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 1,081 records · Page 60Linked to original sources
PubMed1997

The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus.

BACKGROUND: Recent experimental and theoretical studies have shown that several small proteins reach the native state by a nucleation-collapse mechanism. Studies based on lattice models have been used to suggest that the critical nucleus is specific, leading to the notion that the transition state may be unique. On the other hand, results of studies using off-lattice models show that the critical nuclei should be viewed as fluctuating mobile structures, thus implying non-unique transition states. RESULTS: The microscopic underpinnings of the nucleation-collapse mechanism in protein folding are probed using minimal off-lattice models and Langevin dynamics. We consider a 46-mer continuum model which has a native beta-barrel-like structure. The fast-folding trajectories reach the native state by a nucleation-collapse process. An algorithm based on the self-organized neural nets is used to identify the critical nuclei for a large number of rapidly folding trajectories. This method, which reduces the determination of the critical nucleus to one of 'pattern recognition', unambiguously shows that the folding nucleus is not unique. The only common characteristics of the mobile critical nuclei are that they are small (containing on average 15-22 residues) and are largely composed of residues near the loop regions of the molecule. The structures of the transition states, corresponding to the critical nuclei, show the existence of spatially localized ordered regions that are largely made up of residues that are close to each other. These structures are stabilized by a few long-range contacts. The structures in the ensemble of transition states exhibit a rather diverse degree of similarity to the native conformation. CONCLUSIONS: The multiplicity of delocalized nucleation regions can explain the two-state folding by a nucleation-collapse mechanism for small single-domain proteins (such as chymotrypsin inhibitor 2) and their mutants. Because there are many distinct critical nuclei, we predict that the folding kinetics of fast-folding proteins will not be drastically changed even if some of the residues in a 'typical' nucleus are altered.

Algorithms↗
PubMed2003

Enhanced photostability of ICG in close proximity to gold colloids.

Photobleaching of fluorophores frequently limits their detectability or observation time. We examined Indocyanine green (ICG) which is widely used in medical testing and is highly unstable. We showed that spatial localization of ICG near metallic gold colloids resulted in increased photostability. This suggests the use of fluorophore-metal conjugates in situations adversely affected by photobleaching.

Gold Colloid↗
PubMed2003

Geography and niche occupancy as determinants of yeast biodiversity: the yeast-insect-morning glory ecosystem of Kīpuka Puaulu, Hawai'i.

Biodiversity theory proposes two types of hypotheses to account for the species composition of a given community. The first encompasses geographic and historical factors. For example, local species richness is thought to be affected by area, proximity to large landmasses, dispersal mechanisms, and climatic history, collectively known as biogeography. The second type, termed niche occupancy rules, deals with the intrinsic properties of the species as they affect their interaction with the habitat and with other members of the community. The yeast-insect-morning glory ecosystem is a good model to explore biodiversity theory in ascomycetous yeasts. Here we focus on beetles that breed or feed in morning glories and a group of ascomycetous yeasts that are associated exclusively with them. Specifically, we analyse the community found in the vicinity of Kīpuka Puaulu, a small patch of disturbed but mature forest situated amidst lava flows on the island of Hawai'i. Major members of the yeast community include Metschnikowia hawaiiensis, Metschnikowia lochheadii, and the related asexual species Candida ipomoeae and Candida kipukae. These species are nearly indistinguishable from one another in terms of nutritional requirements and abilities, although their phylogenetic range is enormous. Their distribution, both global and local, is far from random. As Kīpuka Puaulu is an island within an island, the principles of island biogeography may be invoked to explain some aspects of its yeast species composition. M. lochheadii, C. ipomoeae, and the rare species Candida hawaiiana are recent introductions from the American continent and therefore exotic, whereas M. hawaiiensis and C. kipukae might be regarded as endemic, as they are yet to be isolated elsewhere. Vectoring by certain nitidulid beetles explains the long-range dispersal of these species. However, niche occupancy rules may account in part for the local spatial distribution of the yeasts within the island of Hawai'i and within the kīpuka itself. We have identified the maximum growth temperature as a potentially critical property of the fundamental niche of these yeasts.

