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PubMed2004

Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT.

BUSTER-TNT is a maximum-likelihood macromolecular refinement package. BUSTER assembles the structural model, scales observed and calculated structure-factor amplitudes and computes the model likelihood, whilst TNT handles the stereochemistry and NCS restraints/constraints and shifts the atomic coordinates, B factors and occupancies. In real space, in addition to the traditional atomic and bulk-solvent models, BUSTER models the parts of the structure for which an atomic model is not yet available ('missing structure') as low-resolution probability distributions for the random positions of the missing atoms. In reciprocal space, the BUSTER structure-factor distribution in the complex plane is a two-dimensional Gaussian centred around the structure factor calculated from the atomic, bulk-solvent and missing-structure models. The errors associated with these three structural components are added to compute the overall spread of the Gaussian. When the atomic model is very incomplete, modelling of the missing structure and the consistency of the BUSTER statistical model help structure building and completion because (i) the accuracy of the overall scale factors is increased, (ii) the bias affecting atomic model refinement is reduced by accounting for some of the scattering from the missing structure, (iii) the addition of a spatial definition to the source of incompleteness improves on traditional Luzzati and sigmaA-based error models and (iv) the program can perform selective density modification in the regions of unbuilt structure alone.

Algorithms↗
PubMed2005

Genetic structure of the cyclic fossorial water vole (Arvicola terrestris): landscape and demographic influences.

Genetic structure can be strongly affected by landscape features and variation through time and space of demographic parameters such as population size and migration rate. The fossorial water vole (Arvicola terrestris) is a cyclic species characterized by large demographic fluctuations over short periods of time. The outbreaks do not occur everywhere at the same time but spread as a wave at a regional scale. This leads to a pattern of large areas (i.e. some hundreds of km2), each with different vole abundances, at any given time. Here, we describe the abundance and genetic structures in populations of the fossorial water vole. We use the data to try to understand how landscape and demographic features act to shape the genetic structure. The spatial variability of vole abundance was assessed from surface indices, collected in spring 2002 (April) in eastern central France. Genetic variability was analysed using eight microsatellite loci at 23 localities sampled between October 2001 and April 2002. We found some congruence between abundance and genetic structures. At a regional scale, the genetic disruptions were associated with both sharp relief and transition between an area of low abundance and another of high abundance. At a local scale, we observed a variation of the isolation-by-distance pattern according to the abundance level of vole populations. From these results we suggest that the dispersal pattern in cyclic rodent populations varies throughout the demographic cycle.

Animals↗
PubMed1993

Responses of the starburst amacrine cells to moving stimuli.

1. Rabbit retinas were isolated from the eye and incubated in the presence of 3H-choline. Samples of retina taken from a defined midperipheral eccentricity were spread over the domed end of a fiberoptic bundle that formed the floor of a superfusion chamber. The rate of release of labeled acetylcholine by the starburst amacrine cells was studied. 2. When the retina was stimulated by moving gratings, the cells vigorously increased their secretion of acetylcholine. Responses were observed when the bars were as small as 60 microns in width. Systematically varying the spatial and temporal frequency of stimulation revealed that temporal frequency was the dominant variable: the cells responded best to stimuli of 1-4 Hz, whether those stimuli were flashing lights, fine gratings moving slowly, or coarse gratings moving rapidly. 3. With temporal frequency constant, the cells' responses decreased as the spatial frequency of the grating increased. The decreased response to fine gratings is most likely due, at least in part, to lateral interactions that become stronger as the light and dark bars become more closely spaced. These could occur in either the outer or inner retina. 4. The velocity tuning curve for the starburst cells' release of acetylcholine matched fairly well the velocity tuning of ON-OFF directionally selective cells in the rabbit. It did not correspond at all well with the tuning curve for the ON directionally selective cells. If the ON cells receive input from the starburst cells, that input appears to be quite indirect.(ABSTRACT TRUNCATED AT 400 WORDS)

Acceleration↗
PubMed1988

Diffraction tomography by a method of image projections.

A method of three-dimensional diffraction tomography based on image projections is derived. Inversion methods based on projections generally are inaccurate due to the spreading nature of the scattered wave. By backpropagating the field onto a single plane in the image region, diffraction effects are reduced and a projection of the weakly scattering object is generated. Consequently, conventional X-ray inversion techniques may be used to image the object. The relationship between the backpropagated field and the projection is derived both for high frequency incident waves and low spatial frequency scatterers. The generalized image kernel allows the use of curved or misaligned recording surfaces. Numerical results are included.

Algorithms↗
PubMed2006

Transparent polymeric cell culture chip with integrated temperature control and uniform media perfusion.

