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At least 1,603 records · Page 89Linked to original sources
PubMed1995

Incidence and spread of Haemophilus influenzae on an Antarctic base determined using the polymerase chain reaction.

A PCR-based method of detecting Haemophilus influenzae in cultures inoculated from throat swabs was evaluated using samples from groups of laboratory staff and medical students and then applied to samples originating from the closed human community of an Antarctic research station. Suitable PCR primers to an H. influenzae gene (ompP2) were used to amplify the gene from DNA preparations made from mixed growth on chocolate agar with added vancomycin. PCR product was reamplified and subjected to restriction endonuclease digestion to allow temporal and spatial mapping of strains over an 8-month period. Eleven different strains of H. influenzae were detected. One particular strain was detected in a third of the base members.

Adult↗
PubMed2003

The lateral spread of epileptiform discharges in rat neocortical slices: effect of focal phencyclidine application.

In vitro and in vivo brain slice techniques were used to examine phencyclidine (PCP) effects on the lateral propagation of epileptiform field potentials (EFP) across adjacent areas of rat frontal neocortex. Epileptiform activity was induced by perfusing slices with Mg 2+-free artificial cerebrospinal fluid. Simultaneous field potential recordings of EFP were obtained from four microelectrodes placed 2-3 mm apart across coronal slices in the third layer. PCP, applied focally between recording sites, blocked rapid propagation across treated areas and resulted in the emergence of spatially separate, independent pacemakers. The characteristics of paroxysmal depolarization shifts did not change significantly by the blockade of lateral propagation of EFP. The same asynchronized pattern of EFP conduction was observed after local application of the N-methyl-D-aspartate (NMDA)-receptor antagonist DL-2-amino-5-phosphono-valeric acid. Local administration of haloperidol as well as NMDA before PCP application reversibly prevented appearance of multiple pacemakers. Focal application of dopamine produced an abnormal pattern of lateral conduction of EFP in 50 % of tested slices. Pacemaker failure as an indicator of functional impairment of cortical integration is the proposed mechanism for developing of schizophrenia-like psychosis associated with epilepsy. Abbreviations. APV: DL-2-amino-5-phosphono-valeric acid EEG:electroencephalogram EFP:epileptiform field potentials NMDA:N-methyl-D-aspartate PCP:phencyclidine SLPE:Schizophrenialike psychosis associated with epilepsy

Animals↗
PubMed2006

pWormgatePro enables promoter-driven knockdown by hairpin RNA interference of muscle and neuronal gene products in Caenorhabditis elegans.

Recent advances in genome research and RNA interference (RNAi) technology have accelerated the adoption of genome-wide experimental approaches for determining gene function in the model organism Caenorhabditis elegans. Despite recent successes, the application of RNAi is limited when gene knockdown causes complex phenotypes or embryonic lethality. Recently, the high-throughput pWormgate cloning system has been introduced as a tool to efficiently generate heat-shock-inducible hairpin RNA constructs using the Gateway recombination technology. We have modified pWormgate into a versatile hairpin cloning plasmid, pWormgatePro, which facilitates temporally and spatially inducible hairpin RNAi using constitutively active, tissue-specific promoters. To demonstrate its utility we knocked down unc-22 in body wall muscles as well as the axon guidance gene unc-5 in the nervous system indicating that promoter-driven hairpins can overcome the neuronal resistance to RNAi. Using pWormgatePro we also show that RNAi in the nervous system of C. elegans is non-autonomous and that spreading of the RNAi signal from neurons to muscle is substantially reduced but not abolished in spreading-defective sid-1 mutant animals. Our findings illustrate the effectiveness of pWormgatePro for gene silencing in muscle cells and neurons and bring forward the possibility of applying tissue-specific RNAi on a genome-wide scale.

Animals↗
PubMed2000

Submolecular organization of DMPA in surface monolayers: beyond the two-layer model.

