Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “connectivity mapping”

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 865 records · Page 48Linked to original sources
PubMed1999

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283-291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coefficient between observed and calculated structure-factor amplitudes and Rfree (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coefficient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the refinement procedure and in assessing structures deposited in databases.

Amino Acid Sequence↗
PubMed2004

Haphazard wiring of simple receptive fields and orientation columns in visual cortex.

The receptive fields of simple cells in visual cortex are composed of elongated on and off subregions. This spatial arrangement is widely thought to be responsible for the generation of orientation selectivity. Neurons with similar orientation preferences cluster in "columns" that tile the cortical surface and form a map of orientation selectivity. It has been proposed that simple cell receptive fields are constructed by the selective pooling of geniculate receptive fields aligned in space. A recent analysis of monosynaptic connections between geniculate and cortical neurons appears to reveal the existence of "wiring rules" that are in accordance with the classical model. The precise origin of the orientation map is unknown, but both genetic and activity-dependent processes are thought to contribute. Here, we put forward the hypothesis that statistical sampling from the retinal ganglion cell mosaic may contribute to the generation of simple cells and provide a blueprint for orientation columns. Results from computer simulations show that the "haphazard wiring" model is consistent with data on the probability of monosynaptic connections and generates orientation columns and maps resembling those found in the cortex. The haphazard wiring hypothesis could be tested by measuring the correlation between the orientation map and the structure of the retinal ganglion cell mosaic of the contralateral eye.

Animals↗
PubMed2006

Non-invasive mapping of corticofugal fibres from multiple motor areas--relevance to stroke recovery.

Recovery of motor function after subcortical stroke appears to be related to the integrity of descending connections from the ipsilesional cortical motor system, a view supported by the observation of greater than normal movement-related activation in ipsilesional motor regions in chronic subcortical stroke patients. This suggests that damage to the descending output fibres from one region of the cortical motor system may be compensated by activity in areas that retain corticofugal outputs. Though the trajectories of corticofugal fibres from each major component of the motor system through the corona radiata and internal capsule are well described in non-human primates, they have not been described fully in humans. Our study set out to map the trajectories of these connections in a group of healthy volunteers (8 male, 4 female; age range = 31-68 years, median = 48.5 years) and establish whether this knowledge can be used to assess stroke-induced disconnection of the cortical motor system and better interpret functional reorganization of the cortical motor system. We describe the trajectories of the connections from each major component of the motor system to the cerebral peduncle using diffusion-weighted imaging and probabilistic tractography in normal subjects. We observed good reproducibility of these connections over subjects. The comparative topography of these connections revealed many similarities between humans and other primates. We then inferred damage to corticofugal pathways in stroke patients (n = 3) by comparing the overlap between regions of subcortical white matter damage with the trajectories of the connections to each motor area. In a small series of case studies, we found that inferred disconnections could explain enhanced hand-grip-related responses, as assessed with functional MRI, in the ipsilesional motor system. These results confirm that selective disruption of motor corticofugal fibres influences functional reorganization and outcome in individual patients.

Adult↗
PubMed1996

Mutations disrupting the ordering and topographic mapping of axons in the retinotectal projection of the zebrafish, Danio rerio.

Retinal ganglion cells connect to their target organ, the rectum, in a highly ordered fashion. We performed a large-scale screen for mutations affecting the retinotectal projection of the zebrafish, which resulted in the identification of 114 mutations. 44 of these mutations disturb either the order of RGC axons in the optic nerve and tract, the establishment of a topographic map on the tectum, or the formation of proper termination fields. Mutations in three genes, boxer, dackel and pinscher, disrupt the sorting of axons in the optic tract but do not affect mapping on the tectum. In these mutants, axons from the dorsal retina grow along both the ventral and the dorsal branch of the optic tract. Mutations in two genes, nevermind and who-cares, affect the dorsoventral patterning of the projection. In embryos homozygous for either of these mutations, axons from dorsal retinal ganglion cells terminate ventrally and dorsally in the tectum. In nevermind, the retinotopic order of axons along the optic nerve and tract is changed in a characteristic way as well, while it appears to be unaffected in who-cares. Two mutations in two complementation groups, gnarled and macho, affect the anteroposterior patterning of the projection. In these mutants, nasodorsal axons branch and terminate too soon in the anterior tectum. In 27 mutants belonging to six complementation groups, retinal axons do not form normal termination fields. Some implications for models concerning the formation of topographic projections are discussed.