Modern microfabrication and microfluidic technologies offer new opportunities in the design and fabrication of miniaturized cell culture systems for online monitoring of living cells. We used laser micromachining and thermal bonding to fabricate an optically transparent, low-cost polymeric chip for long-term online cell culture observation under controlled conditions. The chip incorporated a microfluidic flow equalization system, assuring uniform perfusion of the cell culture media throughout the cell culture chamber. The integrated indium-tin-oxide heater and miniature temperature probe linked to an electronic feedback system created steady and spatially uniform thermal conditions with minimal interference to the optical transparency of the chip. The fluidic and thermal performance of the chip was verified by finite element modeling and by operation tests under fluctuating ambient temperature conditions. HeLa cells were cultured for up to 2 weeks within the cell culture chip and monitored using a time-lapse video recording microscopy setup. Cell attachment and spreading was observed during the first 10-20 h (lag phase). After approximately 20 h, cell growth gained exponential character with an estimated doubling time of about 32 h, which is identical to the observed doubling time of cells grown in standard cell culture flasks in a CO2 incubator.

Cell Culture Techniques↗
PubMed1982

[Spatial organization of the interaction between transcallosal and thalamocortical flows of excitation].

In 10 immobilized cats, the interaction between transcallosal potentials and responses to stimulation of the n. ischiadicus was studied in 85 points of the sensomotor cortex. The interaction effect of these responses is determined by their configuration in a given point as well as by time interval between them. The interaction has an obvious spatial-temporal character. Facilitating influences localized mainly in the area of overlapping of EP focuses whereas peripheral areas of the cortex were under a greater depressing effect of the transcallosal flow. The intermediate areas were subject alternately to facilitating and depressing influences. The above effects of interaction seem to reveal a modulating function of transcallosal flow which actualizes the concentration and contrasting of the excitation spreading over ascending projections.

Animals↗
PubMed1996

Parallel discrete event simulation of Lyme disease.

Our research concerns the dynamic processes underlying the rapid increase in the geographic distribution of Lyme disease, currently the most frequently reported vector-borne disease of humans in the United States [10, 1]. More specifically, we ask how spatially localized ecological interactions drive the Lyme disease epidemic at extended spatial and temporal scales. We have developed a parallel discrete event simulation system in C++ for the IBM SP2. The simulation model discussed here models the mouse-tick interaction, an essential element of the epidemic's ecology. The main entities of the simulation are ticks in various stages of development (larval, nymphal, and adult) and mice. We track the behavior of mice and the spread of disease over the course of 180 days (late spring, summer, and early fall). Our goal is to understand patterns in the Lyme disease epidemic at the regional scale through studying the spread of the pathogen across a single white-footed mouse deme.

Animals↗
PubMed2006

Long-time behavior of spreading solutions of Schrödinger and diffusion equations.

We investigate the asymptotic time behavior of the solutions of a large class of linear differential equations that generalize the free-particle Schrödinger and diffusion equations, containing the standard ones as particular cases. We find general scalings that depend only on characteristic features of both the arbitrary initial condition and the Green function associated with the evolution equation. Basically, the amplitude of a long-time solution can be expressed in terms of low order moments of the initial condition (if finite) and low order spatial derivatives of the Green function. These derivatives can also be of the fractional type, which naturally arise when moments are divergent. We apply our results to a large class of differential equations that includes the fractional Schrödinger and Lévy diffusion equations. In particular, we show that, except for threshold cases, the amplitude of a packet may follow the asymptotic law t-alpha, with arbitrary positive alpha.

Journal Article↗
PubMed1996

Integrin-dependent adhesive activity is spatially controlled by inductive signals at gastrulation.

Integrins mediate cell-ECM interactions essential for morphogenesis, however, the extent to which integrin adhesive activities are regulated in the embryo has not been addressed. We report that integrin-dependent cell adhesion to the Arg-Gly-Asp (RGD) containing central cell-binding domain of fibronectin is required for gastrulation in Xenopus. Although all cells of the early embryo retain the ability to attach to this region, only involuting cells arising from the dorsal and ventral lips of the blastopore are able to spread and migrate on fibronectin in vitro. This change in adhesive behavior is mimicked by treating animal cap cells with activin-A. Activin-induced changes in adhesion are independent of new transcription, translation, or changes in receptor expression at the cell surface. We demonstrate that ectopic expression of integrin alpha4beta1 in animal cap cells results in attachment to the non RGD-containing V-region of fibronectin. Further, these cells acquire the ability to spread on the V-region following activin induction. Thus, alpha4beta1 adhesion to the V-region, like endogenous integrin binding to the central cell-binding domain, is responsive to activin signalling. These data indicate that cell adhesion to the central cell-binding domain is regulated in both space and time, and is under the control of inductive signals that initiate gastrulation movements. We suggest that position-specific inductive interactions are likely to represent a novel and general mechanism by which integrin adhesion is modulated throughout development.

