitogen‐activated protein kinase (MAPK) cascades are involved in plant defense responses. Analysis of the completed Arabidopsis thaliana genome sequence has revealed the existence of 20 MAPKs, 10 MAPKKs and 60 MAPKKKs, implying a high level of complexity in MAPK signaling pathways, and making the assignment of gene functions difficult. The MAP kinase kinase 7 (MKK7) gene of Arabidopsis has previously been shown to negatively regulate polar auxin transport. Here we provide evidence that MKK7 positively regulates plant basal and systemic acquired resistance (SAR). The activation‐tagged bud1 mutant, in which the expression of MKK7 is increased, accumulates elevated levels of salicylic acid (SA), exhibits constitutive pathogenesis‐related (PR) gene expression, and displays enhanced resistance to both Pseudomonas syringae pv. maculicola (Psm) ES4326 and Hyaloperonospora parasitica Noco2. Both PR gene expression and disease resistance of the bud1 plants depend on SA, and partially depend on NPR1. We demonstrate that the constitutive defense response in bud1 plants is a result of the increased expression of MKK7, and requires the kinase activity of the MKK7 protein. We found that expression of the MKK7 gene in wild‐type plants is induced by pathogen infection. Reducing mRNA levels of MKK7 by antisense RNA expression not only compromises basal resistance, but also blocks the induction of SAR. Intriguingly, ectopic expression of MKK7 in local tissues induces PR gene expression and resistance to Psm ES4326 in systemic tissues, indicating that activation of MKK7 is sufficient for generating the mobile signal of SAR.