Animals↗
PubMed1995

Population structure, fitness surfaces, and linkage in the shifting balance process.

Wright first introduced the idea that random genetic drift and classical mass-action selection might combine in such a way as to allow populations to find the highest peak in complicated adaptive surfaces. His theory assumes large but structured populations, in which mating is spatially local. If gene flow is sufficiently low, and the subpopulations (demes) are small enough, they will be subject to genetic drift. Distant demes drift independently, allowing many independent searches of the adaptive surface to take place. A deme that has shifted to a higher peak can, by emigration, cause the rest of the demes to shift to the higher peak. The probability of this shift depends on the migration rate. Previous studies have concluded that very little migration is necessary to effect the shift in adaptive peaks that characterizes the last phase of Wright's Shifting Balance Process (SBP). Here we present the results of a computer study that investigates the roles of dispersal distance, the degree of epistasis in the fitness surface, and recombination on the shifting balance process. In particular, we measure their effect on the population's mean fitness. We show that over a range of dispersal distances the advantage of the SBP is a monotonically increasing function of the amount of epistasis. Our results show that the extent of dispersal that results in the greatest effect of the SBP in increasing mean fitness depends on the extent of epistasis. Finally, for low levels of epistasis, higher recombination performs better, while for intermediate levels, lower recombination results in a greater advantage of the SBP.

Adaptation, Biological↗
PubMed1990

Intact "biological motion" and "structure from motion" perception in a patient with impaired motion mechanisms: a case study.

A series of psychophysical tests examining early and later aspects of image-motion processing were conducted in a patient with bilateral lesions involving the posterior visual pathways, affecting the lateral parietal-temporal-occipital cortex and the underlying white matter (as shown by magnetic resonance imaging studies and confirmed by neuro-ophthalmological and neuropsychological examinations). Visual acuity, form discrimination, color, and contrast-sensitivity discrimination were normal whereas spatial localization, line bisection, depth, and binocular stereopsis were severely impaired. Performance on early motion tasks was very poor. These include seeing coherent motion in random noise (Newsome & Paré, 1988), speed discrimination, and seeing two-dimensional form from relative speed of motion. However, on higher-order motion tasks the patient was able to identify actions from the evolving pattern of dots placed at the joints of a human actor (Johansson, 1973) as well as discriminating three-dimensional structure of a cylinder from motion in a dynamic random-dot field. The pattern of these results is at odds with the hypothesis that precise metrical comparison of early motion measurements is necessary for higher-order "structure from motion" tasks.

Cerebral Cortex↗
PubMedDate not supplied

Light-evoked changes in near-infrared transmission by the ON and OFF channels of the anuran retina.

We have developed an optical method to monitor the activity of the ON and OFF channels in the anuran retina. The change in the fraction of near infrared that is transmitted transversely through the retina in an eyecup slice is monitored during stimulation by visible, green light. Near-infrared transmission increases both at the onset and at the termination of a step stimulus. This "ON/OFF" response is maximal in the neural retina. Sodium L-aspartate, which blocks the light-evoked activity of post-photoreceptor neurons, abolishes the "ON/OFF" response. L-AP4, used as a selective blocker of the ON channel, reduces the "ON" component and has little or no effect on the "OFF" component. The "ON" and "OFF" processes observed optically are distinct from those that generate the b- and d-waves of the electroretinogram, and the "ON" and "OFF" components may be superior to the b- and d-waves as indicators of ON and OFF channel activity. The optical method is almost as simple as electroretinography and has the advantages that responses can be spatially localized with ease.

Aminobutyrates↗
PubMedDate not supplied

Contributions of cat posterior parietal cortex to visuospatial discrimination.