Activins↗
PubMed2002

Generalisation: mechanistic and functional explanations.

An overview of mechanistic and functional accounts of stimulus generalisation is given. Mechanistic accounts rely on the process of spreading activation across units representing stimuli. Different models implement the spread in different ways, ranging from diffusion to connectionist networks. A functional account proposed by Shepard analyses the probabilistic structure of the world for invariants. A universal law based on one such invariant claims that under a suitable scaling of the stimulus dimension, generalisation gradients should be approximately exponential in shape. Data from both vertebrates and invertebrates so far uphold Shepard's law. Some data on spatial generalisation in honeybees are presented to illustrate how Shepard's law can be used to determine the metric for combining discrepancies in different stimulus dimensions. The phenomenon of peak shift is discussed. Comments on mechanistic and functional approaches to generalisation are given.

Adaptation, Physiological↗
PubMed2006

Primary and secondary hyperalgesia can be differentiated by postnatal age and ERK activation in the spinal dorsal horn of the rat pup.

Noxious C-fibre stimulation produces increased sensitivity within the injured area (primary hyperalgesia), and a surrounding zone of secondary hyperalgesia. As significant changes in nociceptive processing occur during development, we compared C-fibre induced primary and secondary hyperalgesia in rat pups aged 3, 10 and 21 postnatal (P) days. Hyperalgesia was measured by electromyography flexion reflex recordings following mustard oil or capsaicin at the site of (primary hyperalgesia), or distant to (secondary hyperalgesia) hindpaw mechanical stimuli. Primary hyperalgesia was induced at all postnatal ages, whereas secondary hyperalgesia could not be demonstrated at P3 but was evident at P10 and P21. At P3, extracellular signal-regulated kinase (ERK) protein is present in the dorsal horn, but hindpaw capsaicin produced minimal ERK activation restricted to the fourth lumbar segment. At P21, capsaicin induced intense phosphoERK expression in the superficial dorsal horn throughout several lumbar segments, consistent with the spread of secondary hyperalgesia. Intrathecal administration of the MEK (ERK kinase) inhibitor PD98059 prevented mustard oil and capsaicin-induced secondary hyperalgesia at P21, but had no effect on primary hyperalgesia at P3 or P21. These results provide evidence that primary and secondary hyperalgesia are differentially modulated during development. Furthermore, since ERK activation is required for secondary hyperalgesia, phosphoERK expression can be used to map the spatial distribution of neuronal activation in the spinal cord. Understanding changing responses to injury in the developing nervous system is important for clinical paediatric practice, and will enhance our ability to target the most effective site with a developmentally appropriate analgesic regime.

Aging↗
PubMed1993

Current source density profiles of optical recording maps: a new approach to the analysis of spatio-temporal neural activity patterns.

Spatio-temporal spreading of activity in the CA1 region of the rat hippocampal slice was studied by two experimental approaches. At identical locations in the tissue we measured both the extracellular field potential distribution with microelectrode recordings and the intracellular potential distribution by optical recording, using voltage-sensitive fluorescent dyes. Current source density analysis (CSD) was applied to the extracellular field potential distributions (eCSD) to enhance the spatial resolution. In order to obtain an analogous improvement for the optical recordings, we developed a new CSD transformation, which calculates the locations of the transmembrane current generators from the intracellular potential distributions (iCSD). Compared to the underlying fluorescence maps, the new iCSD profiles exhibit a considerable improvement in spatial resolution. Results can be directly interpreted in terms of physiological membrane processes, such as postsynaptic potentials and action potentials. The iCSD profiles show a surprisingly good correspondence with the classical eCSD profiles both qualitatively and quantitatively, the only difference being that cell body activity is reduced in amplitude. Thus, this new optical CSD analysis paves the way for a quantitative interpretation, rather than the hitherto predominantly qualitative interpretation of spatio-temporal activity profiles from optical recording measurements.

Action Potentials↗
PubMed1992

Rapid in vivo reactivation of herpes simplex virus in latently infected murine ganglionic neurons after transient hyperthermia.

A rapid and physiologically relevant hyperthermia-based induction procedure has been utilized to develop an in vivo model of induced herpes simplex virus (HSV) reactivation in outbred Swiss Webster mice. This procedure was found to efficiently reactivate latent virus from both trigeminal and lumbosacral ganglia. Examination of the time between hyperthermia and virus production demonstrated that detectable levels of infectious virus were present in ganglia as soon as 14 h posttreatment, with peak percent recoveries at 24 h. These data indicated that the switch from latent to active viral gene transcription occurred rapidly following treatment. Immunohistochemical staining for HSV type 1 antigens revealed rare antigen-positive ganglionic neurons 24 h postinduction. HSV antigens were not detected in any other cell type, and lateral spread of the infection was not observed. This is the first report of the detection of HSV antigens in vivo following induced reactivation in the intact nervous system and demonstrates that the neuron is the site of infectious virus production. In addition, our data strongly suggest that at least some neurons in which HSV antigens are detected during reactivation do not survive. Because the temporal and spatial characteristics of HSV reactivation have been clearly defined, this model is uniquely suited for the molecular dissection of the reactivation process.