Animals↗
PubMed1991

Thalamocortical responses of mouse somatosensory (barrel) cortex in vitro.

We have developed a novel slice preparation of the mouse somatosensory forebrain. This preparation is unique in including both the ventrobasal nucleus of the thalamus and the sensorimotor "barrel" cortex in a 400-microns-thick slice with the functional connectivity between them preserved, and in allowing direct visualization of the various components of the barrel system in unstained living tissue. Thalamocortical connectivity was demonstrated by recording the laminar profile of cortical field potentials evoked electrically from the ventrobasal nucleus. Current-source density analysis of this profile showed that the largest and earliest sinks were coextensive with the two known sites of thalamocortical terminals, layer IV and the junction of layers V and VI. The sink in layer IV could be dissociated experimentally into a small, early sink of presynaptic origin (most probably a presynaptic spike volley in the thalamocortical terminals) and a later, larger sink generated postsynaptically. By mapping the subcortical stimulation sites that elicited a response at different layer IV recording sites we concluded that the thalamus-to-cortex projection preserves the general dorsoventral relationship of the afferents. Intracellularly recorded responses elicited by thalamic stimulation included (but were not limited to) monosynaptic excitatory and disynaptic inhibitory postsynaptic potentials. The thalamus-to-cortex connections were also mapped with the axonal fluorescent tracer dioctadecyl-tetramethylindocarbocyanine perchlorate. The thalamo-cortical slice is a very suitable system for studying the physiology and pharmacology of the thalamocortical synapse and for exploring the synaptic circuitry of the somatosensory cortex.

Animals↗
PubMed1991

Rostrocaudal and lateromedial density distributions of superior colliculus neurons projecting in the predorsal bundle and to the spinal cord: a retrograde HRP study in the cat.

Efferent neurons of the cat superior colliculus (SC) which project in the predorsal bundle (PDB) and to the spinal cord (PDB neurons) form a major pathway by which the SC controls the changes of the direction of gaze in response to stimuli of visual and other modalities. Knowledge of rostrocaudal and lateromedial density distributions of different groups of PDB neurons within the SC is necessary to analyse their relationships with the topography of sensory and motor maps. Density gradients may also bear on the efficacy of connections originating from topographically different collicular regions. In the present study, large injections of HRP/WGA-HRP were made in the C1 segment of the spinal cord and in the pontobulbar tegmentum. Judged by several morphological criteria, axons of passage, including those not subjected to a direct mechanical damage, were participating in the uptake of tracers. Therefore, labeled SC neurons corresponded to the nearly total populations of contralaterally projecting tectospinal neurons (TSNs) and neurons projecting in the PDB, respectively. Subtraction of the TSN density map from that of the whole PDB population was used to infer the distribution of tectal neurons terminating in the rhombencephalic tegmentum (TRhN). This subtotal labeling method proved useful in resolving the contradictions between the earlier HRP studies on the TSN and TRhN topography. The following density distributions were obtained for different groups of PDB neurons: 1) The mean TSN density is more than two times higher in the lateral half of the SC, representing the lower visual field. In this region the density remains constant from rostral to caudal, i.e., from the representation of vertical meridian to large contralateral azimuths. In the medial half, the average density decreases from rostral to caudal. Consequently, TSNs do not show the caudalward increment predicted by the higher efficacy of caudal stimulation points in eliciting head movements. 2) The distribution of PDB neurons is symmetrical with respect to the representation of the horizontal meridian. It is close to homogeneous at all azimuths of the retinotopic map and within the zone limited by small (10-15 degrees) upward and downward elevations.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2002

Lateral connectivity and contextual interactions in macaque primary visual cortex.

