Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “spatial domain identification”

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 37 records · Page 2Linked to original sources
PubMed2000

Nuclear topology of murine, cerebellar Purkinje neurons: changes as a function of development.

The interphase nucleus is a structurally ordered, three-dimensional structure, in which specific chromatin domains occupy distinct spatial positions that can, in turn, be modified with changes in cell function. A fundamental goal in developmental neurobiology is the identification of mechanisms that dictate the orderly expression of genes in a cell-specific manner. Given that different neuronal populations feature a characteristic spatial topology of centromeric sequences, the positioning of specific DNA sequences may constitute such a mechanism. We tested the hypothesis that the cell-specific nuclear topology in fully differentiated neurons is acquired before or during that stage at which neuron-specific sequences are first expressed. For this, we assessed the number and spatial distribution of centromeric domains in the murine, cerebellar Purkinje neuron as a function of postnatal development. Centromeric domains were localized by immunofluorescence of centromere-associated kinetochore proteins and visualized by confocal microscopy. Kinetochores are known to cluster in Purkinje neurons. Thus, the number of signals discerned is always less than the chromosome complement of the species. The number of signals observed in adults (10.8 +/- 0.46) (mean +/- SEM) is established by postnatal day 15 (P15), after a transient decrease from 11.44 +/- 0.44 at P0 to 8.78 +/- 0.24 at P3. The distribution of signals characteristic of the adult, with the majority located at the nucleolus, is established by P5 and is associated with a decrease in the fraction of signals at the nuclear periphery. These changes are temporally associated with the onset of processes such as dendritic differentiation and synaptic maturation and might serve the process of differentiation by placing specific sequences into transcriptionally competent, nuclear sites.

Aging↗
PubMed1997

Molecular structure of the sarcomeric M band: mapping of titin and myosin binding domains in myomesin and the identification of a potential regulatory phosphorylation site in myomesin.

The M band of sarcomeric muscle is a highly complex structure which contributes to the maintenance of the regular lattice of thick filaments. We propose that the spatial coordination of this assembly is regulated by specific interactions of myosin filaments, the M band protein myomesin and the large carboxy-terminal region of titin. Corresponding binding sites between these proteins were identified. Myomesin binds myosin in the central region of light meromyosin (LMM, myosin residues 1506-1674) by its unique amino-terminal domain My1. A single titin immunoglobulin domain, m4, interacts with a myomesin fragment spanning domains My4-My6. This interaction is regulated by phosphorylation of Ser482 in the linker between myomesin domains My4 and My5. Myomesin phosphorylation at this site by cAMP-dependent kinase and similar or identical activities in muscle extracts block the association with titin. We propose that this demonstration of a phosphorylation-controlled interaction in the sarcomeric cytoskeleton is of potential relevance for sarcomere formation and/or turnover. It also reveals how binding affinities of modular proteins can be regulated by modifications of inter-domain linkers.

Alanine↗
PubMed2004

Genome-wide identification of Arabidopsis coiled-coil proteins and establishment of the ARABI-COIL database.

Increasing evidence demonstrates the importance of long coiled-coil proteins for the spatial organization of cellular processes. Although several protein classes with long coiled-coil domains have been studied in animals and yeast, our knowledge about plant long coiled-coil proteins is very limited. The repeat nature of the coiled-coil sequence motif often prevents the simple identification of homologs of animal coiled-coil proteins by generic sequence similarity searches. As a consequence, counterparts of many animal proteins with long coiled-coil domains, like lamins, golgins, or microtubule organization center components, have not been identified yet in plants. Here, all Arabidopsis proteins predicted to contain long stretches of coiled-coil domains were identified by applying the algorithm MultiCoil to a genome-wide screen. A searchable protein database, ARABI-COIL (http://www.coiled-coil.org/arabidopsis), was established that integrates information on number, size, and position of predicted coiled-coil domains with subcellular localization signals, transmembrane domains, and available functional annotations. ARABI-COIL serves as a tool to sort and browse Arabidopsis long coiled-coil proteins to facilitate the identification and selection of candidate proteins of potential interest for specific research areas. Using the database, candidate proteins were identified for Arabidopsis membrane-bound, nuclear, and organellar long coiled-coil proteins.

Algorithms↗
PubMed2004

Identification of PCIF1, a POZ domain protein that inhibits PDX-1 (MODY4) transcriptional activity.