Animals↗
PubMed2000

Plasmodesmata: gatekeepers for cell-to-cell transport of developmental signals in plants.

Cell walls separate individual plant cells. To enable essential intercellular communication, plants have evolved membrane-lined channels, termed plasmodesmata, that interconnect the cytoplasm between neighboring cells. Historically, plasmodesmata were viewed as facilitating traffic of low-molecular weight growth regulators and nutrients critical to growth. Evidence for macromolecular transport via plasmodesmata was solely based on the exploitation of plasmodesmata by plant viruses during infectious spread. Now plasmodesmata are revealed to transport endogenous proteins, including transcription factors important for development. Two general types of proteins, non-targeted and plasmodesmata-targeted, traffic plasmodesmata channels. Size and subcellular location influence non-targeted protein transportability. Superimposed on cargo-specific parameters, plasmodesmata themselves fluctuate in aperture between closed, open, and dilated. Furthermore, plasmodesmata alter their transport capacity temporally during development and spatially in different regions of the plant. Plasmodesmata are exposed as major gatekeepers of signaling molecules that facilitate or regulate developmental programs, maintain physiological status, and respond to pathogens.

Biological Transport↗
PubMed1989

[The effect of stimulus velocity on inhibition efficiency in the responses of the retinal ganglion cells in the frog].

Responses of 3 class ganglion cells evoked by dark bars of different vertical size moving with different velocity were studied in Frog's retina. The data obtained shows that effect of inhibition diminished with increasing of the velocity over 40 degrees/sec. The on- and off-inhibitory zones of receptive fields seem to have different spatial-temporal properties. An on-inhibitory zone has homogeneous structure and is not far from the central zone of receptive field. An off-inhibitory zone consisted of near and distant subzones. The effect of a near subzone hardly depended on the velocity of moving visual stimuli. The effect of a distant off-inhibitory subzone weakly depended on the velocity of moving stimuli and spread to 20 degrees from the central excitatory zone.

Animals↗
PubMed2000

Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language.

Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.

Africa, Northern↗
PubMed2004

Global hot spots of biological invasions: evaluating options for ballast-water management.

Biological invasions from ballast water are a severe environmental threat and exceedingly costly to society. We identify global hot spots of invasion based on worldwide patterns of ship traffic. We then estimate the rate of port-to-port invasion using gravity models for spatial interactions, and we identify bottlenecks to the regional exchange of species using the Ford-Fulkerson algorithm for network flows. Finally, using stochastic simulations of different strategies for controlling ballast-water introductions, we find that reducing the per-ship-visit chance of causing invasion is more effective in reducing the rate of biotic homogenization than eliminating key ports that are the epicentres for global spread.

Biodiversity↗
PubMed2006

Development of gap junctions in hippocampal astrocytes: evidence that whole cell electrophysiological phenotype is an intrinsic property of the individual cell.

Gap junction communication between astrocytes is prevalent and has been proposed to be involved in several astrocyte functions. One such proposal involves gap junctions in potassium spatial buffering. However, little is known about the developmental time course of gap junction coupling and how much the syncytium affects whole cell measurements of ion currents. Our previous work described three types of hippocampal astrocyte, each with a distinct electrophysiological profile when recorded in whole cell voltage-clamp mode. In the current study we correlated post-whole cell recording immunohistochemistry for GLAST and the spread of injected dye from the recorded cell with the measured electrophysiological phenotype to quantify cell coupling of astrocytes and the type of astrocyte coupled, in the rat hippocampus. We found that passive astrocytes, which predominate after 3 wk postnatally, have much lower membrane resistances (Rm) and are more frequently dye coupled and to more cells, than outwardly and variably rectifying astrocytes that predominate in early postnatal development. Dye coupling in GLAST(+) cells was first detected in the first postnatal week and the degree of coupling peaked before the complete transition to the low Rm, passive electrophysiological type. Also, the degree of dye coupling did not correlate with the passive electrophysiological phenotype. Passive cells were also detected after pretreatment with a gap junction inhibitor. Further evidence that cell coupling does not contribute to the mature astrocyte electrophysiological phenotype came from recording of excised membrane patches, which predominantly corresponded to the ion channel expression profiles of their cells of origin. These findings imply that in the hippocampus, interastrocyte cell coupling likely contributes little to the overall whole cell current profile of diverse glia, and the electrophysiological passivity reflects the intrinsic ion channel expression of the mature astrocyte.

Animals↗