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At least 1,081 records · Page 60Linked to original sources

PubMed2005

Prospective correction of affine motion for arbitrary MR sequences on a clinical scanner.

The concept of prospective 3D affine motion correction was generalized, based on the Bloch equations, for signal excitation and sampling using arbitrary MR sequences. The technique was implemented on a clinical MRI scanner for Cartesian, radial, and spiral imaging sequences, as well as for 2D spatially selective RF excitation pulses. A patient-specific motion model steered by real-time navigators was employed to account for the additional degrees of freedom provided by the affine motion model. Different navigator concepts (multiple spatial and temporal navigators, quadratic navigators and other motion sensors) were investigated, with the aim of improving the correlation between navigator information and the motion model. Experiments on moving phantoms are presented to prove the technical feasibility of the approach. In vivo experiments on coronary MRA and renal MRI show the potential of the method for cardiac and abdominal applications hampered by respiratory motion.

Adult↗

PubMed2006

Single breath-hold whole-heart MRA using variable-density spirals at 3T.

Multislice breath-held coronary imaging techniques conventionally lack the coverage of free-breathing 3D acquisitions but use a considerably shorter acquisition window during the cardiac cycle. This produces images with significantly less motion artifact but a lower signal-to-noise ratio (SNR). By using the extra SNR available at 3 T and undersampling k-space without introducing significant aliasing artifacts, we were able to acquire high-resolution fat-suppressed images of the whole heart in 17 heartbeats (a single breath-hold). The basic pulse sequence consists of a spectral-spatial excitation followed by a variable-density spiral readout. This is combined with real-time localization and a real-time prospective shim correction. Images are reconstructed with the use of gridding, and advanced techniques are used to reduce aliasing artifacts.

Artifacts↗

PubMed1998

Opposite behavior of two isozymes when refolding in the presence of non-ionic detergents.

GroEL has a greater affinity for the mitochondrial isozyme (mAAT) of aspartate aminotransferase than for its cytosolic counterpart (cAAT) (Mattingly JR Jr, Iriarte A, Martinez-Carrion M, 1995, J Biol Chem 270:1138-1148), two proteins that share a high degree of sequence similarity and an almost identical spatial structure. The effect of detergents on the refolding of these large, dimeric isozymes parallels this difference in behavior. The presence of non-ionic detergents such as Triton X-100 or lubrol at concentrations above their critical micelle concentration (CMC) interferes with reactivation of mAAT unfolded in guanidinium chloride but increases the yield of cAAT refolding at low temperatures. The inhibitory effect of detergents on the reactivation of mAAT decreases progressively as the addition of detergents is delayed after starting the refolding reaction. The rate of disappearance of the species with affinity for binding detergents coincides with the slowest of the two rate-limiting steps detected in the refolding pathway of mAAT. Limited proteolysis studies indicate that the overall structure of the detergent-bound mAAT resembles that of the protein in a complex with GroEL. The mAAT folding intermediates trapped in the presence of detergents can resume reactivation either upon dilution of the detergent below its CMC or by adding beta-cyclodextrin. Thus, isolation of otherwise transient productive folding intermediates for further characterization is possible through the use of detergents.

Anilino Naphthalenesulfonates↗

PubMed2005

Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data.

The number of structures of protein-protein complexes deposited to the Protein Data Bank is growing rapidly. These structures embed important information for predicting structures of new protein complexes. This motivated us to develop the PPISP method for predicting interface residues in protein-protein complexes. In PPISP, sequence profiles and solvent accessibility of spatially neighboring surface residues were used as input to a neural network. The network was trained on native interface residues collected from the Protein Data Bank. The prediction accuracy at the time was 70% with 47% coverage of native interface residues. Now we have extensively improved PPISP. The training set now consisted of 1156 nonhomologous protein chains. Test on a set of 100 nonhomologous protein chains showed that the prediction accuracy is now increased to 80% with 51% coverage. To solve the problem of over-prediction and under-prediction associated with individual neural network models, we developed a consensus method that combines predictions from multiple models with different levels of accuracy and coverage. Applied on a benchmark set of 68 proteins for protein-protein docking, the consensus approach outperformed the best individual models by 3-8 percentage points in accuracy. To demonstrate the predictive power of cons-PPISP, eight complex-forming proteins with interfaces characterized by NMR were tested. These proteins are nonhomologous to the training set and have a total of 144 interface residues identified by chemical shift perturbation. cons-PPISP predicted 174 interface residues with 69% accuracy and 47% coverage and promises to complement experimental techniques in characterizing protein-protein interfaces. .

