Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “spatial localization”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,225 records · Page 68Linked to original sources

Molecular genetic abnormalities in premalignant lung lesions: biological and clinical implications.

Lung cancer is a leading cause of cancer death worldwide; however, despite major advances in cancer treatment during the past two decades, the prognostic outcome of lung cancer patients has improved only minimally. This is largely due to the inadequacy of the traditional screening approach, which detects only well-established overt cancers and fails to identify precursor lesions in premalignant conditions of the bronchial tree. In recent years this situation has fundamentally changed with the identification of molecular abnormalities characteristic of premalignant changes; these concern tumour suppressor genes, loss of heterozygosity at crucial sites and activation of oncogenes. After considering the morphological modifications that occur in premalignant lesions of the bronchial tree, we analyse the alterations occurring in a series of relevant genes: p53 and its functional regulation by MDM2 and p14ARF, p16INK4, p15INK4b, FHIT, as well as LOH at important sites such as 3p, 8p, 9p and 5q. Activation of oncogenes is considered for K-ras, the cyclin D1, the heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2/B1), and finally the c-myc oncogene. The expression of c-myc is influenced strongly by the presence of growth factors (GFs), among which EGF is of prime importance, as well as its receptor coded for by the c-erbB-2 oncogene. Basic knowledge at the molecular level has extremely important clinical implications with regard to early diagnosis, risk assessment and prevention, and therapeutic targets. The novel techniques for early diagnosis and screening of premalignant lung lesions, such as fluorescence bronchoscopy, endobronchial ultrasound, spiral computed tomography combined with precise spatial localization techniques, should basically change the approach to the problems raised by this disease and allow for an increased discovery rate of incipient lesions. Sequential applications will lead to the identification of individuals/populations at high risk, while the availability of accurate 'intermediate end points' will enable the effects of preventive trials to be monitored. Finally, the same molecular abnormalities may serve as 'starting points' for innovative treatments designed to restore the altered functions to normality. Recent developments in our knowledge and understanding of the molecular genetic abnormalities in premalignant lung lesions open an era of hope.

Gene Expression Regulation, Neoplastic↗

Coupling of changes in cerebral blood flow with neural activity: what must initially dip must come back up.

Activation flow coupling, increases in neuronal activity leading to changes in cerebral blood flow (CBF), is the basis of many neuroimaging methods. An early rise in deoxygenation, the "initial dip," occurs before changes in CBF and cerebral blood volume (CBV) and may provide a better spatial localizer of early neuronal activity compared with subsequent increases in CBF. Imaging modality, anesthetic, degree of oxygenation, and species can influence the magnitude of this initial dip. The observed initial dip may reflect a depletion of mitochondrial oxygen (O(2)) buffers caused by increased neuronal activity. Changes in CBF mediated by nitric oxide (NO) or other metabolites and not caused by a lack of O(2) or energy depletion most likely lead to an increased delivery of capillary O(2) in an attempt to maintain intracellular O(2) buffers.

Animals↗

Glutamatergic neurotransmission and neuronal glucose oxidation are coupled during intense neuronal activation.

13C nuclear magnetic resonance (NMR) experiments have previously shown that glutamatergic neurotransmitter flux (Vcycle(Glu/Gln)) changes proportionately with neuronal glucose oxidation (CMRglc(ox)N) in the nonactivated cortex of anesthetized rats. Positron Emission Tomography measurements of glucose and oxygen uptake during sensory stimulation had shown that the incremental glucose utilization is greater than oxygen leading to the suggestion that the energy required for stimulated neuronal activity arises from nonoxidative glucose metabolism. In this study, the authors used spatially localized 1H-observed, 13C-edited NMR spectroscopy during an infusion of [1,6-13C2]glucose to assess the relationship between changes in Vcycle(Glu/Gln) and glucose utilization (CMRglc(ox)N and CMRglc(nonox)) during the intense cortical activity associated with bicuculline-induced seizures. Metabolic fluxes were determined by model-based analysis of the 13C-enrichment time courses of glutamate-C4 and glutamine-C4 (CMRglc(ox)N, Vcycle(Glu/Gln)) and lactate-C3 (CMRglc(nonox)). The exchange rate between alpha-ketoglutarate and glutamate was found to be significantly faster than TCA cycle flux both for control (41 micromol.g(-1).min(-1); 95% CI, 5 to 109 micromol.g(-1).min(-1)) and during seizures (21 micromol.g(-1).min(-1); 95% CI, 4.4 to 51.8 micromol.g(-1).min(-1)). During seizures, total glucose utilization (CMRglc(ox+nonox)) increased substantially (466% between 0 and 6 minutes; 277% between 6 and 55 minutes). Glucose oxidation (CMRglc(ox)N) also increased (214%; from 0.26 +/- 0.02 to 0.57 +/- 0.07 micromol.g(-1).min(-1)) but to a lesser degree, resulting in a large increase in cortical lactate concentration. Vcycle(Glu/Gln) increased 233% (from 0.22 +/- 0.04 to 0.52 +/- 0.07 micromol.g(-1).min(-1)), which was similar to the increase in glucose oxidation. The value of Vcycle(Glu/Gln) and CMRglc(ox)N obtained here lie on the line predicted in a previous study. These results indicate that neuronal glucose oxidation and not total glucose utilization is coupled to the glutamate/glutamine cycle during intense cortical activation.