A new approach to the data refinement of X-ray reflection measurements from lipid surface monolayers, applied to DMPA on pure water, reveals the structural organization of the lipid in unprecedented detail and provides new insights into headgroup conformation and hydration as a function of lateral pressure. While conventional box models are incapable of modeling the experimental data at high momentum transfer satisfactorily, a quasimolecular composition-space refinement approach using distribution functions to map the spatial organization of submolecular headgroup fragments yields a much better description and overcomes inherent difficulties of box models. Upon going from the fluid liquid-expanded (LE) phase to the hexatic liquid-condensed (LC) phase, the orientation of the headgroup is tightly coupled to the ordering of the acyl chains. Headgroups tilt toward the surface normal to accommodate for the large reduction in available area per lipid molecule. The spread of the headgroup fragment distribution is considerably larger than the global interface roughness and increases slightly with compression. In distinction to earlier work on DMPE using the two-box approach, we find that the phosphate hydration stays essentially constant across the whole isotherm. The discrepancy between the results observed with the different models is attributed to intrinsic deficiencies of the box model.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2003

Modulation of object-based attention by spatial focus under endogenous and exogenous orienting.

In R. Egly, J. Driver, and R. D. Rafal's (1994) influential double-rectangle spatial-cuing paradigm, exogenous cues consistently induce object-based attention, whereas endogenous cues generally induce space-based attention. This difference suggests an interdependency between mode of orienting (endogenous vs exogenous) and mode of selection (object based vs space based). However, mode of orienting is generally confounded with initial focus of attention: Endogenous orienting begins with attention focused on a central cue, whereas exogenous orienting begins with attention widely spread. In this study, an attentional-focusing hypothesis is examined and supported by experiments showing that for both endogenous and exogenous cuing, object-based effects are obtained under conditions that encourage spread attention, but they are attenuated under conditions that encourage focused attention. General implications for object-based attention are discussed. ((c) 2003 APA, all rights reserved)

Adult↗
PubMed2004

Mammographic image restoration using maximum entropy deconvolution.

An image restoration approach based on a Bayesian maximum entropy method (MEM) has been applied to a radiological image deconvolution problem, that of reduction of geometric blurring in magnification mammography. The aim of the work is to demonstrate an improvement in image spatial resolution in realistic noisy radiological images with no associated penalty in terms of reduction in the signal-to-noise ratio perceived by the observer. Images of the TORMAM mammographic image quality phantom were recorded using the standard magnification settings of 1.8 magnification/fine focus and also at 1.8 magnification/broad focus and 3.0 magnification/fine focus; the latter two arrangements would normally give rise to unacceptable geometric blurring. Measured point-spread functions were used in conjunction with the MEM image processing to de-blur these images. The results are presented as comparative images of phantom test features and as observer scores for the raw and processed images. Visualization of high resolution features and the total image scores for the test phantom were improved by the application of the MEM processing. It is argued that this successful demonstration of image de-blurring in noisy radiological images offers the possibility of weakening the link between focal spot size and geometric blurring in radiology, thus opening up new approaches to system optimization.

Algorithms↗
PubMed2001

The role of bacterial motility in the survival and spread of Pseudomonas fluorescens in soil and in the attachment and colonisation of wheat roots.

Motile and non-motile strains of Pseudomonas fluorescens SBW25 were constructed using different combinations of the lacZY, xylE and aph marker genes which allowed their detection and differentiation in soil, root and seed samples. The survival of motile and non-motile strains was investigated in both non-competitive and competitive assays in water and non-sterile soil. Although there was no difference between strains in water, the motile strain survived in significantly greater numbers than the non-motile strain after 21 days in soil. There was no significant difference between competitive assays, where motile and non-motile cells were co-inoculated into soil, and non-competitive assays where strains were inoculated separately. Bacterial survival decreased as matric potential increased from -224 to -17 kPa but matric potential had no significant effect on motile compared to non-motile strains. Vertical spread of both motile and non-motile strains was detected 6.4 mm from the inoculum zone after 14 days in the absence of percolating water. There was no significant difference, for either strain, in distance moved from the inoculum zone after 14, 26 or 40 days. The motile strain had a significant advantage in attachment to sterile wheat roots in both non-competitive and competitive studies. When the spatial colonisation of wheat root systems was assessed in non-sterile soil, there was no significant difference between the motile and non-motile strain from either seed or soil inoculum. However, when the whole root system was assessed as one sample unit, differences could be detected. Bacterial motility could contribute to survival in soil and the initial phase of colonisation, where attachment and movement onto the root surface are important.

