bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of the absorption of concentrated dyes and their use for quantitative imaging of surface topography
Authors: MODEL M. A. , KHITRIN A. K. , BLANK J. L. 
Published: July 2008

SummaryWe propose a method to image the surface topography of transparent objects. The space between the object and the opposite closely positioned surface (such as a cover glass or a slide) is filled with a strongly absorbing dye. The contrast is generated by recording a transmission image at a wavelength where the dye absorbs. Since the transmitted intensity depends on the depth of the dye layer, it carries information about the relief of the tested surface. With sufficiently concentrated dyes, nanometre unevenness of a surface can be detected. By using less‐concentrated solutions, it is possible to image and measure larger objects, such as biological cells. At the present stage, biological applications of the method are only semi‐quantitative, but the method still provides detailed information about cell shapes that is not readily obtainable with other imaging techniques. Conversion of the image grey scale into the units of vertical distance requires knowledge of the absorption coefficient of the dye. The same method that is used for imaging can be adapted to measure the absorption coefficient of concentrated dyes. The solution to be analyzed is placed between a glass slide and a spherical lens of known radius. The absorption coefficient is determined from attenuation of transmitted intensity as a function of the distance to the centre. At the same time, the interference pattern in the reflected image allows measurement of the refractive index of the dye.
Climbing the steps of viral atomic force microscopy: visualization of Dengue virus particles
Authors: FERREIRA G. P. , TRINDADE G. S. , VILELA J. M. C. , DA SILVA M. I. N. , ANDRADE M. S. , KROON E. G. 
Published: July 2008

SummaryIn recent years, the application of atomic force microscopy (AFM) to biological systems has highlighted the potential of this technology. AFM provides insights into studies of biological structures and interactions and can also identify and characterize a large panel of pathogens, including viruses. The Flaviviridae family contains a number of viruses that are important human and animal pathogens. Among them, Dengue virus causes epidemics with fatal outcomes mainly in the tropics. In this study, Dengue virus is visualized for the first time using the in air AFM technique. Images were obtained from a potassium‐tartrate gradient‐purified virus. This study enhances the application of AFM as a novel tool for the visualization and characterization of virus particles. Because flavivirus members are closely related, studies of the morphologic structure of the Dengue virus can reveal strategies that may be useful to identify and study other important viruses in the family, including the West Nile virus.
A simple technique to minimize heat damage to specimens during thermal polymerization of LR White in plastic and gelatin capsules
Authors: BOWLING A. J. , VAUGHN K. C. 
Published: July 2008

SummaryLondon Resin (LR) White is a commonly used resin for embedding specimens to be used for immuno‐ and/or cytochemical studies. In some instances, due to either the properties of the specimen or the availability of various reagents and equipment, it becomes necessary and/or more convenient to polymerize LR White using heat rather than chemical accelerators or UV light. It is known, however, that heat can reduce or even eliminate the anti genicity of the tissue being embedded. It is therefore desirable to polymerize specimens at the lowest temperature possible and to remove the specimens from the oven as soon as polymerization is complete. We have developed a technique that provides a visual marker that allows the exothermic polymerization of LR White to be monitored, thus minimizing the amount of time a specimen must stay in the oven while excluding oxygen from capsules of polymerizing LR White.
Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata
Authors: DESALVO M. K. , VOOLSTRA C. R. , SUNAGAWA S. , SCHWARZ J. A. , STILLMAN J. H. , COFFROTH M. A. , SZMANT A. M. , MEDINA M. 
Published: July 2008

AbstractThe declining health of coral reefs worldwide is likely to intensify in response to continued anthropogenic disturbance from coastal development, pollution, and climate change. In response to these stresses, reef‐building corals may exhibit bleaching, which marks the breakdown in symbiosis between coral and zooxanthellae. Mass coral bleaching due to elevated water temperature can devastate coral reefs on a large geographical scale. In order to understand the molecular and cellular basis of bleaching in corals, we have measured gene expression changes associated with thermal stress and bleaching using a complementary DNA microarray containing 1310 genes of the Caribbean coral Montastraea faveolata. In a first experiment, we identified differentially expressed genes by comparing experimentally bleached M. faveolata fragments to control non‐heat‐stressed fragments. In a second experiment, we identified differentially expressed genes during a time course experiment with four time points across 9 days. Results suggest that thermal stress and bleaching in M. faveolata affect the following processes: oxidative stress, Ca2+ homeostasis, cytoskeletal organization, cell death, calcification, metabolism, protein synthesis, heat shock protein activity, and transposon activity. These results represent the first medium‐scale transcriptomic study focused on revealing the cellular foundation of thermal stress‐induced coral bleaching. We postulate that oxidative stress in thermal‐stressed corals causes a disruption of Ca2+ homeostasis, which in turn leads to cytoskeletal and cell adhesion changes, decreased calcification, and the initiation of cell death via apoptosis and necrosis.
Specific residues in the N‐terminal domain of FimH stimulate type 1 fimbriae assembly in Escherichia coli following the initial binding of the adhesin to FimD usher
Authors: Munera Diana , Palomino Carmen , Fernández Luis Ángel 
Published: July 2008