Binding Sites↗

PubMed2002

HBXAP, a novel PHD-finger protein, possesses transcription repression activity.

The PHD/LAP (plant homology domain/leukemia associated protein) finger motif is characteristically defined by a histidine and seven cysteines that are spatially arranged in a C4HC3 consensus sequence. This unique zinc finger, found primarily in a wide variety of chromatin-associated proteins, is considered to mediate protein-protein interactions. We have isolated a novel human PHD-finger protein, HBXAP (for hepatitis B virus x associated protein). HBXAP has three alternatively spliced isoforms. We also identified the Drosophila melanogaster HBXAP ortholog, gene CG8677. Based on alignment of four different proteins, we found a novel conserved domain in HBXAP that we designated the HBXAP conserved domain (XCD). We show that HBXAP represses transcription when recruited to DNA via the DNA binding of GAL4. Furthermore, the PHD finger alone suffices to repress transcription, thus attributing a functional role to this domain. The gene HBXAP is localized to the long arm of human chromosome 11 between q13.4 and q14.1. This region is amplified and rearranged in many tumors, suggesting a role for HBXAP in tumorigenesis similar to that of other PHD-containing proteins.

Amino Acid Motifs↗

PubMed1988

Prediction of probable pathways of folding in globular proteins.

A method is described for the prediction of probable folding pathways of globular proteins, based on the analysis of distance maps. It is applicable to proteins of unknown spatial structure but known amino acid sequence as well as to proteins of known structure. It is based on an objective procedure for the determination of the boundary of compact regions that contain high densities of interresidue contacts on the distance map of a globular protein. The procedure can be used both with contact maps derived from a known three-dimensional protein structure and with predicted contact maps computed by means of a statistical procedure from the amino acid sequence alone. The computed contact map can also be used to predict the location of compact short-range structures, viz. alpha-helices and beta-turns, thereby complementing other statistical predictive procedures. The method provides an objective basis for the derivation of a theoretically predicted pathway of protein folding, proposed by us earlier [Tanaka and Scheraga (1977) Macromolecules 10, 291-304; Némethy and Scheraga (1979) Proc. Natl. Acad. Sci., U.S.A. 76, 6050-6054].

Adenylate Kinase↗

PubMed1990

Molecular anatomy: phyletic relationships derived from three-dimensional structures of proteins.

A distance measure that reflects the dissimilarity among structures has been developed on the basis of the three-dimensional structures of similar proteins, this being totally independent of sequence in the sense that only the relative spatial positions of mainchain alpha-carbon atoms need be known. This procedure leads to phyletic relationships that are in general correlated with the sequence phylogenies based on residue type. Such relationships among known protein three-dimensional structures are also a useful aid to their classification and selection in knowledge-based modeling using homologous structures. We have applied this approach to six homologous sets of proteins: immunoglobulin fragments, globins, cytochromes c, serine proteinases, eye-lens gamma crystallins, and dinucleotide-binding domains.

Amino Acid Sequence↗

PubMed2006

[MRI in staging of lung cancer].

PURPOSE: Overview of magnetic resonance imaging (MRI) in staging of lung cancer. MATERIAL AND METHODS: Currently available methods of imaging lung cancer, lymph node and distant metastases by MRI are explained. At present, MRI is mainly used in the detection of cerebral metastases and assessment of infiltration of the thoracic wall and of the mediastinum. The capabilities of T2-weighted single-shot TSE (HASTE) and T1-weighted 3D gradient echo techniques (VIBE) are demonstrated. RESULTS: With the advent of new fast sequences like HASTE and VIBE the spatial resolution comes close to that of computed tomography but with an outstanding soft tissue contrast and without radiation exposure. The introduction of lymph node specific contrast media will improve sensitivity and specificity in N staging. Additionally, whole-body MRI is capable of detecting distant metastases, in particular in the organs at risk, i.e. brain, upper abdomen and musculoskeletal system. CONCLUSION: MRI is gaining importance as part of a multimodal imaging approach for staging of lung cancer.

