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PubMed1995

Transactivation domain 2 (TA2) of p65 NF-kappa B. Similarity to TA1 and phorbol ester-stimulated activity and phosphorylation in intact cells.

The p65 subunit of the inducible transcription factor NF-kappa B contains at least two strong transactivation domains (TADs) within its C terminus. The first domain, TA1, is contained within the last 30 amino acids of p65, whereas TA2 comprises the adjacent 90 amino acids. In this study, squelching experiments revealed that both TADs of p65, as well as the related subunit c-Rel, compete for the same cofactor(s) mediating transactivation. Both TADs of p65 share a common sequence motif, which is evolutionarily conserved and displays a remarkable degree of spatial organization when aligned on an alpha-helical surface. The functional importance of the common sequence motif was confirmed by deletion analysis of TA2. Within the conserved sequence motif, a 7-amino-acid repeat was noted. Idealized heptad repeats fused to the DNA binding domain of Gal4 were transcriptionally active, but only as multimers. Phosphorylation and transcriptional activity of a defined region within the TA2 domain was found to be stimulated by phorbol ester treatment of cells. In contrast, TA1 was constitutively phosphorylated, and its activity did not significantly respond to phorbol ester stimulation. The stimulatory effect of phorbol ester on transcription of the TA2 domain was completely blocked by the protein kinase C inhibitor. These data suggest that protein kinase C has a dual effect on NF-kappa B activity. It not only causes removal of I kappa B-alpha from cytoplasmic NF-kappa B but also augments the transactivation potential of activated nuclear NF-kappa B.

Amino Acid Sequence↗

PubMed2006

Fine-scale genetic structure among genetic individuals of the clone-forming monotypic genus Echinosophora koreensis (Fabaceae).

BACKGROUND AND AIMS: For rare endemics or endangered plant species that reproduce both sexually and vegetatively it is critical to understand the extent of clonality because assessment of clonal extent and distribution has important ecological and evolutionary consequences with conservation implications. A survey was undertaken to understand clonal effects on fine-scale genetic structure (FSGS) in two populations (one from a disturbed and the other from an undisturbed locality) of Echinosophora koreensis, an endangered small shrub belonging to a monotypic genus in central Korea that reproduces both sexually and vegetatively via rhizomes. METHODS: Using inter-simple sequence repeats (ISSRs) as genetic markers, the spatial distribution of individuals was evaluated using Ripley's L(d)-statistics and quantified the spatial scale of clonal spread and spatial distribution of ISSR genotypes using spatial autocorrelation analysis techniques (join-count statistics and kinship coefficient, F(ij)) for total samples and samples excluding clones. KEY RESULTS: A high degree of differentiation between populations was observed (phi(ST(g)) = 0.184, P < 0.001). Ripley's L(d)-statistics revealed a near random distribution of individuals in a disturbed population, whereas significant aggregation of individuals was found in an undisturbed site. The join-count statistics revealed that most clones significantly aggregate at < or = 6-m interplant distance. The Sp statistic reflecting patterns of correlograms revealed a strong pattern of FSGS for all four data sets (Sp = 0.072-0.154), but these patterns were not significantly different from each other. At small interplant distances (< or = 2 m), however, jackknifed 95% CIs revealed that the total samples exhibited significantly higher F(ij) values than the same samples excluding clones. CONCLUSION: The strong FSGS from genets is consistent with two biological and ecological traits of E. koreensis: bee-pollination and limited seed dispersal. Furthermore, potential clone mates over repeated generations would contribute to the observed high F(ij) values among genets at short distance. To ensure long-term ex situ genetic variability of the endangered E. koreensis, individuals located at distances of 10-12 m should be collected across entire populations of E. koreensis.

Conservation of Natural Resources↗

PubMed2004

[Spatial distribution pattern of Chilo suppressalis analyzed by classical method and geostatistics].

Two original samples of Chilo suppressalis and their grid, random and sequence samples were analyzed by classical method and geostatistics to characterize the spatial distribution pattern of C. suppressalis. The limitations of spatial distribution analysis with classical method, especially influenced by the original position of grid, were summarized rather completely. On the contrary, geostatistics characterized well the spatial distribution pattern, congregation intensity and spatial heterogeneity of C. suppressalis. According to geostatistics, the population was up to Poisson distribution in low density. As for higher density population, its distribution was up to aggregative, and the aggregation intensity and dependence range were 0.1056 and 193 cm, respectively. Spatial heterogeneity was also found in the higher density population. Its spatial correlativity in line direction was more closely than that in row direction, and the dependence ranges in line and row direction were 115 and 264 cm, respectively.