SummaryType 1 fimbriae are assembled by the chaperone–usher pathway where periplasmic protein complexes formed between fimbrial subunits and the FimC chaperone are recruited by the outer membrane protein FimD (the usher) for their ordered polymerization and export. FimH adhesin initiates and stimulates type 1 fimbriae polymerization by interacting with FimD. Previously we showed that the N‐terminal lectin domain of FimH (N‐FimH) is necessary for binding of the adhesin to FimD. In this work, we have selected mutants in N‐FimH that reduce the levels of adhesin and type 1 fimbriae displayed in Escherichia coli without altering the levels of FimH in the periplasm. The selected mutations are mostly concentrated in residues G15, N46 and D47. In contrast to other mutations isolated that simply affect binding of FimH to FimD (e.g. C3Y), these variants associate to FimD and alter its susceptibility to trypsin digestion similarly to wild‐type FimH. Importantly, their mutant phenotype is rescued when FimD is activated in vivo by the coexpression of wild‐type FimH. Altogether, these data indicate that residues G15, N46 and D47 play an important role following initial binding of FimH to FimD for efficient type 1 fimbriae polymerization by this outer membrane usher.
Halite cementation and carbonate diagenesis of intra‐salt reservoirs from the Late Neoproterozoic to Early Cambrian Ara Group (South Oman Salt Basin)
Authors: SCHOENHERR JOHANNES , REUNING LARS , KUKLA PETER A. , LITTKE RALF , URAI JANOS L. , SIEMANN MICHAEL , RAWAHI ZUWENA 
Published: July 2008

AbstractLate Neoproterozoic to Early Cambrian carbonates of the Ara Group form important intra‐salt ‘stringer’ reservoirs in the South Oman Salt Basin. Differential loading of thick continental clastics above the six carbonate to evaporite cycles of the Ara Group led to the formation of salt diapirs, encasing a predominantly self‐charging hydrocarbon system within partly highly overpressured carbonate bodies (‘stringers’). These carbonates underwent a complex diagenetic evolution, with one stage of halite cementation in a shallow (early) and another in a deep (late) burial environment. Early and late halite cements are defined by their microstructural relationship with solid bitumen. The early phase of halite cementation is post‐dated by solid reservoir bitumen. This phase is most pervasive towards the top of carbonate stringers, where it plugs nearly all available porosity in facies with initially favourable poroperm characteristics. Bromine geochemistry revealed significantly higher bromine contents (up to 280 p.p.m.) in the early halite compared with the late halite (173 p.p.m.). The distribution patterns and the (high) bromine contents of early halite are consistent with precipitation caused by seepage reflux of highly saturated brines during deposition of the overlying rock salt interval. Later in burial history, relatively small quantities of early halite were dissolved locally and re‐precipitated as indicated by inclusions of streaky solid bitumen within the late halite cements. Late halite cement also seals fractures which show evidence for repeated reopening. Initially, these fractures formed during a period of hydrothermal activity and were later reopened by a crack‐seal mechanism caused by high fluid overpressures. Porosity plugging by early halite cements affects the poroperm characteristics of the Ara carbonates much more than the volumetrically less important late halite cement. The formation mechanisms and distribution patterns of halite cementation processes in the South Oman Salt Basin can be generalized to other petroliferous evaporite basins.
Peroxisomal Δ3,Δ2‐enoyl CoA isomerases and evolution of cytosolic paralogues in embryophytes
Authors: Goepfert Simon , Vidoudez Charles , Tellgren‐Roth Christian , Delessert Syndie , Hiltunen J. Kalervo , Poirier Yves 
Published: July 2008