Hox factors are evolutionarily conserved homeodomain-containing transcription factors that activate and repress gene expression in a precise temporally and spatially regulated manner during development and differentiation. Pancreatic-duodenal homeobox 1 (PDX-1) is a Hox-type protein that is a critical requirement for normal pancreas development and for proper differentiation of the endocrine pancreas. In humans, PDX-1 gene mutation causes pancreatic agenesis and early- and late-onset type 2 diabetes. PDX-1 consists of an N-terminal transactivation domain, a homeodomain responsible for DNA binding and nuclear localization, and a conserved C terminus that is mutated in human diabetes but whose function is poorly understood. We have identified a novel POZ domain protein, PDX-1 C terminus-interacting factor 1 (PCIF1)/SPOP, that interacts with PDX-1 both in vitro and in vivo. PCIF1 is localized to the nucleus in a speckled pattern, and coexpression of PDX-1 alters the subnuclear distribution of PCIF1. Functionally, PCIF1 inhibits PDX-1 transactivation of established target gene promoters in a specific and dose-dependent manner that requires critical amino acids in the PDX-1 C terminus. PCIF1 is expressed in adult pancreatic insulin-producing beta cells, and overexpression of PCIF1 inhibits the rat insulin 1 and rat insulin 2 promoters in the MIN6 insulinoma beta cell line. The coexpression of PCIF1 with PDX-1 in beta cells and the ability of PCIF1 to repress PDX-1 transactivation suggest that modulation of PDX-1 function by PCIF1 may regulate normal beta cell differentiation.

Adaptor Proteins, Signal Transducing↗
PubMed2003

Weave-repeat identification by structural analysis of fabric images.

Two descriptions of the image of a web structure, a convolution model and an additive model, in both the spatial and frequency domains, are combined in the design of a method to extract information about the fabric structure by image analysis. The method allows the extraction of the conventional and also the minimal weave repeats, their size in terms of number of threads, their interlacing patterns, and their patterns of repetition. It is applicable to fabrics with square and nonsquare conventional weave repeat. Experimental results with image of real samples are presented and discussed.

Journal Article↗
PubMed1988

Prediction of the location of structural domains in globular proteins.

The location of structural domains in proteins is predicted from the amino acid sequence, based on the analysis of a computed contact map for the protein, the average distance map (ADM). Interactions between residues i and j in a protein are subdivided into several ranges, according to the separation [i-j[ in the amino acid sequence. Within each range, average spatial distances between every pair of amino acid residues are computed from a data base of known protein structures. Infrequently occurring pairs are omitted as being statistically insignificant. The average distances are used to construct a predicted ADM. The ADM is analyzed for the occurrence of regions with high densities of contacts (compact regions). Locations of rapid changes of density between various parts of the map are determined by the use of scanning plots of contact densities. These locations serve to pinpoint the distribution of compact regions. This distribution, in turn, is used to predict boundaries of domains in the protein. The technique provides an objective method for the location of domains both on a contact map derived from a known three-dimensional protein structure, the real distance map (RDM), and on an ADM. While most other published methods for the identification of domains locate them in the known three-dimensional structure of a protein, the technique presented here also permits the prediction of domains in proteins of unknown spatial structure, as the construction of the ADM for a given protein requires knowledge of only its amino acid sequence.

Adenylate Kinase↗
PubMed2003

The ScPex13p SH3 domain exposes two distinct binding sites for Pex5p and Pex14p.

Pex13p is an essential component of the peroxisomal protein import machinery and interacts via its C-terminal SH3 domain with the type II SH3-ligand Pex14p and the non-PXXP protein Pex5p. We report the solution structure of the SH3 domain of Pex13p from Saccharomyces cerevisiae and the identification of a novel-binding pocket, which binds a non-PXXP-peptide representing the binding site of Pex5p. Chemical shift assays revealed the binding sites for Pex5p and Pex14p ligand peptides to be distinct and spatially separated. Competition assays demonstrated that the two ligand peptides can bind simultaneously to the SH3 domain.

Amino Acid Motifs↗
PubMed1990

Immunochemical characterization of antigenic domains on human interferon-beta: spatially distinct epitopes are associated with both antiviral and antiproliferative activities.