Algorithms↗

PubMed2003

REST-PEEP: reduced scan time phase-encoded echo planar imaging.

Echo planar methodology can be used for rapid acquisition in three dimensions of k-space. There are two groups of sequences which have thus far been implemented. The first group is characterized by three-dimensional acquisition from a single RF excitation. Echo planar shift mapping and echo volume imaging are single-shot chemical shift imaging and three-dimensional spatial imaging techniques, respectively. Even though these methods are extremely fast, their spatial and spectral resolutions are poor. In the second group of sequences, echo planar imaging acquisition is repeated for every phase-encode gradient step to improve upon the spatial resolution and signal-to-noise ratio at the expense of acquisition time. Here we report a novel combination of these two groups of sequences aimed at providing additional flexibility in trade-offs between the spectral bandwidth, signal-to-noise ratio, spatial resolution and imaging time. Preliminary results for both chemical shift imaging and three-dimensional spatial imaging are presented. The chemical shift imaging was optimized for excitation of the N-acetyl aspartate (NAA). An interesting consequence of our approach is that the Nyquist ghost is transferred from the spectrum to the metabolite image.

Algorithms↗

PubMed1987

MR sequence parameter optimization: an algorithmic approach.

The MR pulsing sequence is often described by terms such as spatial resolution, signal-to-noise, coverage, acquisition time, and contrast. These might be considered "secondary" parameters because they are not set directly but are instead specified indirectly by setting the "primary" parameters: field of view; projections (phase-encoded or readout); slice thickness and gap; number of excitations; and the sequence parameter times--repetition, echo delay, and inversion. Together, the primary and secondary parameters specify the MR pulsing sequence. Many of these parameters are interrelated such that setting one parameter indirectly affects another. Parameter specification is thus an iterative procedure that involves compromises to achieve an optimum relative to some predefined criteria. In this article, we examine the interrelationships between the primary and secondary parameters that specify the spin-echo pulsing sequence and suggest an algorithmic approach for selecting the best sequence parameters.

Algorithms↗

PubMed1994

Towards a clarification of spatial processing.

Three experiments that adopt an interference paradigm to investigate characteristics of a type of movement causing interference with spatial processing are reported. Experiment 1 illustrates the importance of distinguishing between movement and attention to movement when investigating the movement characteristics of spatial processing. The technique of passive movement is used to minimize attention in the subsequent experiments. Experiment 2 confirms earlier experiments showing that passive movement causes interference in spatial processing. However, it extends the previous findings by demonstrating that passive movement is detrimental to spatial processing only when the movement is to a sequence of locations known in advance by the subjects. Experiment 3 demonstrates that the movement interference cannot be interpreted as a general interference effect but that it is selective for spatial processing. The results of these experiments permit a more precise delineation of the disruptive effects of movement in spatial processing and allow an explicit definition of spatial processing to be put forward.

Attention↗

PubMed1999

Homologues of the Cf-9 disease resistance gene (Hcr9s) are present at multiple loci on the short arm of tomato chromosome 1.

The tomato Cf-4 and Cf-9 genes map at a genetically complex locus on the short arm of chromosome 1 and confer resistance against Cladosporium fulvum through recognition of different pathogen-encoded avirulence determinants. Cf-4 and Cf-9 are members of a large gene family (Hcr9s, Homologues of Cladosporium fulvum resistance gene Cf-9), some of which encode additional distinct recognition specificities. A genetic analysis of the majority of Hcr9s suggests that their distribution is spatially restricted to the short arm of chromosome 1. Two loci of clustered Hcr9 genes have been analyzed physically that mapped distal (Northern Lights) and proximal (Southern Cross) to the Cf-4/9 locus (Milky Way). Sequence homologies between intergenic regions at Southern Cross and Milky Way indicate local Hcr9 duplication preceded cluster multiplication. The multiplication of clusters involved DNA flanking Hcr9 sequences as indicated by conserved lipoxygenase sequences at Southern Cross and Milky Way. The similar spatial distribution of Hcr9 clusters in different Lycopersicon spp. suggests Hcr9 cluster multiplication preceded speciation.

Base Sequence↗

PubMed2003

Determinant for endoplasmic reticulum retention in the luminal domain of the human cytomegalovirus US3 glycoprotein.