SummaryΔ3,Δ2‐enoyl CoA isomerase (ECI) is an enzyme that participates in the degradation of unsaturated fatty acids through the β‐oxidation cycle. Three genes encoding Δ3,Δ2‐enoyl CoA isomerases and named AtECI1, AtECI2 and AtECI3 have been identified in Arabidopsis thaliana. When expressed heterologously in Saccharomyces cerevisiae, all three ECI proteins were targeted to the peroxisomes and enabled the yeast Δeci1 mutant to degrade 10Z‐heptadecenoic acid, demonstrating Δ3,Δ2‐enoyl CoA isomerase activity in vivo. Fusion proteins between yellow fluorescent protein and AtECI1 or AtECI2 were targeted to the peroxisomes in onion epidermal cells and Arabidopsis root cells, but a similar fusion protein with AtECI3 remained in the cytosol for both tissues. AtECI3 targeting to peroxisomes in S. cerevisiae was dependent on yeast PEX5, while expression of Arabidopsis PEX5 in yeast failed to target AtECI3 to peroxisomes. AtECI2 and AtECI3 are tandem duplicated genes and show a high level of amino acid conservation, except at the C‐terminus; AtECI2 ends with the well conserved peroxisome targeting signal 1 (PTS1) terminal tripeptide PKL, while AtECI3 possesses a divergent HNL terminal tripeptide. Evolutionary analysis of ECI genes in plants revealed several independent duplication events, with duplications occurring in rice and Medicago truncatula, generating homologues with divergent C‐termini and no recognizable PTS1. All plant ECI genes analyzed, including AtECI3, are under negative purifying selection, implying functionality of the cytosolic AtECI3. Analysis of the mammalian and fungal genomes failed to identify cytosolic variants of the Δ3,Δ2‐enoyl CoA isomerase, indicating that evolution of cytosolic Δ3,Δ2‐enoyl CoA isomerases is restricted to the plant kingdom.
Physiological Role of Exogenously Applied Glycinebetaine to Improve Drought Tolerance in Fine Grain Aromatic Rice (Oryza sativa L.)
Authors: Farooq M. , Basra S. M. A. , Wahid A. , Cheema Z. A. , Cheema M. A. , Khaliq A. 
Published: July 2008

AbstractRice performance under drought stress is mainly impeded by oxidative damage and hampered plant water status, which may be improved by exogenous use of osmoprotectants. In this study, the role of glycinebetaine (GB) to improve drought tolerance in rice (Oryza sativa L.) cultivar Super‐basmati was evaluated. GB was used both as seed and foliar application. For priming, seeds were soaked in 50, 100 and 150 mg l−1 aerated solution of GB for 48 h. At four‐leaf stage, one set of plants was subjected to drought stress, while the other set kept at full field capacity. Drought was maintained at 50 % of field capacity by watering when needed. For exogenous application, 50, 100 and 150 mg l−1 GB levels were applied at five‐leaf stage. Drought stress greatly reduced the rice growth while GB application improved it both under well‐watered and drought conditions. Drought tolerance in rice was strongly related to the maintenance of tissue water potential and antioxidant system, which improved the integrity of cellular membranes and enabled the plant to maintain high photosynthesis. Foliar treatments were more effective than the seed treatments, while among the GB treatment, foliar application with 100 mg l−1 was the most effective.
Breakpoints for posaconazole susceptibility testing: background and discussion about the need of establishing values
Authors: Fleck R. , Hof H. 
Published: July 2008

SummaryPosaconazole is a new antifungal agent, which exhibits a broad spectrum of activity against fungi including Aspergillus terreus, some zygomycetes and dematiaceous fungi. Out of the group of triazole antifungal agents, it is the only compound for which interpretive breakpoints have not been established have not yet been established for Candida spp. As reliable breakpoints are useful in the practical management of patients with fungal infections, it is desirable to establish the same for all available substances. However, the underlying data of the existing breakpoints for other antifungal agents are of varying quality because of limited clinical data available. Furthermore, these breakpoints are not equally suitable for all testing methods available and they may not be suitable for all species to be tested. From the practical point of view, it is therefore important not only to establish breakpoints for the reference method but also for the inexpensive and easy to perform testing methods, which are suitable for smaller laboratories.
Learning‐associated regulation of polysialylated neural cell adhesion molecule expression in the rat prefrontal cortex is region‐, cell type‐ and paradigm‐specific
Authors: Ter Horst Judith P. F. , Loscher Jennifer S. , Pickering Mark , Regan Ciaran M. , Murphy Keith J. 
Published: July 2008