The use of a panel of monoclonal antibodies (mAb) raised against recombinant (serine-17) human interferon-beta (rHuIFN-beta ser) has permitted the identification of three epitopes on HuIFN-beta, designated as sites I, II and III, based solely on functional differences, i.e., the neutralization of antiviral and antiproliferative activities of natural and recombinant HuIFN-beta (Redlich, P.N. and Grossberg, S. E., J. Immunol. 1989. 143: 1887). Site I- and II-directed mAb possessed neutralizing activity whereas none was noted by mAb recognizing site III. To characterize further these epitopes by immunochemical means, we studied their (a) spatial relationship by competitive binding assays, (b) antigenic structure by Western blotting, and (c) sensitivity to chemical modification by the measurement of mAb reactivity after radioiodination. Competitive antibody binding studies revealed site II to be spatially distinct from sites I and III. Furthermore, site I- and II-directed mAb could easily recognize rHuIFN-beta ser on a Western blot, suggesting that both these epitopes are primarily sequential in structure or denaturation resistant. Chemical modification by radioiodination, which did not alter the biologic activity of rHuIFN-beta ser, had likewise little effect on mAb reactivity to site I; however, reactivity to site II was diminished and reactivity to site III was minimal following the radioiodination process. Both site I- and II-directed mAb inhibited the binding of 125I-rHuIFN-beta ser to intact Daudi cells, suggesting that inhibition of receptor binding is their mechanism of neutralization. Thus, we conclude that epitopes I and II, which are associated with both antiviral and antiproliferative activities of rHuIFN-beta, are spatially and immunochemically distinct.

Antibodies, Monoclonal↗
PubMed1990

Nonlinear analysis of spatial vision using first-and-second-order Volterra transfer functions measurement.

The harmonic input method of nonlinear system identification is modified to allow the Volterra series approach to be used for psychophysical investigation of various aspects of human pattern vision in the spatial frequency domain. While it is well known that only one modulation transfer function provides a complete characterization of a linear system, a number of multidimensional transfer functions are needed to identify a nonlinear system. We have shown, that so far as the contrast sensitivity to sine-wave gratings may be used for an empirical estimate of the first-order modulation transfer function of the human visual system, the contrast sensitivity to difference harmonics may be used as an empirical estimate of the second-order modulation transfer function. A difference harmonic arises from a mixture of two sine-wave gratings resulting from the nonlinearity of the visual system. Difference harmonic, experienced as some periodic beatlike structure, may still be observed if frequencies of the component gratings are higher than the maximum visual acuity. The visibility of the low-frequency beatlike pattern produced by pairs of sine-wave gratings, which themselves are of spatial frequencies too high to be resolved, could be accounted for either by a difference frequency distortion product (Burton, 1973) or by a special beat detector (Derrington & Badcock, 1985). We found that increasing the contrast of one component grating may be compensated for by reducing the contrast of the other component grating, the beatlike pattern being at threshold. This is exactly what would be expected if the beatlike pattern is detected because of the difference harmonics produced by nonlinearity of the visual system. We have determined contrast thresholds for the difference harmonics which occur between two unresolved different spatial frequencies. The contrast sensitivity function for difference harmonics was found to have a marked similarity both in the shape and position of peak sensitivity to the contrast sensitivity function for single sine-wave gratings. Another important characteristic of the contrast sensitivity function for difference harmonics is that it depends only on the frequency difference, delta f = f1 - f2, rather than on the value of either f1 or f2. All this indicates that a difference harmonic arises from local nonlinearities in the visual system. More specifically, the visual system may be represented as a cascade system, composed of a linear system with transfer function O (f) followed by a nonlinear element, r(.), without spatial spread in cascade with another linear system with transfer function P (f).(ABSTRACT TRUNCATED AT 400 WORDS)

Contrast Sensitivity↗
PubMed2005

The receptor site of the spider toxin PcTx1 on the proton-gated cation channel ASIC1a.

Acid-sensing ion channels (ASICs) are excitatory neuronal cation channels, involved in physiopathological processes related to extracellular pH fluctuation such as nociception, ischaemia, perception of sour taste and synaptic transmission. The spider peptide toxin psalmotoxin 1 (PcTx1) has previously been shown to inhibit specifically the proton-gated cation channel ASIC1a. To identify the binding site of PcTx1, we produced an iodinated form of the toxin ((125)I-PcTx1Y(N)) and developed a set of binding and electrophysiological experiments on several chimeras of ASIC1a and the PcTx1-insensitive channels ASIC1b and ASIC2a. We show that (125)I-PcTx1Y(N) binds specifically to ASIC1a at a single site, with an IC(50) of 128 pM, distinct from the amiloride blocking site. Results obtained from chimeras indicate that PcTx1 does not bind to ASIC1a transmembrane domains (M1 and M2), involved in formation of the ion pore, but binds principally on both cysteine-rich domains I and II (CRDI and CRDII) of the extracellular loop. The post-M1 and pre-M2 regions, although not involved in the binding site, are crucial for the ability of PcTx1 to inhibit ASIC1a current. The linker domain between CRDI and CRDII is important for their correct spatial positioning to form the PcTx1 binding site. These results will be useful for the future identification or design of new molecules acting on ASICs.