Animals↗

Proprioception in extraocular muscles.

Human extraocular muscles are richly endowed with sensory receptors. The precise role of afferent signals derived from these proprioceptors in ocular motor control and spatial localization has been the subject of considerable debate for more than a century. Laboratory-based and clinical studies have increasingly suggested that proprioceptive signals from extraocular muscles influence visuomotor behavior.

Animals↗

Coexistence under positive frequency dependence.

Negative frequency dependence resulting from interspecific interactions is considered a driving force in allowing the coexistence of competitors. While interactions between species and genotypes can also result in positive frequency dependence, positive frequency dependence has usually been credited with hastening the extinction of rare types and is not thought to contribute to coexistence. In the present paper, we develop a stochastic cellular automata model that allows us to vary the scale of frequency dependence and the scale of dispersal. The results of this model indicate that positive frequency dependence will allow the coexistence of two species at a greater rate than would be expected from chance. This coexistence arises from the generation of banding patterns that will be stable over long time-periods. As a result, we found that positive frequency-dependent interactions over local spatial scales promote coexistence over neutral interactions. This result was robust to variation in boundary conditions within the simulation and to variation in levels of disturbance. Under all conditions, coexistence is enhanced as the strength of positive frequency-dependent interactions is increased.

Animals↗

Gaia as a complex adaptive system.

We define the Gaia system of life and its environment on Earth, review the status of the Gaia theory, introduce potentially relevant concepts from complexity theory, then try to apply them to Gaia. We consider whether Gaia is a complex adaptive system (CAS) in terms of its behaviour and suggest that the system is self-organizing but does not reside in a critical state. Gaia has supported abundant life for most of the last 3.8 Gyr. Large perturbations have occasionally suppressed life but the system has always recovered without losing the capacity for large-scale free energy capture and recycling of essential elements. To illustrate how complexity theory can help us understand the emergence of planetary-scale order, we present a simple cellular automata (CA) model of the imaginary planet Daisyworld. This exhibits emergent self-regulation as a consequence of feedback coupling between life and its environment. Local spatial interaction, which was absent from the original model, can destabilize the system by generating bifurcation regimes. Variation and natural selection tend to remove this instability. With mutation in the model system, it exhibits self-organizing adaptive behaviour in its response to forcing. We close by suggesting how artificial life ('Alife') techniques may enable more comprehensive feasibility tests of Gaia.

Earth, Planet↗

The mechanics of cell fate determination in petals.

The epidermal cells of petals of many species are specialized, having a pronounced conical shape. A transcription factor, MIXTA, is required for the formation of conical cells in Antirrhinum majus; in shoot epidermal cells of several species, expression of this gene is necessary and sufficient to promote conical cell formation. Ectopic expression has also shown MIXTA to be able to promote the formation of multicellular trichomes, indicating that conical cells and multicellular trichomes share elements of a common developmental pathway. Formation of conical cells or trichomes is also mutually exclusive with stomatal formation. In Antirrhinum, MIXTA normally only promotes conical cell formation on the inner epidermal layer of the petals. Its restricted action in cell fate determination results from its specific expression pattern. Expression of MIXTA, in turn, requires the activity of B-function genes, and biochemical evidence suggests that the products of DEFICIENS, GLOBOSA and SEPALLATA-related genes directly activate MIXTA expression late in petal development, after the completion of cell division in the petal epidermis. A MIXTA-like gene, AmMYBML1, is also expressed in petals. AmMYBML1 expression is high early in petal development. This gene may direct the formation of trichomes in petals. In specifying the fates of different cell types in petals, regulatory genes like MIXTA may have been duplicated. Changes in the timing and spatial localization of expression then provides similar regulatory genes which specify different cell fates.

Antirrhinum↗

Characterization of microbial consortia in a terephthalate-degrading anaerobic granular sludge system.