US3 of human cytomegalovirus is an endoplasmic reticulum resident transmembrane glycoprotein that binds to major histocompatibility complex class I molecules and prevents their departure. The endoplasmic reticulum retention signal of the US3 protein is contained in the luminal domain of the protein. To define the endoplasmic reticulum retention sequence in more detail, we have generated a series of deletion and point mutants of the US3 protein. By analyzing the rate of intracellular transport and immunolocalization of the mutants, we have identified Ser58, Glu63, and Lys64 as crucial for retention, suggesting that the retention signal of the US3 protein has a complex spatial arrangement and does not comprise a contiguous sequence of amino acids. We also show that a modified US3 protein with a mutation in any of these amino acids maintains its ability to bind class I molecules; however, such mutated proteins are no longer retained in the endoplasmic reticulum and are not able to block the cell surface expression of class I molecules. These findings indicate that the properties that allow the US3 glycoprotein to be localized in the endoplasmic reticulum and bind major histocompatibility complex class I molecules are located in different parts of the molecule and that the ability of US3 to block antigen presentation is due solely to its ability to retain class I molecules in the endoplasmic reticulum.

Amino Acid Motifs↗

PubMed1990

Stereo and motion cues in preattentive vision processing--some experiments with random-dot stereographic image sequences.

Low-level preattentive vision processing is of special interest since it seems the logical starting point of all vision processing. Exploration of the human visual processing system at this level is, however, extremely difficult, but can be facilitated by the use of stroboscopic presentation of sequences of random-dot stereograms, which contain only local spatial and temporal information and therefore limit the processing of these images to the low level. Four experiments are described in which such sequences were used to explore the relationships between various cues (optical flow, stereo disparity, and accretion and deletion of image points) at the low level. To study these relationships in more depth, especially the resolution of conflicting information among the cues, some of the image sequences presented information not usually encountered in 'natural' scenes. The results indicate that the processing of these cues is undertaken as a set of cooperative processes.

Attention↗

PubMed1993

The regulation of myogenin gene expression during the embryonic development of the mouse.

The myogenic program can be activated in cultured cells by each of four basic-helix-loop-helix (bHLH) transcription factors, the expression of which is strictly controlled, both temporally and spatially, during embryonic development. To begin to understand the mechanisms by which these regulators are regulated themselves, we have used transgenic animals to define the minimal sequences required for the complete recapitulation of the temporal and spatial expression pattern of the myogenin gene during embryogenesis. We show that this can be achieved with only 133 bp of 5'-flanking DNA and identify two essential motifs, which are consensus binding sites for the bHLH proteins and for the proteins of the RSRF family. We show further that these sequences, when juxtaposed to a heterologous promoter, are capable of imposing the myogenin expression pattern. We conclude that the proper regulation of myogenin requires a bHLH protein, most probably Myf-5, the only myogenic bHLH factor known to be present in the embryo at the time that myogenin is activated, and an RSRF-like binding activity. Furthermore, the expression pattern of a mutant myogenin promoter lacking the RSRF site reveals the existence of at least two populations of cells within the myotomes and of novel rostrocaudal gradients of expression.

Animals↗

PubMed1993

Comparative protein modelling by satisfaction of spatial restraints.

We describe a comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures. The three-dimensional (3D) model is obtained by optimally satisfying spatial restraints derived from the alignment and expressed as probability density functions (pdfs) for the features restrained. For example, the probabilities for main-chain conformations of a modelled residue may be restrained by its residue type, main-chain conformation of an equivalent residue in a related protein, and the local similarity between the two sequences. Several such pdfs are obtained from the correlations between structural features in 17 families of homologous proteins which have been aligned on the basis of their 3D structures. The pdfs restrain C alpha-C alpha distances, main-chain N-O distances, main-chain and side-chain dihedral angles. A smoothing procedure is used in the derivation of these relationships to minimize the problem of a sparse database. The 3D model of a protein is obtained by optimization of the molecular pdf such that the model violates the input restraints as little as possible. The molecular pdf is derived as a combination of pdfs restraining individual spatial features of the whole molecule. The optimization procedure is a variable target function method that applies the conjugate gradients algorithm to positions of all non-hydrogen atoms. The method is automated and is illustrated by the modelling of trypsin from two other serine proteinases.

Amino Acid Sequence↗

PubMed2001

Magnetic resonance imaging-based assessment of cartilage loss in severe osteoarthritis: accuracy, precision, and diagnostic value.