Acid Sensing Ion Channels↗
PubMed2002

Mental maps in memory retrieval and comprehension.

How do people use spatial information stored in maps? This question has been explored in a number of domains, such as memory and language comprehension, with differing results. Some studies of how experimentally learned maps are organised in memory, using primed recognition, have found temporal information to influence mental map organisation. In contrast, studies of narrative comprehension, using probe identification and anaphoric reading times, have observed spatial effects. This study combines these two research traditions and shows that the organisation observed in long-term memory differs from the organisation in narrative comprehension, even when both tasks refer to the same map.

Cognition↗
PubMed2006

Classification images for detection, contrast discrimination, and identification tasks with a common ideal observer.

We consider three simple forced-choice visual tasks--detection, contrast discrimination, and identification--in Gaussian white noise. The three tasks are designed so that the difference signal in all three cases is the same difference-of-Gaussians (DOG) profile. The distribution of the image noise implies that the ideal observer uses the same DOG filter to perform all three tasks. But do human observers also use the same visual strategy to perform these tasks? We use classification image analysis to evaluate the visual strategies of human observers. We find significantly different subject classification images across the three tasks. The domain of greatest variability appears to be low spatial frequencies [<5 cycles per degree (cpd)]. In this range, we find frequency enhancement in the detection task, and frequency suppression and reversal in the contrast discrimination task. In the identification task, subject classification images agree reasonably well with the ideal observer filter. We evaluate the effect of nonlinear transducers and intrinsic spatial uncertainty to explain divergence from the ideal observer found in detection and contrast discrimination tasks.

Choice Behavior↗
PubMed1995

[A new approach for the automatic detection of health event clusters].

The Italian Morality Atlas at municipality level, sponsored by the Health Ministry and realized by the Emilia-Romagna region in collaboration with the Institute of Medical Statistics of Milano, is aimed at: 1) supporting and stimulating the local production of mortality maps and the use of geographical data; 2) providing a working and research tool to local health planners; 3) setting a routine procedure for the detection of spatial clusters. This procedure is organized in several steps: the definition of the spatial domain and of the spatial distance metrics; the choice of the effect indicator and the standard population; the estimate of the density risk surface via kernel methods; the identification of "local maxima"; the analysis of local maxima for cluster detection; the description of the identified clusters. The paper investigates the meaning and the characteristics of spatial clusters, describes the procedure for their identification and discusses the opportunity to use an automated approach for map reading.

Cervical Atlas↗
PubMed2004

Characterization of palmprints by wavelet signatures via directional context modeling.

The palmprint is one of the most reliable physiological characteristics that can be used to distinguish between individuals. Current palmprint-based systems are more user friendly, more cost effective, and require fewer data signatures than traditional fingerprint-based identification systems. The principal lines and wrinkles captured in a low-resolution palmprint image provide more than enough information to uniquely identify an individual. This paper presents a palmprint identification scheme that characterizes a palmprint using a set of statistical signatures. The palmprint is first transformed into the wavelet domain, and the directional context of each wavelet subband is defined and computed in order to collect the predominant coefficients of its principal lines and wrinkles. A set of statistical signatures, which includes gravity center, density, spatial dispersivity and energy, is then defined to characterize the palmprint with the selected directional context values. A classification and identification scheme based on these signatures is subsequently developed. This scheme exploits the features of principal lines and prominent wrinkles sufficiently and achieves satisfactory results. Compared with the line-segments-matching or interesting-points-matching based palmprint verification schemes, the proposed scheme uses a much smaller amount of data signatures. It also provides a convenient classification strategy and more accurate identification.

Algorithms↗
PubMed1999

Vertebrate odorant receptors.

Olfactory transduction begins with the binding of an odorous molecule to a protein receptor--odorant receptor--on the cell surface of olfactory neuron. Odorant receptors are encoded by a large gene family belonging to the superfamily of G-protein-coupled, seven-transmembrane-domain receptors. Since the identification of the receptor gene family in 1991, a considerable amount of progress has been made in the study of odorant receptors, including aspects of spatial and temporal expression pattern, the genomic organization of the receptor genes, regulation of expression, and receptor function. These studies are of critical importance in understanding how the olfactory system recognizes and distinguishes thousands of odors.