The microbial composition and spatial distribution in a terephthalate-degrading anaerobic granular sludge system were characterized using molecular techniques. 16S rDNA clone library and sequence analysis revealed that 78.5% of 106 bacterial clones belonged to the delta subclass of the class Proteobacteria; the remaining clones were assigned to the green non-sulfur bacteria (7.5%), Synergistes (0.9%) and unidentified divisions (13.1%). Most of the bacterial clones in the delta-Proteobacteria formed a novel group containing no known bacterial isolates. For the domain Archaea, 81.7% and 18.3% of 72 archaeal clones were affiliated with Methanosaeta and Methanospirillum, respectively. Spatial localization of microbial populations inside granules was determined by transmission electron microscopy and fluorescent in situ hybridization with oligonucleotide probes targeting the novel delta-proteobacterial group, the acetoclastic Methanosaeta, and the hydrogenotrophic Methanospirillum and members of Methanobacteriaceae. The novel group included at least two different populations with identical rod-shape morphology, which made up more than 87% of the total bacterial cells, and were closely associated with methanogenic populations to form a nonlayered granular structure. This novel group was presumed to be the primary bacterial population involved in the terephthalate degradation in the methanogenic granular consortium.

Anaerobiosis↗

beta-Glucuronidase (GUS) transposons for ecological and genetic studies of rhizobia and other gram-negative bacteria.

A series of transposons are described which contain the gusA gene, encoding beta-glucuronidase (GUS), expressed from a variety of promoters, both regulated and constitutive. The regulated promoters include the tac promoter which can be induced by IPTG, and nifH promoters which are symbiotically activated in legume nodules. One transposon contains gusA with a strong Shine-Dalgarno translation initiation context, but no promoter, and thus acts as a promoter-probe transposon. In addition, a gus operon deletion strain of Escherichia coli, and a transposon designed for use in chromosomal mapping using PFGE, are described. The GUS transposons are constructed in a mini-Tn5 system which can be transferred to Gram-negative bacteria by conjugation, and will form stable genomic insertions. Due to the absence of GUS activity in plants and many bacteria of economic importance, these transposons constitute powerful new tools for studying the ecology and population biology of bacteria in the environment and in association with plants, as well as for studies of the fundamental molecular basis of such interactions. The variety of assays available for GUS enable both quantitative assays and spatial localization of marked bacteria to be carried out.

Base Sequence↗

Spatial Metabolomics Reveals the Role of Penicillic Acid in Cheese Rind Microbiome Disruption by a Spoilage Fungus.

Microbial interactions in cheese rinds influence community structure, food safety, and product quality. But the chemical mechanisms that mediate microbial interactions in cheeses and other fermented foods are generally not known. Here, we investigate how the spoilage mold Aspergillus westerdijkiae chemically inhibits beneficial cheese-rind bacteria using a combination of omics technologies. In cheese rind community and co-culture experiments, A. westerdijkiae strongly inhibited most cheese rind community members. In co-culture with Staphylococcus equorum, A. westerdijkiae strongly affected bacterial gene expression, including upregulation of a putative bceAB gene cluster that is associated with resistance to antimicrobial compounds in other bacteria. Mass spectrometry imaging (MSI) revealed spatially localized production of secondary metabolites, including penicillic acid and ochratoxin B at the fungal-bacterial interface. Integration of LC-MS/MS and genome annotations confirmed the presence of additional bioactive metabolites, such as notoamides and circumdatins. Fungal metabolic responses varied by bacterial partner, suggesting species-specific chemical strategies. Notably, penicillic acid levels increased 2.5-fold during interaction with Brachybacterium, and experiments with purified penicillic acid showed inhibition of a range of cheese rind bacteria. These findings show that A. westerdijkiae deploys a context-dependent arsenal of mycotoxins and other metabolites, disrupting microbial community assembly in cheese rinds.

Aspergillus westerdijkiae↗

StuA is required for cell pattern formation in Aspergillus.

The stunted (stuA) gene product is required for the orderly differentiation and spatial organization of cell types of the Aspergillus nidulans conidiophore. Expression of the stuA gene is complex. Two transcripts, stuA alpha and stuA beta, are initiated from separate promoters. Transcription of both RNAs increases approximately 50-fold during the establishment of developmental competence. Induction-dependent transcriptional and post-transcriptional regulatory mechanisms further enhance expression 15-fold. Consistent with the latter observation, both transcripts have structural features characteristic of RNAs subject to translational control. Conidiophore morphogenesis requires regulatory interactions between the products of the stuA, bristle (brlA), and abacus (abaA) genes. Enhanced stunted expression is cell type specific and dependent on a functional BrlA protein. StuA affects the spatial localization of AbaA by acting directly, or indirectly, to repress abaA expression.

Amino Acid Sequence↗

A duplicated zone of polarizing activity in polydactylous mouse mutants.