Two components of cortical circuits could mediate contour integration in primary visual cortex (V1): intrinsic horizontal connections and feedback from higher cortical areas. To distinguish between these, we combined functional mapping with a new technique for labeling axons, a recombinant adenovirus bearing the gene for green fluorescent protein (GFP), to determine the extent, density, and orientation specificity of V1 intrinsic connections and V2 to V1 feedback. Both connections cover portions of V1 representing regions of visual space up to eight times larger than receptive fields as classically defined, though the intrinsic connections are an order of magnitude denser than the feedback. Whereas the intrinsic connections link similarly oriented domains in V1, V2 to V1 feedback displays no such specificity. These findings suggest that V1 intrinsic horizontal connections provide a more likely substrate for contour integration.

Adenoviridae↗
PubMed2002

Brain function in the vegetative state.

Positron emission tomography (PET) techniques represent a useful tool to better understand the residual brain function in vegetative state patients. It has been shown that overall cerebral metabolic rates for glucose are massively reduced in this condition. However, the recovery of consciousness from vegetative state is not always associated with substantial changes in global metabolism. This finding led us to hypothesize that some vegetative patients are unconscious not just because of a global loss of neuronal function, but rather due to an altered activity in some critical brain regions and to the abolished functional connections between them. We used voxel-based Statistical Parametric Mapping (SPM) approaches to characterize the functional neuroanatomy of the vegetative state. The most dysfunctional brain regions were bilateral frontal and parieto-temporal associative cortices. Despite the metabolic impairment, external stimulation still induced a significant neuronal activation (i.e., change in blood flow) in vegetative patients as shown by both auditory click stimuli and noxious somatosensory stimuli. However, this activation was limited to primary cortices and dissociated from higher-order associative cortices, thought to be necessary for conscious perception. Finally, we demonstrated that vegetative patients have impaired functional connections between distant cortical areas and between the thalami and the cortex and, more importantly, that recovery of consciousness is paralleled by a restoration of this cortico-thalamo-cortical interaction.

Cerebral Cortex↗
PubMed2000

Effects of acute and chronic ethanol exposure on spatial cognitive processing and hippocampal function in the rat.

Animals, including rats, have a predisposition to process and use spatial information to organize and guide behavior. The hippocampus and related structures are critically involved in this function, and, consequently, it has been proposed that one function of the hippocampus is to construct "spatial cognitive maps" of environments. Lesions to the hippocampus or its connections produce a pattern of alterations in behavior which include shifts from the use of spatial information to guide behavior to the use of cue- or taxon-based information to guide behavior. Recently it was demonstrated that ethanol interacts with a specific group of neurotransmitter systems, i.e., N-methyl-D-aspartate receptors and GABA(A) receptors that exist in high proportions in the hippocampus and related structures. In this review, we seek to summarize the literature demonstrating that one effect of acute and chronic ethanol exposure is to produce behavioral alterations that are strikingly similar to those found following lesions to the hippocampal system. Furthermore, cellular and anatomical alterations resulting from similar ethanol exposure paradigms will be reviewed and offered as possible mechanisms for producing the alterations in behavior. Finally, several unanswered questions concerning the interaction between ethanol and spatial cognitive processing will be identified.

Acute Disease↗
PubMed1989

Organization of the projection from the superficial to the deep layers of the hamster's superior colliculus as demonstrated by the anterograde transport of Phaseolus vulgaris leucoagglutinin.

Anterograde tracing with Phaseolus vulgaris leucoagglutinin (PHA-L) was employed to describe the projection from the superficial to the deep layers of the hamster's superior colliculus (SC). Deposits of PHA-L in the stratum griseum superficiale (SGS) resulted in labelled terminal swellings in the stratum opticum and all of the deep laminae (the stratum griseum intermediate [SGI], stratum albumin intermedium [SAI], stratum griseum profundum [SGP], and stratum albumin profundum [SAP]). Labelled terminals were also visible in the periaqueductal gray (PAG). Reconstructions of individual axons showed that many collateral in the deep laminae arose from axons that projected to targets outside the colliculus. The projection from the superficial to the deep laminae had a loose topographic organization, and the trajectories of interlaminar axons were generally deflected laterally from "projection" lines that were orthogonal to the SC surface. Physiological recording and receptive field mapping were used to determine actual projection lines, which connect neurons in the superficial and deep layers that have receptive fields with the same elevation. These projection lines closely matched the trajectory of the pathway from the superficial to the deep laminae.

Animals↗
PubMed1978

Bromouracil mutagenesis and mismatch repair in mutator strains of Escherichia coli.