The purpose of the present study was to examine the contributions made by cat posterior parietal cortex to the analyses of the relative position of objects in visual space. Two cats were trained on a landmark task in which they learned to report the position of a landmark object relative to a right or left food-reward chamber. Subsequently, three pairs of cooling loops were implanted bilaterally in contact with visuoparietal cortices forming the crown of the middle suprasylvian gyrus (MSg; architectonic area 7) and the banks of the posterior-middle suprasylvian sulcus (pMS sulcal cortex) and in contact with the ventral-posterior suprasylvian (vPS) region of visuotemporal cortex. Bilateral deactivation of pMS sulcal cortex resulted in a profound impairment for all six tested positions of the landmark, yet bilateral deactivation of neither area 7 nor vPS cortex yielded any deficits. In control tasks (visual orienting and object discrimination), there was no evidence for any degree of attentional blindness or impairment of form discrimination during bilateral deactivation of pMS cortex. Therefore, we conclude that bilateral cooling of pMS cortex, but neither area 7 nor vPS cortex, induces a specific deficit in spatial localization as examined with the landmark task. These observations have significant bearing on our understanding of visuospatial processing in cat, monkey, and human cortices.

Animals↗
PubMedDate not supplied

Sign-conserving amacrine neurons in the fly's external plexiform layer.

Amacrine cells in the external plexiform layer of the fly's lamina have been intracellulary recorded and dye-filled for the first time. The recordings demonstrate that like the lamina's short photoreceptors R1-R6, type 1 lamina amacrine neurons exhibit nonspiking, "sign-conserving" sustained depolarizations in response to illumination. This contrasts with the sign-inverting responses that typify first-order retinotopic relay neurons: monopolar cells L1-L5 and the T1 efferent neuron. The contrast frequency tuning of amacrine neurons is similar to that of photoreceptors and large lamina monopolar cells. Initial observations indicate that lamina amacrine receptive fields are also photoreceptor-like, suggesting either that their inputs originate from a small number of neighboring visual sampling units (VSUs), or that locally generated potentials decay rapidly with displacement. Lamina amacrines also respond to motion, and in one recording these responses were selective for the orientation of moving edges. This functional organization corresponds to the anatomy of amacrine cells, in which postsynaptic inputs from several neighboring photoreceptor endings are linked by a network of very thin distal processes. In this way, each VSU can receive convergent inputs from a surround of amacrine processes. This arrangement is well suited for relaying responses to local intensity fluctuations from neighboring VSUs to a central VSU where amacrines are known to be presynaptic to the dendrites of the T1 efferent. The T1 terminal converges at a deeper level with that of the L2 monopolar cell relaying from the same optic cartridge. Thus, the localized spatial responses and receptor-like temporal response properties of amacrines are consistent with possible roles in lateral inhibition, motion processing, or orientation processing.

Amacrine Cells↗
PubMed2006

Spatial negative priming in early Alzheimer's disease: evidence for reduced cognitive inhibition.

Some studies of negative priming and other tasks assumed to reflect inhibitory functions suggest a decline in inhibitory processes in Alzheimer's disease. However, none of the measures used in previous studies can be interpreted as an unambiguous reflection of distractor inhibition. The present study investigates whether reductions in negative priming associated with Alzheimer's disease reflect reduced distractor inhibition, rather than perceptual review processes. Individuals with early Alzheimer's disease were predicted to show reduced negative priming on a spatial localization task designed to provide an unambiguous measure of distractor inhibition. Sixteen clinical participants showed significantly less negative priming than old and young healthy control groups, which is interpreted as evidence for reduced distractor inhibition in early dementia. A second analysis indicated that, within the clinical sample only, negative priming effect size was significantly correlated with prime trial response speed. Clinical participants showing the least negative priming were slower to respond to an initial stimulus. The results may mean that people with early Alzheimer's disease have a reduced capacity to use excitatory as well as inhibitory processes in selection.