Humans↗

PubMed2002

Selective attention to pain: a psychophysical investigation.

Laboratory research suggests that the processing of painful stimuli can be modulated by selective attention to a particular sensory modality. However, alternative accounts for previous findings remain possible in terms of task-switching and spatial attention effects. In the present study, we examined whether attention can be selectively directed to the pain modality in order to facilitate the processing of the sensory-discriminative aspects of painful laser heat stimuli when these alternatives were ruled out. Participants made speeded spatial discrimination responses to an unpredictable sequence of painful laser heat and visual stimuli presented on the left forearm. On each trial, a symbolic cue predicted the likely modality for the upcoming target on the majority of trials. Participants responded more rapidly when the target was presented in the expected as opposed to the unexpected modality, demonstrating that selective attention can modulate the processing of painful stimuli. These findings are discussed in relation to contemporary theories of crossmodal attention and multisensory information-processing.

Attention↗

PubMed2004

Molecular diversity among communities of freshwater microchlorophytes.

Current hypotheses on the distribution of freshwater microchlorophytes lead to predictions of low diversity and wide environmental tolerances. Thus, the same few species should be found worldwide in many different habitats. However, these hypotheses are based on a morphospecies concept, which precludes the possibility of numerous cryptic species among these organisms. In this study, we examined the diversity of coccoid green microalgae and chlamydomonads (Chlorophyta) isolated from sites in Minnesota and North Dakota (USA) using techniques of 18S rDNA sequence analysis. Of 93 distinct 18S rDNA sequences identified from among 273 isolates examined by molecular techniques, all but four are new to science. The spatial distribution of organisms represented by these 18S rDNA sequences was not uniform, because some lakes and ponds yielded distinct 18S rDNA types not found at other sites. In addition, organisms generally considered to be cosmopolitan, such as Chlamydomonas reinhardtii and Chlorella vulgaris, were not found. These results challenge predictions of low species number and wide environmental tolerances among these eukaryotic microorganisms.

Base Sequence↗

PubMed1992

Tissue-restricted accumulation of a ribosomal protein mRNA is not coordinated with rRNA transcription and precedes growth of the sea urchin pluteus larva.

We have identified an mRNA that encodes a protein, SpS24, of the small ribosomal subunit in the sea urchin, Strongylocentrotus purpuratus. RNA blot and in situ hybridization analyses show that the SpS24 gene is active during early oogenesis, downregulated in the mature egg and during cleavage, and reactivated in the early blastula. The mRNA then increases in abundance at least 100-fold. Later in development, expression of SpS24 mRNA becomes restricted primarily to cells in the oral ectoderm and endoderm of the pluteus larva, and the message is undetectable in aboral ectoderm cells and most mesenchyme cells. To determine whether transcription of the ribosomal RNA genes occurs at a higher rate in oral ectoderm and endoderm tissues, a probe for the transcribed spacer was used in RNase protection and in situ hybridization assays. High concentrations of rRNA-processing intermediates were observed in unfertilized eggs and shown to reside primarily, if not exclusively, in the cytoplasm. The spatial and temporal distributions of these sequences strongly suggest that they are associated with heavy bodies. New embryonic rRNA transcripts are first detectable at the very early blastula stage. In later embryos, the content of this transcribed spacer sequence is similar in all but a few cells, which implies that they synthesize rRNA at a similar low rate. Comparison of available estimates of rRNA transcription rate with the potential rate of SpS24 protein synthesis, calculated from SpS24 mRNA prevalence, shows that oral ectoderm and endoderm cells have the capacity to synthesize 15- to 30-fold more SpS24 protein than is required to keep pace with rRNA synthesis in these cells. Because the sea urchin embryo develops from an egg to a pluteus larva in the absence of growth, this stockpiling of SpS24 mRNA anticipates rather than accompanies the onset of growth, which does not begin until after feeding. Upregulation of this gene is therefore part of the developmental program, rather than a physiological response to nutrient availability.

Amino Acid Sequence↗

PubMed1995

Differential effects of molecular chaperones on refolding of homologous proteins.