AbstractThe prefrontal cortex (PFC) is an interconnected set of cortical areas that function in the synthesis of a diverse range of information and production of complex behaviour. It is now clear that these frontal structures, through bidirectional excitatory communication with the hippocampal formation, also play a substantial role in long‐term memory consolidation. In the hippocampus, morphological synaptic plasticity, supported by regulation of neural cell adhesion molecule (NCAM) polysialylation status, is crucial to information storage. The recent description of polysialylated neurons in the various fields of the medial PFC suggests these structures to possess a similar capacity for synaptic plasticity. Here, using double‐labelling immunohistochemistry with glutamic acid decarboxylase 67, we report that the nature of NCAM polysialic acid‐positive neurons in the PFC is region‐specific, with a high proportion (30–50%) of a γ‐aminobutyric acid (GABA)ergic phenotype in the more ventral infralimbic, orbitofrontal and insular cortices compared with just 10% in the dorsal structures of the cingulate, prelimbic and frontal cortices. Moreover, spatial learning was accompanied by activations in polysialylation expression in ventral PFC structures, while avoidance conditioning involved downregulation of this plasticity marker that was restricted to the dorsomedial PFC – the cingulate and prelimbic cortices. Thus, in contrast to other structures integrated functionally with the hippocampus, memory‐associated plasticity mobilized in the PFC is region‐, cell type‐ and task‐specific.
Pre‐ and postsynaptic regulation of locus coeruleus neurons after chronic morphine treatment: a study of GIRK‐knockout mice
Authors: Torrecilla Maria , Quillinan Nidia , Williams John T. , Wickman Kevin 
Published: July 2008

AbstractWhile the acute inhibitory effect of opioids on locus coeruleus (LC) neurons is mediated primarily by the activation of G protein‐gated inwardly‐rectifying K+(GIRK) channels, the 3′‐5′‐cyclic adenosine monophosphate (cAMP) system has been implicated in the effects of chronic morphine exposure. Presently, the impact of chronic morphine treatment on GIRK‐dependent and GIRK‐independent mechanisms underlying the opioid‐induced inhibition of LC neurons is unclear. Here, opioid‐induced postsynaptic inhibition was studied in LC neurons from wild‐type and GIRK2/GIRK3−/−mice at baseline and following chronic morphine treatment. The postsynaptic inhibition of LC neurons caused by the opioid agonist [Met]5enkephalin (ME) was unaffected by chronic morphine treatment in mice of either genotype. Furthermore, chronic morphine treatment had no effect on the forskolin augmentation of the ME‐induced current in wild‐type LC neurons and only a minor effect on the ME‐induced current in LC neurons from GIRK2/GIRK3−/−mice. Chronic morphine treatment did, however, lead to an increased frequency of spontaneous excitatory postsynaptic currents (EPSCs) in the LC. Interestingly, while forskolin augmented the EPSC frequency similarly in untreated and morphine‐treated wild‐type mice, as well as untreated GIRK2/GIRK3−/−mice, it failed to increase the frequency of EPSCs in morphine‐treated GIRK2/GIRK3−/−mice. Altogether, the findings suggest that chronic morphine treatment exerts little impact on ion channels and signaling pathways that mediate the postsynaptic inhibitory effects of opioids but does enhance excitatory neurotransmission in the mouse LC.
Nitric oxide dependence of glutamate‐mediated modulation at a vertebrate neuromuscular junction
Authors: Pinard Audrée , Robitaille Richard 
Published: July 2008