The positional signaling along the anteroposterior axis of the developing vertebrate limb is provided by the zone of polarizing activity (ZPA) located at the posterior margin. Recently, it was established that the Sonic hedgehog (Shh) mediates ZPA activity. Here we report that a new mouse mutant, Recombination induced mutant 4 (Rim4), and two old mutants, Hemimelic extra toes (Hx) and Extra toes (Xt), exhibit mirror-image duplications of the skeletal pattern of the digits. In situ hybridization of the embryos of these mutants revealed ectopic expression of Shh and fibroblast growth factor-4 (Fgf-4) genes at the anterior margin of limb buds. The new mutation, Rim4, was mapped to chromosome 6 with linkage to HoxAbut segregated from HoxA. No linkage to other known polydactylous mutations was detected. In this mutant, ectopic expression of the Hoxd-11 gene, thought to be downstream of ZPA, was also observed at the anterior margin of the limb buds. All results indicate the presence of an additional ZPA at the anterior margin of limb buds in these mutants. Thus, it appears that multiple endogenous genes regulate the spatial localization of the ZPA in the developing mouse limb bud.

Animals↗

Deterministic transport in ratchets.

We present the deterministic transport properties of driven overdamped particles in a simple piecewise-linear ratchet potential. We consider the effects on the stationary current due to local spatial asymmetry, time asymmetry in the driving force, and we include the possibility of a global spatial asymmetry. We present an extremely simple scheme for evaluating the current that is established on the ratchet within an "adiabatic" approximation, and compare the results with exact numerical integration of the process.

Journal Article↗

Stability analysis for extended models of gap solitary waves

A numerical linear stability analysis has been carried out for stationary spatially localized solutions of several systems of coupled nonlinear partial differential equations (PDE's) with two and more complex variables. These coupled PDE's have recently been discussed in the literature, mostly in the context of physical systems with a frequency gap in the dispersion relation of their linear excitations, and they are extensions of the Mills-Trullinger gap soliton model. Translational and oscillatory instabilities are identified, and their associated growth rates are computed as functions of certain parameters characterizing the solitary waves.

Journal Article↗

Electromagnetic contributions to single-molecule sensitivity in surface-enhanced raman scattering

We examine whether single molecule sensitivity in surface-enhanced Raman scattering (SERS) can be explained in the framework of classical electromagnetic theory. The influence of colloid particle shape and size, composition (Ag or Au) and interparticle separation distance on the wavelength-dependent SERS enhancement factor is reported. Our calculations indicate that the maximum enhancement factor achievable through electromagnetics is of the order 10(11). This is obtained only under special circumstances, namely at interstitial sites between particles and at locations outside sharp surface protrusions. The comparative rarity of such sites, together with the extreme spatial localization of the enhancement they provide, can qualitatively explain why only very few surface sites seem to contribute to the measured signal in single-molecule SERS experiments. Enhancement factors of the order 10(14)-10(15), which have been reported in recent experiments, are likely to involve additional enhancement mechanisms such as chemisorption induced resonance Raman effects.

Journal Article↗

Quasidiagonal approach to the estimation of lyapunov spectra for spatiotemporal systems from multivariate time series

We describe methods of estimating the entire Lyapunov spectrum of a spatially extended system from multivariate time-series observations. Provided that the coupling in the system is short range, the Jacobian has a banded structure and can be estimated using spatially localized reconstructions in low embedding dimensions. This circumvents the "curse of dimensionality" that prevents the accurate reconstruction of high-dimensional dynamics from observed time series. The technique is illustrated using coupled map lattices as prototype models for spatiotemporal chaos and is found to work even when the coupling is not strictly local but only exponentially decaying.

Journal Article↗

Target waves in the complex ginzburg-landau equation

We introduce a spatially localized inhomogeneity into the two-dimensional complex Ginzburg-Landau equation. We observe that this can produce two types of target wave patterns: stationary and breathing. In both cases, far from the target center, the field variables correspond to an outward propagating periodic traveling wave. In the breathing case, however, the region in the vicinity of the target center experiences a periodic temporal modulation at a frequency, in addition to that of the wave frequency of the faraway outward waves. Thus at a fixed point near the target, the breathing case yields a quasiperiodic time variation of the field. We investigate the transition between stationary and breathing targets, and note the existence of hysteresis. We also discuss the competition between the two types of target waves and spiral waves.

Journal Article↗

Stability criterion for multicomponent solitary waves

We obtain the most general matrix criterion for stability and instability of multicomponent solitary waves by considering a system of N incoherently coupled nonlinear Schrodinger equations. Soliton stability is studied as a constrained variational problem which is reduced to finite-dimensional linear algebra. We prove that unstable (all real and positive) eigenvalues of the linear stability problem for multicomponent solitary waves are connected with negative eigenvalues of the Hessian matrix. The latter is constructed for the energetic surface of N-component spatially localized stationary solutions.

Journal Article↗