Journal Article↗
PubMed1996

Distinct stages of melanocyte differentiation revealed by anlaysis of nonuniform pigmentation patterns.

The injection of an antagonistic anti-murine c-kit monoclonal antibody ACK2 during mouse embryonic development produced three distinctive pigmentation patterns on the coat of the offspring. Pattern 1 consisted of pigmentation in craniofacial and caudal regions and was induced by an ACK2 injection between 9.5 and 11.5 days post coitum (dpc). In pattern 2, the entire coat was unpigmented and was induced by the injection at around 13.0 dpc. Pattern 3 consisted of pigmented patches spreading ventrolaterally from the dorsoanterior trunk regions towards the anterior and posterior directions and it was induced by ACK2 administered at 14.5-15.0 dpc. We investigated the embryological basis of these nonuniform pigmentation patterns to elucidate the process of melanoblast differentiation between lineage commitment and colonization into developing hair follicles. The results showed the following. (1) Melanocyte differentiation at the embryonic stage from 10.5 to 12.5 dpc progresses in a spatially nonuniform fashion, being faster in the craniofacial and caudal regions than in the trunk; pattern 1 reflects this. (2) Melanoblasts are activated to proliferate synchronously upon entering into the epidermis; pattern 2 correlates with this process. (3) c-kit functions as a survival signal for proliferating melanoblasts in the epidermis. (4) The melanoblasts that enter developing hair follicles can survive without a c-kit signal; pattern 3 essentially represents the hair follicles colonized by these cells. Analysis of the melanoblast distribution of ls/ls embryos that bear a loss-of-function mutation in the endothelin 3 gene suggested that endothelin 3 is required for early melanoblast differentiation before entering into the epidermis, whereas proliferation in the epidermis takes place without this molecule. Based on these data, we propose 4 distinct steps of embryonic melanocyte differentiation: (1) migration in the dermis, which requires both c-kit and endothelin 3; (2) a state before epidermal entry that is resistant to anti-c-kit mAb; (3) cell proliferation after entering the epidermal layer, which requires c-kit and endothelin receptor B but not endothelin 3 and (4) integration into developing hair follicles, which renders melanoblasts resistant to anti-c-kit mAb. Thus, melanoblast differentiation proceeds by alternately repeating c-kit -dependent and c-kit-independent stages and c-kit functions as a survival factor for the proliferating melanoblasts.

Animals↗
PubMed2006

Ultra-high resolution imaging by fluorescence photoactivation localization microscopy.

Biological structures span many orders of magnitude in size, but far-field visible light microscopy suffers from limited resolution. A new method for fluorescence imaging has been developed that can obtain spatial distributions of large numbers of fluorescent molecules on length scales shorter than the classical diffraction limit. Fluorescence photoactivation localization microscopy (FPALM) analyzes thousands of single fluorophores per acquisition, localizing small numbers of them at a time, at low excitation intensity. To control the number of visible fluorophores in the field of view and ensure that optically active molecules are separated by much more than the width of the point spread function, photoactivatable fluorescent molecules are used, in this case the photoactivatable green fluorescent protein (PA-GFP). For these photoactivatable molecules, the activation rate is controlled by the activation illumination intensity; nonfluorescent inactive molecules are activated by a high-frequency (405-nm) laser and are then fluorescent when excited at a lower frequency. The fluorescence is imaged by a CCD camera, and then the molecules are either reversibly inactivated or irreversibly photobleached to remove them from the field of view. The rate of photobleaching is controlled by the intensity of the laser used to excite the fluorescence, in this case an Ar+ ion laser. Because only a small number of molecules are visible at a given time, their positions can be determined precisely; with only approximately 100 detected photons per molecule, the localization precision can be as much as 10-fold better than the resolution, depending on background levels. Heterogeneities on length scales of the order of tens of nanometers are observed by FPALM of PA-GFP on glass. FPALM images are compared with images of the same molecules by widefield fluorescence. FPALM images of PA-GFP on a terraced sapphire crystal surface were compared with atomic force microscopy and show that the full width at half-maximum of features approximately 86 +/- 4 nm is significantly better than the expected diffraction-limited optical resolution. The number of fluorescent molecules and their brightness distribution have also been determined using FPALM. This new method suggests a means to address a significant number of biological questions that had previously been limited by microscope resolution.