Age Factors↗
PubMed2005

monitoring activity-dependent peptide release from the CNS using single-bead solid-phase extraction and MALDI TOF MS detection.

To investigate dynamic peptidergic cell-cell communication, single micrometer-sized solid-phase extraction (SPE) beads were used to collect peptides from specific locations of well-characterized neurosecretory structures and even individual neuronal processes for off-line MALDI MS analyses. Peptide binding parameters of single SPE beads, including limits of collection, detection, and saturation capacity, were tested with 14C-labeled cytochrome c as well as with mixtures of multiple neuropeptides (bradykinin, Aplysia acidic peptide 1-20, and insulin). MALDI MS detection of secreted peptides was demonstrated in two well-characterized neurosecretory structures, the rat pituitary gland and single cultured Aplysia bag cell neurons. With cultured cells, precise placement of SPE beads allowed peptide collection from distinct neurites with spatial localization on the order of 200 microm, and SPE beads could be replaced within time frames that allowed analyte collection before and after cell stimulation paradigms. Comparison between pre- and poststimulation peptide profiles in both model systems allowed a directed strategy to determine which compounds were released with neuronal activity. Single SPE bead MALDI MS offers a novel approach to investigate peptide signaling that allows the detection and discovery of unknown intercellular signals secreted from a large variety of biological tissues.

Animals↗
PubMed2005

Optical probes for biological applications based on surface-enhanced Raman scattering from indocyanine green on gold nanoparticles.

We report surface-enhanced Raman scattering (SERS) studies on indocyanine green (ICG) on colloidal silver and gold and demonstrate a novel optical probe for applications in living cells. In addition to its own detection by the characteristic ICG SERS signatures, the ICG gold nanoprobe delivers spatially localized chemical information from its biological environment by employing SERS in the local optical fields of the gold nanoparticles. The probe offers the potential to increase the spectral specificity and selectivity of current chemical characterization approaches of living cells and biomaterials based on vibrational information.

Animals↗
PubMed2005

A scalable addressable positive-dielectrophoretic cell-sorting array.

We present the first known implementation of a passive, scalable architecture for trapping, imaging, and sorting individual microparticles, including cells, using a positive dielectrophoretic (p-DEP) trapping array. Our array-based technology enables "active coverslips" where, when scaled, many individually held cells can be sorted based upon imaged spatial or temporally variant characteristics. Our design incorporates a unique "ring-dot" p-DEP trap geometry organized in a row/column array format. This trap design, implemented in a two-level metal process, provides strong and highly spatially localized holding fields enabling single-cell capture for all traps in the array. We release individual trapped microparticles during sorting using a passive transistor-independent approach where we electrically ground the row and column electrodes associated with specific traps in the array. The demand for chip-to-world electrical connections in our arrays scales proportionally with the square root of the number of traps in a given array, delivering a substantial improvement over prior designs. We demonstrate capture, holding, and release operations with both beads and cells in small arrays of this new architecture.

Cell Separation↗
PubMed2000

Femtosecond studies of electron dynamics at interfaces.

A delocalized electron at a metal-dielectric interface interacts with the adlayer and spatially localizes or self-traps on the femtosecond time scale into what is termed a small polaron. The dynamics can be studied by two-photon photoemission. Theoretical and experimental analyses reveal the interaction energy and the lattice vibrational mode that mediates electron localization. These results contribute to a fundamental understanding of electron behavior in weakly bonded solids and can lead to a better understanding of carrier dynamics in many different systems, including organic light-emitting diodes.

Absorptiometry, Photon↗
PubMed1994

Specific nucleus as the transition state for protein folding: evidence from the lattice model.