A screening procedure based on the formation of papillae on individual bacterial colonies was used to isolate mutants of Escherichia coli with high mutation rates in the presence of bromouracil. Most of the mutants obtained had high spontaneous mutation rates and mapped close to the previously known mutators mutT, mutS, mutR, uvrE and mutL. Except for mutants of mutT type, these mutators also showed high mutability by bromouracil. Transfection experiments were performed with heteroduplex lambda DNA to test for mismatch repair. The results suggest a reduced efficiency of repair of mismatched bases in mutators mutS, mutR, uvrE and mutL, whereas mutants mapping as mutT appear normal. The results support a connection between spontaneous and bromouracil-induced mutability and repair of mismatched bases in DNA.

Bromouracil↗
PubMed1980

Stabilizing and rapid thionin staining of TMB-based HRP reaction product.

Tetramethyl benzidine (TMB) as a substrate for horseradish peroxidase (HRP) histochemistry offers a great advantage over other substrates in its sensitivity but the reaction product is unstable in alcohol. Immersing TMB-reacted sections in methyl salicylate renders the reaction product stable enough so that exposure to ethanol for 10 min causes no detectable loss of HRP labelled neurons. A rapid thionin stain is introduced which, after stabilizing the TMB-based reaction product in methyl salicylate, causes no detectable loss of HRP labelled neurons. These procedures should prove valuable to users of the popular HRP techniques for studying neural connections.

Benzidines↗
PubMed2026

Extracellular Vesicles From Glioblastoma Cells Reflect 2D vs. 3D Culture Adaptation and Resistance to Temozolomide.

Glioblastoma (GBM) is an aggressive brain tumor marked by extensive heterogeneity, resistance to therapy, and dismal prognosis. Extracellular vesicles (EVs) have emerged as key players in GBM biology, mediating intercellular communication and therapy adaptation. However, the exact functions and molecular impact of EVs in GBM remain incompletely understood. In this study, we performed a comparative proteomic analysis of U87MG GBM cells grown in two-dimensional (2D) monolayers and three-dimensional (3D) spheroids following temozolomide (TMZ) treatment, alongside characterization of EVs derived from both culture systems. 3D-spheroids secreted more EVs of smaller size and exhibited a more TMZ-resistant, stem-like proteome under TMZ-induced genotoxic stress. In contrast, 2D cell cultures demonstrated greater proteome remodeling, with EVs enriched in protein families involved in DNA repair, oxidative stress adaptation, and methylation processes. Notably, several methyltransferases were decreased intracellularly but selectively retained in EVs, suggesting active sorting to influence the tumor microenvironment or modulate epigenetic states in recipient cells. EVs also carried adhesion molecules and signaling proteins linked to migration, invasion, and Wnt pathway activation, as well as metabolic enzymes connecting serine metabolism and redox control to TMZ resistance. Mapping EV and cellular proteomes onto The Cancer Genome Atlas (TCGA) dataset identified prognostic protein families associated with either poor or favorable patient outcomes. Our data demonstrate that EV cargo composition mirrors TMZ-induced phenotypic adaptation and reveals molecular mechanisms underlying therapeutic resistance. These EV-associated signatures may serve as clinically actionable biomarkers for patient stratification and offer potential targets to overcome chemoresistance in GBM.

Humans↗
PubMed2000

The structure of the H(+)-ATP synthase from chloroplasts and its subcomplexes as revealed by electron microscopy.

The electron microscopic data available on CF(0)F(1) and its subcomplexes, CF(0), CF(1), subunit III complex are collected and the CF(1) data are compared with the high resolution structure of MF(1). The data are based on electron microscopic investigation of negatively stained isolated CF(1), CF(0)F(1) and subunit III complex. In addition, two-dimensional crystals of CF(0)F(1) and CF(0)F(1) reconstituted liposomes were investigated by cryo-electron microscopy. Progress in the interpretation of electron microscopic data from biological samples has been made with the introduction of image analysis. Multi-reference alignment and classification of images have led to the differentiation between different conformational states and to the detection of a second stalk. Recently, the calculation of three-dimensional maps from the class averages led to the understanding of the spatial organisation of the enzyme. Such three-dimensional maps give evidence of the existence of a third connection between the F(0) part and F(1) part.