Aluminum Oxide↗
PubMed2001

Endocrine, paracrine and autocrine regulation of trophoblastic metalloproteinases.

Gelatinase A and B (MMP-2 and MMP-9) are secreted by cytotrophoblast (CTB); these enzymes digest the major constituents of the endometrial extracellular matrices (ECM). Direct evidence links the expression of MMPs to the metastatic phenotype of tumour cells and tissue inhibitor of metalloproteinases (TIMP) to the inhibition of metastatisation. Gelatinase B (MMP-9, and no other MMP) has been shown in vitro to mediate CTB invasion. ECM components are known to influence adhesion, spreading, migration and differentiation of cells through specific cell surface receptors called integrins. While CTB migrate from the villous into the decidua they modulate their integrin repertoire, secrete MMP-9 and acquire the capacity to digest their environment. Although CTB behave like metastatic cells, in vivo they are only transiently invasive (first trimester) and their invasion is essentially limited to the endometrium and to the proximal myometrium. This temporal and spatial regulation seems to be mediated in a paracrine way by uterine factors and in an autocrine way by trophoblastic factors. We investigated the effects of endometrial regulators such as leukaemia inhibitory factor (LIF), tumour necrosis factor (TNF), transforming growth factor beta (TGFb), interleukin-1 and 6 (IL-1, IL-6) and insulin-like growth factor binding protein-1 (IGFBP-1) as well as trophoblastic factors such as hCG and leptin. All these factors markedly influenced the secretion and/or activation of MMP-2 and MMP-9. Most cytokines influence cell behaviour by modulating phosphorylation of transcription factors. Among these we identified two oncogene products (Jun and Fos) which were activated by TNF or phorbol esters and which promoted the synthesis of MMP-9. We conclude that decidual and trophoblastic products are autocrine or paracrine regulators of trophoblastic invasion of the endometrium and that some of these products act by activating the transcription of early response genes such as transcription factors.

Chorionic Gonadotropin↗
PubMed2003

Properties and functional role of voltage-dependent potassium channels in dendrites of rat cerebellar Purkinje neurons.

We characterized the properties and functional roles of voltage-dependent potassium channels in the dendrites of Purkinje neurons studied in rat cerebellar slices. Using outside-out patches formed <or=250 microm away from the soma, we found that depolarization-activated potassium channels were present at high density throughout the dendritic tree. Currents required relatively large depolarizations for activation (midpoint, approximately -10 mV), had rapid activation and deactivation kinetics, and inactivated partially (20-70% over 200 msec) with both fast (time constant, 15-20 msec) and slow (300-400 msec) components. Inactivating and noninactivating components were both blocked potently by external tetraethylammonium (half-block by 150 microm) and 4-aminopyridine (half-block by 110 microm). The voltage dependence, kinetics, and pharmacology suggest a predominant contribution by Kv3 family subunits, and immunocytochemical experiments showed staining for both Kv3.3 and Kv3.4 subunits in the dendritic tree. In the proximal dendrite, potassium channels were activated by passively spread sodium spikes recorded at the same position, and experiments using dual recordings showed that the channels serve to actively dampen back-propagation of somatic sodium spikes. In more distal dendrites, potassium currents were activated by voltage waveforms taken from climbing fiber responses, suggesting that they help shape these responses as well. The requirement for large depolarizations allows dendritic Kv3 channels to shape large depolarizing events while not disrupting spatial and temporal summation of smaller excitatory postsynaptic potentials.

Action Potentials↗
PubMed2004

Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.

BACKGROUND: Hidden Markov Models (HMMs) have proven very useful in computational biology for such applications as sequence pattern matching, gene-finding, and structure prediction. Thus far, however, they have been confined to representing 1D sequence (or the aspects of structure that could be represented by character strings). RESULTS: We develop an HMM formalism that explicitly uses 3D coordinates in its match states. The match states are modeled by 3D Gaussian distributions centered on the mean coordinate position of each alpha carbon in a large structural alignment. The transition probabilities depend on the spread of the neighboring match states and on the number of gaps found in the structural alignment. We also develop methods for aligning query structures against 3D HMMs and scoring the result probabilistically. For 1D HMMs these tasks are accomplished by the Viterbi and forward algorithms. However, these will not work in unmodified form for the 3D problem, due to non-local quality of structural alignment, so we develop extensions of these algorithms for the 3D case. Several applications of 3D HMMs for protein structure classification are reported. A good separation of scores for different fold families suggests that the described construct is quite useful for protein structure analysis. CONCLUSION: We have created a rigorous 3D HMM representation for protein structures and implemented a complete set of routines for building 3D HMMs in C and Perl. The code is freely available from http://www.molmovdb.org/geometry/3dHMM, and at this site we also have a simple prototype server to demonstrate the features of the described approach.