We have studied the folding mechanism of lattice model 36-mer proteins. Using a simulated annealing procedure in sequence space, we have designed sequences to have sufficiently low energy in a given target conformation, which plays the role of the native structure in our study. The sequence design algorithm generated sequences for which the native structures is a pronounced global energy minimum. Then, designed sequences were subjected to lattice Monte Carlo simulations of folding. In each run, starting from a random coil conformation, the chain reached its native structure, which is indicative that the model proteins solve the Levinthal paradox. The folding mechanism involved nucleation growth. Formation of a specific nucleus, which is a particular pattern of contacts, is shown to be a necessary and sufficient condition for subsequent rapid folding to the native state. The nucleus represents a transition state of folding to the molten globule conformation. The search for the nucleus is a rate-limiting step of folding and corresponds to overcoming the major free energy barrier. We also observed a folding pathway that is the approach to the native state after nucleus formation; this stage takes about 1% of the simulation time. The nucleus is a spatially localized substructure of the native state having 8 out of 40 native contacts. However, monomers belonging to the nucleus are scattered along the sequence, so that several nucleus contacts are long-range while other are short-range. A folding nucleus was also found in a longer chain 80-mer, where it also constituted 20% of the native structure. The possible mechanism of folding of designed proteins, as well as the experimental implications of this study is discussed.

Algorithms↗
PubMed1984

Ketogenesis in the living rat followed by 13C NMR spectroscopy.

The metabolic fate of 13C1-labeled butyrate in the liver of living rats has been studied by 13C NMR. The formation of the ketone bodies acetoacetate and beta-hydroxybutyrate was observed in vivo as well as resonances from glutamate, glutamine, and carbonate. The observed time course of these metabolites demonstrates the potential of the technique to measure enzyme kinetics in vivo and also to measure the enzyme capacity of a given organ to metabolize a substrate. The in vivo spectra were compared to in vitro spectra of the excised liver and perchloric acid extracts of the liver. Observation of the metabolites and monitoring of their time course in vivo would not have been possible without distinct improvements in the spectral resolution and the spatial localization of the radio-frequency field within the liver. As a novel approach, we have selected the carbonyl region of the 13C NMR spectra for identifying the ketone bodies and other oxidation products in the liver.

3-Hydroxybutyric Acid↗
PubMed2001

Reduced temperature dependence of collective conformational opening in a hyperthermophile rubredoxin.

Spatially localized differences in the conformational dynamics of the rubredoxins from the hyperthermophile Pyrococcus furiosus (Pf) and the mesophile Clostridium pasteurianum (Cp) are monitored via amide exchange measurements. As shown previously for the hyperthermophile protein, nearly all backbone amides of the Cp rubredoxin exhibit EX(2) hydrogen exchange kinetics with conformational opening rates of >1 s(-)(1). Significantly slower amide exchange is observed for Pf rubredoxin in the region surrounding the metal site and the proximal end of the three-stranded beta-sheet, while for the rest of the structure, the exchange rates at 23 degrees C are similar for both proteins. For the multiple-turn region comprising residues 14-32 in both rubredoxins, the uniformity of both the exchange rate constants and the values of the activation energy at the slowly exchanging sites is consistent with a model of solvent exposure via a subglobal cooperative conformational opening. In contrast to the common expectation of increased rigidity in the hyperthermophile proteins, below room temperature Pf rubredoxin exhibits a larger apparent flexibility in this multiple-turn region. The smaller enthalpy for the conformational opening process of this region in Pf rubredoxin reflects the much weaker temperature dependence of the underlying conformational equilibrium in the hyperthermophile protein.

Clostridium↗
PubMed1998

Exonuclease-polymerase active site partitioning of primer-template DNA strands and equilibrium Mg2+ binding properties of bacteriophage T4 DNA polymerase.