Three homologous aspartate aminotransferases with virtually identical spatial structures and pairwise amino acid sequence identities of > 40% differ markedly with respect to the yield of renaturation upon dilution from 6 M guanidine hydrochloride (mitochondrial << cytosolic < Escherichia coli). The enzymes also respond differently to molecular chaperones. GroEL/GroES, the Hsp60 homolog of E. coli, increased considerably the yield of renaturation of mitochondrial aspartate aminotransferase and to a lesser extent that of its cytosolic counterpart, but not that of the E. coli enzyme. DnaK/DnaJ/GrpE, the Hsp70 system of E. coli, also increased the yield of renaturation of mitochondrial aspartate aminotransferase. Apparently, specific features in the amino acid sequence or the folding pathway which are independent of the final secondary and tertiary structure determine the interactions of the folding proteins with the chaperone systems.

Animals↗

PubMed1993

The dimensionality of texture-defined motion: a single channel theory.

We examine apparent motion carried by textural properties. The texture stimuli consist of a sequence of grating patches of various spatial frequencies and amplitudes. Phases are randomized between frames to insure that first-order motion mechanisms directly applied to stimulus luminance are not systematically engaged. We use ambiguous apparent motion displays in which a heterogeneous motion path defined by alternating patches of texture s (standard) and texture v (variable) competes with a homogeneous motion path defined solely by patches of texture s. Our results support a one-dimensional (single-channel) model of motion-from-texture in which motion strength is computed from a single spatial transformation of the stimulus--an activity transformation. The value assigned to a point in space-time by this activity transformation is directly proportional to the modulation amplitude of the local texture and inversely proportional to local spatial frequency (within the range of spatial frequencies examined). The activity transformation is modeled as the rectified output of a low-pass spatial filter applied to stimulus contrast. Our data further suggest that the strength of texture-defined motion between a patch of texture s and a patch of texture v is proportional to the product of the activities of s and v. A strongly counterintuitive prediction of this model borne out in our data is that motion between patches of different texture can be stronger than motion between patches of similar texture (e.g. motion between patches of a low contrast, low frequency texture 1 and patches of high contrast, high frequency texture h can be stronger than motion between patches of similar texture h).

Contrast Sensitivity↗

PubMed1994

Conductive cation transport in apical membrane vesicles prepared from fetal lung.

In order to characterise the apically-located conductive cation pathway of the type II pneumocyte, apical plasma membranes were prepared from mature fetal guinea pig lung. The protocol yielded purified apical membranes that enriched 19-fold with the brush border enzyme marker alkaline phosphatase; there was no significant contamination with other cellular membranes. A technique for imposing an outwardly-directed electrochemical Na+ gradient was used to amplify conductive 22Na+ uptake into vesicles. Uptake of 22Na+ was time-dependent, proportional to the magnitude of the Na+ gradient, specific and sensitive to the amiloride analogues phenamil and EIPA (apparent minimum Ki values of 50 nM and 10 microM, respectively, with maximum uptake inhibition of 42% and 39% at 100 microM). Uptake experiments in which the outwardly-directed Na+ gradient was replaced by outwardly-directed gradients of small monovalent cations and molecular cations were performed. The Na+/K+ permeability ratio was 1.2:1, and over the extended range of small monovalent cations, a permeability sequence of Na+ > K+ > Li+ > Rb+ > Cs+ was observed, indicating the presence of fixed negative charge in or spatially close to the pore. The molecular cation permeability sequence of NH4+ > methylamine+ > dimethylamine+ > choline+ > N-methyl-D-glucamine+ > tetraethylammonium+ > tetramethylammonium+, after transformation, gives an estimate of 8 A for the conducting pore diameter. These data are consistent with the presence in the apical membrane of fetal type II pneumocytes of a cation specific channel with low Na+ selectivity and amiloride sensitivity.

Animals↗

PubMed1978

Chemical analysis of stalk components of Dictostelium discoideum.

Structural components of the stalks of mature fruiting bodies of Dictyostelium discoideum have been isolated and characterized after solubilizing non-structural components with urea and sodium dodecyl sulfate. The urea/sodium dodecyl sulfate-insoluble stalks are composed of about 52% cellulose, 15% protein and 3% of a non-cellulosic heteropolymer in a covalently bound matrix. Non-covalently bound fatty acid containing material was also found. The composition and structural interrelationships of these components are essentially identical to that of the urea/sodium dodecyl sulfate-insoluble surface sheath which is produced earlier in development before culmination. These results suggest that the same components are involved in making structural elements which differ substantially in their functional role in the developmental sequence as well as in their spatial and temporal localization and morphological appearance.