Algorithms↗
PubMed2004

TRIM: TR independent multislice imaging.

This article introduces a novel concept to overcome the dependence of image contrast on spatial positioning parameters such as the number of slices and slice separation in multislice measurements: TR-independent multislice (TRIM) acquisition allows the number of slices in a single measurement to remain independent of the repetition time TR. Ramped TRIM (rTRIM) allows the distance between the sections excited in each repetition to remain independent of the distance between the reconstructed slices. Even images from overlapping slices can be acquired without crosstalk between the images of adjacent slices due to spatially overlapping excitation profiles. This concept is based on a special reordering scheme: Within a single TR acquisition, steps are only taken from a fraction of all slices. This necessitates attribution of different phase-encoding steps to different slices within each repetition cycle. The reordering scheme can be derived by the use of a design matrix. The imaging properties of the technique are discussed theoretically and illustrated by a point spread function analysis based on simulations and phantom measurements. Potential sources of artifacts are identified and methods for their prevention are developed. Optimized implementations with different T(1)-weighted sequences such as spin echo (SE), turbo spin echo (TSE), and spoiled gradient echo acquisitions are shown on normal volunteers with imaging parameters used in routine diagnosis.

Humans↗
PubMed2006

Landscape mosaic induces traveling waves of insect outbreaks.

The effect of landscape mosaic on recurrent traveling waves in spatial population dynamics was studied via simulation modeling across a theoretical landscape with varying levels of connectivity. Phase angle analysis was used to identify locations of wave epicenters on patchy landscapes. Simulations of a tri-trophic model of the larch budmoth (Zeiraphera diniana) with cyclic population dynamics on landscapes with a single focus of high-density habitat produced traveling waves generally radiating outwardly from single and multiple foci and spreading to isolated habitats. We have proposed two hypotheses for this result: (1) immigration subsidies inflate population growth rates in the high connectivity habitat and, thus, reduce the time from valleys to peaks in population cycles; (2) populations in the high connectivity habitat crash from peaks to valleys faster than in an isolated habitat due to over-compensatory density dependence. While population growth rates in the high connectivity habitat benefitted from immigration subsidies, times from population valleys to peaks were greater in high connectivity habitat due to a greater magnitude of fluctuations. Conversely, the mean time of the crash from population peaks to valleys was shorter in high connectivity habitat, supporting the second hypothesis. Results of this study suggest over-compensatory density dependence as an underlying mechanism for recurrent traveling waves originating in high connectivity habitats aggregated around a single focus.

Animals↗
PubMed1985

Responses of cultured neural retinal cells to substratum-bound laminin and other extracellular matrix molecules.

The responses of cultured chick embryo retinal neurons to several extracellular matrix molecules are described. Retinal cell suspensions in serum-free medium containing the "N1" supplement (J. E. Bottenstein, S. D. Skaper, S. Varon, and J. Sato, 1980, Exp. Cell Res. 125, 183-190) were seeded on tissue culture plastic surfaces pretreated with polyornithine (PORN) and with one of the factors to be tested. Substantial cell survival could be observed after 72 hr in vitro on PORN pretreated with serum or laminin, whereas most cells appeared to be degenerating on untreated PORN, PORN-fibronectin, and PORN-chondronectin. Cell attachment, although quantitatively similar for all these substrata, was temperature-dependent on serum and laminin but not on fibronectin or untreated PORN. In a short-term bioassay, neurite development was abundant on laminin, scarce on serum and fibronectin, and absent on PORN. No positive correlation between cell spreading and neurite production could be seen: cell spreading was more extensive on PORN and fibronectin than on laminin or serum, while on laminin-treated dishes, spreading was similar for neurite-bearing and non-neurite-bearing cells. Laminin effects on retinal neurons were clearly substratum dependent. When bound to tissue culture plastic, laminin showed a dose-dependent inhibitory effect on cell attachment and did not stimulate neurite development. PORN-bound laminin, on the other hand, did not affect cell attachment but caused marked stimulation of neurite development, suggesting that laminin conformation and/or the spatial distribution of active sites play an important role in the neurite-promoting function of this extracellular matrix molecule. Investigation of the embryonic retina with ELISA and immunocytochemical methods showed that laminin is present in this organ during development. Therefore, in vivo and in vitro observations are consistent with the possibility that laminin might influence neuronal development in the retina.