AbstractRecent evidence has revealed a contribution of glutamate in the stereotyped cholinergic neuromuscular transmission. Indeed, receptors, transporters and glutamate itself are present at the neuromuscular junction (NMJ) while glutamate activation of metabotropic receptors (mGluRs) decreases synaptic transmission and mediates depression through presynaptic mechanisms. However, we have shown that the mGluRs are located postsynaptically, inconsistent with the presynaptic action of glutamate. In the present study, we tested whether nitric oxide (NO) serves as a retrograde messenger mediating the distant effect of glutamate. Glutamate or an mGluR agonist [trans‐(1S,3R)‐aminocyclopentanedicarboxylic acid (ACPD)] failed to reduce synaptic transmission in the presence of an NOS inhibitor (3Br7NINa, 3‐bromo‐7‐nitroindazole sodium salt). Moreover, application of 3Br7NINa precluded the effect of the mGluR antagonist MCPG [(S)‐alpha‐methyl‐4‐carboxyphenylglycine] on high‐frequency‐induced synaptic depression. Iontophoretic injections of BAPTA [1,2‐bis(2‐aminophenoxy)ethane‐N,N,N′‐tetraacetic acid] in muscle fibres abolished the effect of trans‐ACPD on synaptic transmission and blocked the mGluR component of depression, indicating the involvement of muscular calcium in mGluR‐induced depression. Also, the use of this protocol unveiled a muscular calcium‐dependent potentiating pathway dependent on cyclo‐oxygenase activity. In addition, local application of trans‐ACPD induced an increase in NO production by muscle fibres visualized with the indicator DAF‐FM (4‐amino‐5‐methylamino‐2′,7′‐difluorofluorescein). This was prevented by 3Br7NINa or the iontophoretic injection of BAPTA. Moreover, motor nerve stimulation (50 Hz, 30 s) induced an increase in DAF‐FM fluorescence that was abolished by 3Br7NINa and MCPG. Hence, the data suggest that the production of the retrograde molecule NO depends on the postsynaptic calcium‐dependent activation of nitric oxide synthase following mGluRs stimulation and is essential for the glutamatergic modulation of synaptic efficacy and plasticity at the NMJ.
Broad neuroprotective profile of nicotinamide in different mouse models of MPTP‐induced parkinsonism
Authors: Anderson D. W. , Bradbury K. A. , Schneider J. S. 
Published: July 2008

AbstractThe factors contributing to substantia nigra pars compacta (SNc) dopamine (DA) neuron death and striatal DA depletion in Parkinson’s disease (PD) are still poorly understood. However, mitochondrial dysfunction, cellular energy depletion and oxidative stress appear to play important roles in the pathogenesis of PD. In view of this, the current study examined the potential of nicotinamide, a form of the B‐complex vitamin niacin, to protect against 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP)‐induced SNc cell loss and striatal DA depletion in two mouse MPTP models that respond differently to putative neuroprotective agents. Adult male C57Bl/6 mice received nicotinamide (125, 250 or 500 mg/kg i.p.) prior to either acute (four injections in 1 day at 2‐h intervals) or sub‐acute (two injections per day at 4‐h intervals for 5 days) MPTP administration. Striatal DA levels, changes in numbers of tyrosine hydroxylase (TH)‐ and cresyl violet‐stained cells in the SNc at 2 and 6 weeks following the last MPTP exposure were analyzed. Nicotinamide administration resulted in a dose‐dependent sparing of striatal DA levels and SNc neurons in acute MPTP‐treated animals. Only the highest dose of nicotinamide had similar effects in sub‐acute MPTP‐treated animals. At 6 weeks after MPTP exposure, there was some spontaneous recovery of striatal DA levels in both models: neuroprotective effects were still apparent in acute but not sub‐acute MPTP‐treated animals. These results show neuroprotective effects of nicotinamide in different mouse Parkinson models associated with different forms of cell death and suggest that nicotinamide may have broad neuroprotective potential in PD.
Huntingtin interacting protein 1 can regulate neurogenesis in Drosophila
Authors: Moores Justin N. , Roy Sophie , Nicholson Donald W. , Staveley Brian E. 
Published: July 2008

AbstractHuntington’s disease (HD) is associated with a range of cellular consequences including selective neuronal death and decreased levels of neurogenesis. Ultimately, these altered processes are dependent upon proteins that interact with Huntingtin (Htt) such as the Huntingtin‐interacting protein 1 (Hip1) which has a reduced binding preference to expanded Htt. These effects are similar to those observed with modified Notch signal transduction. As Hip1 plays a key role in endocytosis and intracellular transport, and activation of the Notch signal requires both, we investigated putative links between Hip1 and Notch signaling in flies. We have identified two forms of Hip1 that may be produced through the use of alternative first exons: a version of Hip1 with a lipid‐binding ANTH domain and Hip1ΔANTH lacking this domain. The directed expression of Hip1 decreases, while expression of Hip1ΔANTH increases, the density of sensory microchaetae on the dorsal notum, a classical model of neurogenesis. A reduction in microchaetae density associated with NotchMicrochaetae Deficient (MCD) (NMCD ) alleles is sensitive to both Hip1 and Hip1ΔANTH levels, as are the bristle phenotypes generated by misexpression of deltex, a key mediator of Notch signaling. Genetic studies further demonstrate that the observed effects of Hip1 and of Hip1ΔANTH are sensitive to achaete gene dosage while insensitive to the levels of E(Spl), suggesting a non‐canonical Notch neurogenic signal through a deltex‐dependent pathway. The novel role we describe for Hip1 in Notch‐mediated neurogenesis provides a functional link between Notch signaling and proteins related to HD.