Amino Acids↗

PubMed1989

Neurogenesis of the peripheral nervous system in Drosophila embryos: DNA replication patterns and cell lineages.

Cell lineages that give rise to the PNS were studied using the thymidine analog 5-bromo-2'-deoxyuridine (BrdU) to visualized DNA replication immunocytochemically. The precursors of the PNS in the body segments of Drosophila embryos replicate their DNA in a spatially and temporally stereotyped pattern. The sequence of DNA replication within developing sensory organs suggests particular lineage relationships of the cells that constitute a sensory organ, i.e., neuron and associated support cells. In embryos that are mutant for the achaete-scute complex or daughterless, in which most or all of the PNS is missing, no BrdU-labeled cells were found in the appropriate regions, suggesting that these PNS precursors either do not form or fail to replicate. Thus, the BrdU technique allows determination as to whether a mutation affects the PNS precursors or terminal differentiation.

Animals↗

PubMed2005

Galanin and perseveration.

Galanin is a 29/30 amino acid neuropeptide that has been shown to impair learning and memory task performance and also have roles in somatosensation, stress responses, sexual behavior, and feeding regulation. However, little is known about galanin involvement in higher cognitive processes, especially executive processes. Perseveration is a classic sign of frontal cortex damage and failure of executive control. Galanin has been shown to disrupt the performance of maze delayed alternation tasks and the operant, spatial delayed nonmatch-to-position (DNMTP) working memory task, tests especially sensitive to perseverative responding. To better understand this potential involvement of galanin in executive control, the present study tested the hypothesis that galanin induces perseveration. The first experiment examined the effects of galanin (10, 20 microg i.c.v.) on the performance of a simple operant response alternation task in which stimuli were assigned to one of two spatially distinct locations to produce extended sequences of presentations to one location, separated by a 10-s intertrial interval. The second experiment looked at the effects of galanin (5, 20 microg i.c.v.) on the performance of non-delayed match-to-position and nonmatch-to-position conditional discrimination operant tasks in which a minimal 1.0 s time interval separated responses. Finally, the effects of galanin (10, 20 microg i.c.v.) on delayed match-to-position (DMTP) performance were examined to determine whether response alternation (i.e., nonmatching) was critical to observing a galanin-induced impairment in this task. Galanin reduced the rate of trial completion in all the tasks, but did not alter simple or conditional discrimination accuracy. Galanin (10 microg) impaired DMTP performance in a delay-independent manner. Together, these data suggest that galanin does not produce perseveration, but are consistent with a galanin-induced decrease in reinforcer strength.

Animals↗

PubMed2006

A computational theory of hippocampal function, and empirical tests of the theory.

The main aim of the paper is to present an up-to-date computational theory of hippocampal function and the predictions it makes about the different subregions (dentate gyrus, CA3 and CA1), and to examine behavioral and electrophysiological data that address the functions of the hippocampus and particularly its subregions. Based on the computational proposal that the dentate gyrus produces sparse representations by competitive learning and via the mossy fiber pathway forces new representations on the CA3 during learning (encoding), it has been shown behaviorally that the dentate gyrus supports spatial pattern separation during learning. Based on the computational proposal that CA3-CA3 autoassociative networks are important for episodic memory, it has been shown behaviorally that the CA3 supports spatial rapid one-trial learning, learning of arbitrary associations where space is a component, pattern completion, spatial short-term memory, and sequence learning by associations formed between successive items. The concept that the CA1 recodes information from CA3 and sets up associatively learned backprojections to neocortex to allow subsequent retrieval of information to neocortex, is consistent with findings on consolidation. Behaviorally, the CA1 is implicated in processing temporal information as shown by investigations requiring temporal order pattern separation and associations across time; computationally this could involve temporal decay memory, and temporal sequence memory which might also require CA3. The perforant path input to DG is implicated in learning, to CA3 in retrieval from CA3, and to CA1 in retrieval after longer time intervals ("intermediate-term memory").

Animals↗