Animals↗
PubMed1990

Comparison between ectoderm-conditioned medium and fibronectin in their effects on chondrogenesis by limb bud mesenchymal cells.

Limb bud ectoderm inhibits chondrogenesis by limb bud mesenchymal cells cultured at high density or on collagen gels. This ectodermal antichondrogenic influence has been postulated to function in vivo in regulating the spatial patterning of cartilage and soft connective tissue in the limb. We have developed a method for preparing ectoderm-conditioned medium containing antichondrogenic activity. Using a simple bioassay, we have investigated some characteristics of the ectodermal products and their effects on limb bud mesenchymal cells. Inhibition of chondrogenesis by ectoderm-conditioned medium was tested on limb bud mesenchymal cells cultured on collagen gels. The antichondrogenic influence involves enhanced cell spreading and is alleviated by agents, such as cytochalasin D, that induce cell rounding. Fibronectin resembles ectoderm-conditioned medium in its ability to inhibit chondrogenesis and promote cell spreading in collagen gel cultures of limb bud mesenchymal cells. However, Western blot analysis shows that the antichondrogenic activity of ectoderm-conditioned medium is not due to fibronectin in the medium. Peptides related to the fibronectin cell-binding domain block the antichondrogenic effect of fibronectin, but not that of ectoderm-conditioned medium. On the other hand, an antibody to an integrin, as well as heparan sulfate, alleviates the antichondrogenic effects of both fibronectin and ectoderm-conditioned medium. The antichondrogenic effect of ectoderm-conditioned medium may be mediated by an integrin and by a cell surface heparan sulfate proteoglycan, but it does not depend directly upon fibronectin-mediated cell spreading.

Amino Acid Sequence↗
PubMed2005

Diffusion and home range parameters from rodent population measurements in Panama.

Simple random walk considerations are used to interpret rodent population data collected in Hantavirus-related investigations in Panama regarding the short-tailed cane mouse, Zygodontomys brevicauda. The diffusion constant of mice is evaluated to be of the order of (and larger than) 200 meters squared per day. The investigation also shows that the rodent mean square displacement saturates in time, indicating the existence of a spatial scale which could, in principle, be the home range of the rodents. This home range is concluded to be of the order of 70 meters. Theoretical analysis is provided for interpreting animal movement data in terms of an interplay of the home ranges, the diffusion constant, and the size of the grid used to monitor the movement. The study gives impetus to a substantial modification of existing theory of the spread of the Hantavirus epidemic which has been based on simple diffusive motion of the rodents, and additionally emphasizes the importance for developing more accurate techniques for the measurement of rodent movement.

Animals↗
PubMed2002

Axial tomographic confocal fluorescence microscopy.

By physical rotation of the sample, axial tomography enables the acquisition of otherwise inaccessible spatial information from an object. In combination with confocal microscopy, the method can fundamentally improve the effective three-dimensional (3D) resolution. In this report we present a novel method for high resolution reconstruction of confocal axial tomographic data. The method automatically determines the relative angles of rotation, aligns the data from different rotational views and reconstructs a single high resolution 3D dataset. The reconstruction makes use of a known point spread function and is based on an unconstrained maximum likelihood deconvolution performed simultaneously from multiple (in our case three) angular views. It was applied to simulated as well as to experimental confocal datasets. The gain in resolution was quantified and the effect of choice of overrelaxation factors on the speed of convergence was investigated. A clearly improved 3D resolution was obtained by axial tomography together with reconstruction as compared with reconstruction of confocal data from only a single angular view.

Algorithms↗