OBJECTIVE: To examine the in vivo accuracy and precision of magnetic resonance imaging (MRI)-based assessment of cartilage loss in patients with severe osteoarthritis (OA) of the knee. METHODS: High-resolution MRI images of the tibial cartilage were obtained in 8 patients prior to total knee arthroplasty, using a water-excitation gradient-echo MRI sequence (acquisition time 6 minutes 19 seconds; spatial resolution 1.2 x 0.31 x 0.31 mm3). The MRI measurements were repeated after joint repositioning. The precision of the cartilage volume and thickness computations was determined after 3-dimensional reconstruction. During surgery, the tibial plateaus were resected, and the MRI data were compared with water displacement of surgically retrieved cartilage. RESULTS: The standard deviation (coefficient of variation) of repeated tibial cartilage volume measurements was 56 mm3 (5.5%) medially and 59 mm3 (3.8%) laterally. The deviation from surgically removed tissue was -13%, on average, with a high linear correlation between both methods (r = 0.98). In patients with varus OA, the tissue loss was estimated to be 1,290 mm3 in the medial tibia and 1,150 mm3 in the lateral tibia, compared with the data in healthy volunteers. CONCLUSION: Noninvasive quantitative MRI-based analysis of cartilage morphometry in severe OA is accurate, precise, and displays high potential diagnostic value.

Aged↗

PubMed2001

High-resolution intracranial and cervical MRA at 3.0T: technical considerations and initial experience.

Initial experience with intracranial and cervical MRA at 3.0T is reported. Phantom measurements (corrected for relaxation effects) show S/N (3.0T) = 2.14 +/- 0.08 x S/N (1.5T) in identical-geometry head coils. A 3.0T 3DTOF intracranial imaging protocol with higher-order autoshimming was developed and compared to 1.5T 3DTOF in 12 patients with aneurysms. A comparison by two radiologists showed the 3.0T to be significantly better (P < 0.001) for visualization of the aneurysms. The feasibility of cervical and intracranial contrast enhanced MR angiography (CEMRA) at 3.0T is also examined. The relaxivity of the gadolinium contrast agent decreases by only about 4-7% when the field strength is increased from 1.5 to 3.0T. Cervical 3.0T CEMRA was obtained in eight patients, two of whom had 1.5T studies available for direct comparison. Image comparison suggests 3.0T to be a favorable field strength for cervical CEMRA. Voxel volumes of 0.62-0.73 mm(3) (not including zero-filling) were readily achieved at 3.0T with the use of a single-channel transmit-receive head or cervical coil, a 25 mL bolus of gadoteridol, and a 3D pulse sequence with a 66% sampling efficiency. This spatial resolution allowed visualization of intracranial aneurysms, carotid dissections, and atherosclerotic disease including ulcerations. Potential drawbacks of 3.0T MRA are increased SAR and T(*)(2) dephasing compared to 1.5T. Image comparison suggests signal loss due to T(*)(2) dephasing will not be substantially more problematic than at 1.5T. The dependence of RF power deposition on TR for CEMRA is calculated and discussed.

Brain↗

PubMed1997

Fluorescence in situ hybridization with comets.

We have adapted the fluorescence in situ hybridization technique to single-cell gel electrophoresis (comet assayed) preparations. Since cells were embedded in agarose, probed regions could be visualized in three dimensions. This system makes it possible to determine the spatial distribution of chromosome-specific DNA sequences at the level of the individual nucleus (nonelectrophoresed) as well as in chromatin fibers of comets (electrostretched chromosomal DNA). This methodology is likely to bring new insights into the field of interphase nuclear ultrastructure. Here, we present the preliminary data obtained with human blood lymphocytes in Gzero after they have been electrophoresed for different times. Chromosome-specific areas (all centromeres, all telomeres, chromosome 7-specific centromere, and long arm of chromosome 3-specific telomere, as well as three segments of the O6-methylguanine-DNA methyltransferase gene) were investigated. Our results are in agreement with the concept that telomeres are in close association with the nuclear membrane and suggest that centromeres are relatively less condensed structures located in the center of the interphase nucleus.

Centromere↗

PubMed1997

Conformation-invariant structures of the alpha1beta1 human hemoglobin dimer.