Animals↗
PubMed2006

Spatial segregation of transport and signalling functions between human endothelial caveolae and lipid raft proteomes.

Lipid rafts and caveolae are biochemically similar, specialized domains of the PM (plasma membrane) that cluster specific proteins. However, they are morphologically distinct, implying different, possibly complementary functions. Two-dimensional gel electrophoresis preceding identification of proteins by MS was used to compare the relative abundance of proteins in DRMs (detergent-resistant membranes) isolated from HUVEC (human umbilical-vein endothelial cells), and caveolae immunopurified from DRM fractions. Various signalling and transport proteins were identified and additional cell-surface biotinylation revealed the majority to be exposed, demonstrating their presence at the PM. In resting endothelial cells, the scaffold of immunoisolated caveolae consists of only few resident proteins, related to structure [CAV1 (caveolin-1), vimentin] and transport (V-ATPase), as well as the GPI (glycosylphosphatidylinositol)-linked, surface-exposed protein CD59. Further quantitative characterization by immunoblotting and confocal microscopy of well-known [eNOS (endothelial nitric oxide synthase) and CAV1], less known [SNAP-23 (23 kDa synaptosome-associated protein) and BASP1 (brain acid soluble protein 1)] and novel [C8ORF2 (chromosome 8 open reading frame 2)] proteins showed different subcellular distributions with none of these proteins being exclusive to either caveolae or DRM. However, the DRM-associated fraction of the novel protein C8ORF2 (approximately 5% of total protein) associated with immunoseparated caveolae, in contrast with the raft protein SNAP-23. The segregation of caveolae from lipid rafts was visually confirmed in proliferating cells, where CAV1 was spatially separated from eNOS, SNAP-23 and BASP1. These results provide direct evidence for the previously suggested segregation of transport and signalling functions between specialized domains of the endothelial plasma membrane.

Caveolae↗
PubMed2006

Arabidopsis TEBICHI, with helicase and DNA polymerase domains, is required for regulated cell division and differentiation in meristems.

In plant meristems, each cell divides and differentiates in a spatially and temporally regulated manner, and continuous organogenesis occurs using cells derived from the meristem. We report the identification of the Arabidopsis thaliana TEBICHI (TEB) gene, which is required for regulated cell division and differentiation in meristems. The teb mutants show morphological defects, such as short roots, serrated leaves, and fasciation, as well as defective patterns of cell division and differentiation in the meristem. The TEB gene encodes a homolog of Drosophila MUS308 and mammalian DNA polymerase theta, which prevent spontaneous or DNA damage-induced production of DNA double strand breaks. As expected from the function of animal homologs, teb mutants show constitutively activated DNA damage responses. Unlike other fasciation mutants with activated DNA damage responses, however, teb mutants do not activate transcriptionally silenced genes. teb shows an accumulation of cells expressing cyclinB1;1:GUS in meristems, suggesting that constitutively activated DNA damage responses in teb lead to a defect in G2/M cell cycle progression. Furthermore, other fasciation mutants, such as fasciata2 and tonsoku/mgoun3/brushy1, also show an accumulation of cells expressing cyclinB1;1:GUS in meristems. These results suggest that cell cycle progression at G2/M is important for the regulation of the pattern of cell division and of differentiation during plant development.

Arabidopsis↗
PubMed1996

A discrete site modulates activation of I domains. Application to integrin alphaMbeta2.

A central characteristic of integrin adhesion receptors is their capacity to become activated, thereby enhancing their affinity for ligands. Here, we report the identification of a discrete site within the I domain of integrin alphaMbeta2, which modulates the adhesive activity of this receptor. Based upon the crystal structure, this region is composed of two short and spatially proximal loops, E162QLKKSKTL and Q190NNPNPRS. Mutations in these loops yield receptors which support spontaneous cell adhesion to fibrinogen, whereas mutation of an adjacent region and wild-type receptors require activation to adhere to this substrate. An activating monoclonal antibody enhanced the adhesive activity of one but not the other loop mutants, suggesting that the activation states of these two mutant receptors were not identical. Given that similar I domains exist in several other integrin alpha subunits and non-integrin proteins, and possibly in all integrin beta subunits, these two loop segments may represent a universal target for controlling integrin activation and the function of other I domain-containing proteins. In support of this hypothesis, several naturally occurring mutations that activate von Willebrand factor map to the same loops of its I(A) domain.

Amino Acid Sequence↗