Chloroplasts↗
PubMedDate not supplied

Conceptual evaluation of the potential role of fractures in unsaturated processes at Yucca Mountain.

A wide array of field observations, in situ testing, and rock and water sampling (and subsequent analyses) within the unsaturated zone (UZ) of Yucca Mountain demonstrate the importance of fractures to flow and transport in the welded tuffs. The abundance of fractures and the spatial variability in their hydraulic properties, along with the heterogeneity within lithologic formations, make evaluation of unsaturated processes occurring within the potential repository horizon complex. Fracture mapping and field testing show that fractures are well connected, yet considerable variation is seen within and between units comprising the potential repository horizon with regard to fracture trace length, spacing, permeability, and capillarity. These variations have important implications for the distribution and movement of water and solutes through the unsaturated zone. Numerical models designed to assess such phenomena as unsaturated flow, transport, and coupled thermal-hydrological processes each require their own conceptual model for fracture networks, in order to identify the subset of all fractures that is relevant to the particular study. We evaluate several process-dependent conceptual models for fractures and identify the relevant fracture subsets related to these processes.

Forecasting↗
PubMed2005

Invariant computations in local cortical networks with balanced excitation and inhibition.

Cortical computations critically involve local neuronal circuits. The computations are often invariant across a cortical area yet are carried out by networks that can vary widely within an area according to its functional architecture. Here we demonstrate a mechanism by which orientation selectivity is computed invariantly in cat primary visual cortex across an orientation preference map that provides a wide diversity of local circuits. Visually evoked excitatory and inhibitory synaptic conductances are balanced exquisitely in cortical neurons and thus keep the spike response sharply tuned at all map locations. This functional balance derives from spatially isotropic local connectivity of both excitatory and inhibitory cells. Modeling results demonstrate that such covariation is a signature of recurrent rather than purely feed-forward processing and that the observed isotropic local circuit is sufficient to generate invariant spike tuning.

Action Potentials↗
PubMed2003

The sensor protein KdpD inserts into the Escherichia coli membrane independent of the Sec translocase and YidC.

KdpD is a sensor kinase protein in the inner membrane of Escherichia coli containing four transmembrane regions. The periplasmic loops connecting the transmembrane regions are intriguingly short and protease mapping allowed us to only follow the translocation of the second periplasmic loop. The results show that neither the Sec translocase nor the YidC protein are required for membrane insertion of the second loop of KdpD. To study the translocation of the first periplasmic loop a short HA epitope tag was genetically introduced into this region. The results show that also the first loop was translocated independently of YidC and the Sec translocase. We conclude that KdpD resembles a new class of membrane proteins that insert into the membrane without enzymatic assistance by the known translocases. When the second periplasmic loop was extended by an epitope tag to 27 amino acid residues, the membrane insertion of this loop of KdpD depended on SecE and YidC. To test whether the two periplasmic regions are translocated independently of each other, the KdpD protein was split between helix 2 and 3 into two approximately equal-sized fragments. Both constructed fragments, which contained KdpD-N (residues 1-448 of KdpD) and the KdpD-C (residues 444-894 of KdpD), readily inserted into the membrane. Similar to the epitope-tagged KdpD protein, only KdpD-C depended on the presence of the Sec translocase and YidC. This confirms that the four transmembrane helices of KdpD are inserted pairwise, each translocation event involving two transmembrane helices and a periplasmic loop.

Adenosine Triphosphatases↗
PubMed2003

Domain movements of HAP2 in the cap-filament complex formation and growth process of the bacterial flagellum.

The cap at the growing end of the bacterial flagellum is essential for its growth, remaining stably attached while permitting the insertion of flagellin transported from the cytoplasm through the narrow central channel. We analyzed the structure of the isolated cap in its frozen hydrated state by electron cryomicroscopy. The 3D density map now shows detailed features of domains and their connections, giving reliable volumes and masses, making assignment of the domains to the amino acid sequence possible. A model of the cap-filament complex built with an atomic model of the filament allows a quantitative analysis of the cap domain movements on cap binding and rotation that promotes the efficient self assembly of flagellin during the filament growth process.

Bacterial Proteins↗