Analysis of the conformational differences between the oxy and deoxy forms of hemoglobin is complicated by shifting coordinate systems and correlated motions between different parts of the molecule. Methods independent of any frame of reference were used to study the differences in structure between the oxy and deoxy forms of the human hemoglobin alphabeta dimer. Differences between the deoxy and oxy dimer structures can be characterized as rearrangements of 15 substructures persisting between the two conformations. Such substructures are of two kinds, either rigid domains or tertiary substructures. Rigid domains are groups of residues for which all inter-residue distances are conformationally invariant. Residues belonging to a rigid domain do not have to be spatially contiguous nor must they have consecutive sequence numbers. The largest such substructure is a rigid core that spans both the alpha and beta monomers and includes 44% of the dimer. Other rigid domains exist within the heme pockets. An alternative but closely related view of the molecule is based on tertiary substructures. Unlike a rigid domain, a tertiary substructure must have consecutively numbered residues and the residue that ends one tertiary substructure begins the next. The decomposition of the dimer into tertiary substructures represents the dimer as a framework of connected stiff structural elements. Viewed as a set of tertiary substructures, the hemoglobin dimer has the same three principal functional elements: the dimer core and the alpha and beta heme pockets, with the heme pockets held to the dimer core by CD and FG corners. The tertiary substructures that comprise the dimer core include 51% of the molecule. When ligands bind at the hemes, the FG corners communicate structural changes in the hemes to the dimer cores, which may mediate heme-heme cooperativity.

Amino Acid Sequence↗

PubMed1997

Distributed large-scale simulation of magnetic resonance imaging.

The concept and the implementation of a parallelized and spin-based simulator for magnetic resonance (MR) imaging is presented. The dynamics of magnetization are modeled using the Bloch equation covering arbitrary radiofrequency (RF) pulses, gradients, main-field inhomogeneity, and relaxation. A temporal decomposition of a given sequence is introduced, leading to basic sequence elements called atoms. A concept of spatial sampling of the object by spins is proposed, in the course of which Shannon's sampling theorem must be respected. In biomedical MR imaging, spins can be modeled as noninteracting entities, permitting an efficient parallelization of the simulation. The simulator ParSpin was implemented on a heterogeneous, interconnected cluster of workstations based on existing message passing libraries. The communication overhead has been kept moderately small. The aggregate computing performance of many processors enables the research into very complex problems (e.g., three-dimensional or steady-state MR experiments requiring up to 10(6) spins). Additionally, ParSpin allows a comprehensive visualization for educational purposes.

Computer Simulation↗

PubMed2002

Fast and ultrafast non-echo-planar MR imaging techniques.

The topic fast and ultrafast MR imaging commonly includes relatively slow gradient-echo techniques with spoiled transverse magnetization (FLASH, FFE-T1, SPGR), gradient-echo techniques with partially refocused transverse magnetization (FISP, FFE, GRASS), gradient-echo techniques with fully refocused transverse magnetization (trueFISP, balanced FFE, FIESTA), the multi-echo spin-echo techniques (RARE, TSE, FSE), a mixture of multi-echo spin-echo and gradient-echo techniques (GRASE, TGSE), and finally single-shot techniques (HASTE, SS-FSE, EPI). This article gives a description of the sequence structures of non-echo-planar fast imaging techniques and a list of potential clinical applications. Recent advances in faster imaging which are not sequence related, such as simultaneous acquisitions of spatial harmonics (SMASH) and sensitivity encoding (SENSE) for fast MRI, are mentioned as well as some novel techniques such as QUEST and BURST. Due to the recent success with gradient-echo techniques with fully refocused transverse magnetization (trueFISP, balanced FFE, FIESTA), this "faster" gradient-echo technique is discussed in more detail followed by multi-echo spin-echo techniques that present the counterpart to the multi-echo gradient-echo (EPI) technique, which is not discussed in this paper. Three major areas appear to be the domain for EPI: diffusion; perfusion; and blood oxygenation level dependent imaging (BOLD, fMRI). For all other applications there is ample room for utilizing other fast and ultrafast imaging techniques, due to some intrinsic problems with EPI.

Echo-Planar Imaging↗

PubMed2003

A feature-integration account of sequential effects in the Simon task.

Recent studies have shown that the effects of irrelevant spatial stimulus-response (S-R) correspondence (i.e., the Simon effect) occur only after trials in which the stimulus and response locations corresponded. This has been attributed to the gating of irrelevant information or the suppression of an automatic S-R route after experiencing a noncorresponding trial-a challenge to the widespread assumption of direct, intentionally unmediated links between spatial stimulus and response codes. However, trial sequences in a Simon task are likely to produce effects of stimulus- and response-feature integration that may mimic the sequential dependencies of Simon effects. Four experiments confirmed that Simon effects are eliminated if the preceding trial involved a noncorresponding S-R pair. However, this was true even when the preceding response did not depend on the preceding stimulus or if the preceding trial required no response at all. These findings rule out gating/suppression accounts that attribute sequential dependencies to response selection difficulties. Moreover, they are consistent with a feature-integration approach and demonstrate that accounting for the sequential dependencies of Simon effects does not require the assumption of information gating or response suppression.

Adolescent↗