The binding of bacteriophage T4 DNA polymerase (T4 pol) to primer-template DNA with 2-aminopurine (2AP) located at the primer terminus results in the formation of a hyperfluorescent 2AP state. Changes in this hyperfluorescent state were utilized to investigate the fractional concentration of primer-templates bound at the exonuclease and statically quenched polymerase sites. In the absence of Mg2+, a hydrophobic exonuclease site dominates over the polymerase site for possession of the primer terminus. The fractional concentration of primer termini in the exonuclease site was found to be 64 and 84% for correct (AP-T) and mismatched (AP-C) primer-templates, respectively. Exonuclease-deficient mutants, polymerase-switching mutants, and nucleoside triphosphates all shift this equilibrium toward the polymerase site. Synthesis of stereospecific hydrolysis resistant phosphorothioate 2AP-labeled DNA allowed Mg2+ ion binding titrations to be performed in the presence of bound DNA without the complication of the excision reaction. High- and low-affinity Mg2+ binding sites were observed in the presence of bound double-stranded (ds) DNA, with dissociation constants in the micromolar (WT Kd = 5.1 microM) and millimolar (WT Kd = 2.5 mM) concentration ranges. Mg2+ binding was found to be a key "conformational switch" for T4 pol. As the high-affinity Mg2+ binding sites are filled, the primer terminus migrates from the exonuclease site to a highly based stacked polymerase active site. Filling the low-affinity Mg2+ sites further shifts the primer terminus into the polymerase site. As the low-affinity Mg2+ sites are filled, T4 pol "loosens its grip" on the primer terminus, as shown by a large amplitude increase in the nanosecond rotational mobility of 2AP within the bound T4 complex. The hyperfluorescent exonuclease site is spatially localized to 2AP positioned on the primer end. The penultimate (n - 1) position, as well as n - 2 and n - 5 positions, reveals no detectable fluorescent enhancement upon binding. The observed position-dependent fluorescence data, when combined with time-resolved total-intensity and anisotropy data, suggest that the creation of the hyperfluorescent state is caused by phenylalanine 120 (F120) of T4 pol intercalating into 2AP primers much like that observed for phenylalanine 123 of RB69 DNA polymerase intercalating into deoxythymidine primers [Wang, J., et al. (1997) Cell 89, 1087-1099]. As Mg2+ binds in the exonuclease site of T4 pol, the primer terminus appears to be "pulled backward" into the active site, decreasing the concentration of F120-intercalated primer termini, and bringing the exonuclease active site residues closer to the primer terminus scissile phosphate bond.

2-Aminopurine↗
PubMed1999

Single-turnover analysis of mutant human apurinic/apyrimidinic endonuclease.

Apurinic/apyrimidinic endonuclease (AP endo) is a key enzyme in the repair of oxidatively damaged DNA. Using single-turnover conditions, we recently described substrate binding parameters for wild type human AP endo. In this study, we utilized four enzyme mutants, D283A, D308A, D283A/D308A, and H309N, and assayed them under steady state and single-turnover conditions. The turnover number of the single aspartate mutants was decreased 10-30-fold in comparison to that of the wild type. The decrease in the turnover number was accompanied by a 17- and 50-fold decrease in the forward rate constant (kon) for substrate binding by D308A and D283A, respectively. The dissociation rate constant for substrate (koff) was unchanged for the D308A mutant but was 10 times faster for the D283A mutant than for the wild type. The apparent Km values for both of the single aspartate mutants were about equal to their respective KD values. To account for the kinetic behavior of the D308A mutant, it was necessary to insert a conformational change into the kinetic scheme. In contrast to the single aspartate mutants, the turnover number for the double mutant was 500-fold lower than that of the wild type, its apparent Km was 2.5-fold higher, and binding to substrate was weak. Mutation of His309 caused the greatest decrease in activity, resulting in a turnover number that was more than 30000-fold lower than that of the wild type and an apparent Km that was 13-fold higher, supporting the notion that His309 is intimately involved in catalysis. Molecular dynamics simulation techniques suggested that conversion of either aspartate to alanine resulted in major shifts in the spatial localization of key amino acids. Despite the fact that the two aspartates flank His309, the movement they engendered was distinct, consistent with the differences in catalytic behavior. We suggest that the conformation of the active site is largely maintained by the two aspartates, which enable efficient binding and cleavage of abasic site-containing DNA.

Alanine↗