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PubMed1993

Overlapping expression of Xwnt-3A and Xwnt-1 in neural tissue of Xenopus laevis embryos.

Xwnt-3A is a member of the Xenopus-Wnt gene family, a class of secreted, cysteine-rich proteins implicated in intercellular signaling during early development. Here we describe the full-length coding sequence of Xwnt-3A, as well as the spatial expression pattern of this Xwnt gene as determined by whole-mount in situ hybridization analysis. While Xwnt-3A shares considerable amino acid identity with both Wnt-3 (87%) and Wnt-3A (85%), its spatial expression pattern is most like that of Wnt-3A. Xwnt-3A, which is first detected at the neurula stage of development, is expressed exclusively along the dorsal midline of the developing brain and neural tube and along the dorsal surface of the otic vesicle. While the expression of Xwnt-1 extensively overlaps that of Xwnt-3A, Xwnt-1 is uniquely expressed along the midbrain/hindbrain boundary and is absent from the otic vesicle. The expression of Xwnt-3A in neural ectoderm is dependent upon neural induction as determined by experiments with recombined ectoderm and mesoderm tissue. These results suggest that Xwnt-3A may participate in patterning the central nervous system during early Xenopus development. Last, the ectopic expression of Xwnt-3A induces the formation of a secondary axis at the anterior end of the embryo.

Amino Acid Sequence↗

PubMed1994

Conserved patterns in the Cu,Zn superoxide dismutase family.

Conserved structural and functional features of Cu,Zn superoxide dismutase enzymes have been studied by comparison of known three-dimensional structures and analysis of the currently available amino acid sequences. For this purpose, the three-dimensional structures of the bovine, spinach and yeast enzymes have been superimposed and the structure-based sequence alignment of 38 different superoxide dismutases has been produced. The evolutionary tree obtained from the alignment indicates that cytosolic and extracellular enzymes followed independent evolutionary paths, and that horizontal gene transfer, if any, occurred at an early stage in eukaryota evolution. Based on the sequence alignment and on the analysis of clusters of spatially neighboring residues, the conservation/variation of functionally relevant intramolecular interactions has been investigated. Seven alternative residue arrangements have been identified in the upper rim of the active site, which form an important determinant of the electrostatic field at the catalytic center. The total nominal charge of this region is constantly -1 through the phyla. The seven residues which coordinate the two metal ions at the active site are conserved, with only one known exception. Among the residues involved in maintenance of the active site structure, Gly59, Gly80, Gly136 and Gly139 are fully conserved; mutations of Gly42 and Pro64 have been observed, concerted with replacements in their structural surroundings. Coordinated mutations affecting residue pairs which maintain the packing geometry of the Greek-key beta-barrel have been identified. Furthermore, the unique disulfide bridge involving Cys55-Cys144 in eukaryota, shows the alternative Cys50A-Cys144 arrangement in prokaryotic enzymes.

Amino Acid Sequence↗

PubMed1998

Volumetric analysis of white matter, gray matter, and CSF using fractional volume analysis.

Quantitative cerebral tissue volumes may be useful for an objective assessment of pathological changes in brain. Accurate determination of tissue volumes is complicated, however, by the partial volume averaging (PVA) effect. We have, therefore, developed a new pulse sequence that minimizes the PVA through the use of inversion-recovery (IR) and double inversion-recovery (DIR) techniques. This pulse sequence simultaneously acquires four different sets of images to provide the necessary information for volumetric analysis and reduces potential spatial misregistration of images due to patient motion. The image sets acquired from the proposed pulse sequence are 1) gray matter visible, 2) white matter visible, 3) FLAIR, and 4) fast spin-echo proton-density weighted images. An algorithm has been implemented to correct for differential T1-weighting and for tissue quantitation.

Artifacts↗

PubMed2006

Hidden Markov multiple event sequence models: A paradigm for the spatio-temporal analysis of fMRI data.

This paper presents a novel, completely unsupervised fMRI brain mapping method that addresses the three problems of hemodynamic response function (HRF) variability, hemodynamic event timing, and fMRI response non-linearity. Spatial and temporal information are directly taken into account into the core of the activation detection process. In practice, activation detection at voxel v is formulated in terms of temporal alignment between sequences of hemodynamic response onsets (HROs) detected in the fMRI signal at v and in the spatial neighborhood of v, and the input sequence of stimuli or stimulus onsets. Event-related and epoch paradigms are considered. The multiple event sequence alignment problem is solved within the probabilistic framework of hidden Markov multiple event sequence models (HMMESMs), a new class of hidden Markov models. Results obtained on real and synthetic data significantly outperform those obtained with the popular statistical parametric mapping (SPM2) method without requiring any prior definition of the expected activation patterns, the HMMESM mapping approach being completely unsupervised.

Adolescent↗

PubMed1996

Molecular dissection of effector cell protease receptor-1 recognition of factor Xa. Assignment of critical residues involved in antibody reactivity and ligand binding.

Receptor-mediated assembly of blood proteases on vascular cells maintains the hemostatic balance and initiates intracellular signal transduction. Effector cell protease receptor-1 (EPR-1) is an approximately 62-kDa vascular cell membrane receptor for the clotting protease factor Xa, participating in thrombin formation and lymphocyte activation. Here, recombinant EPR-1 fragments were engineered in the frame of intercellular adhesion molecule-1, transfected in mammalian cells, and analyzed for antibody recognition and ligand binding. Chimeric transfectants containing the EPR-1 sequence Met1-Arg60 bound the immunosuppressive anti-EPR-1 monoclonal antibody (mAb) 2E1. In contrast, transfected cells expressing the EPR-1 sequence Pro120-Ala154 were recognized by the functionally inhibitory anti-EPR-1 mAbs 9D4 and B6, bound 125I-factor Xa in a reaction quantitatively indistinguishable from that of wild-type EPR-1 transfectants, and promoted factor Xa concentration-dependent prothrombin activation in the absence of exogenous factor V/Va. Chimeric transfectants expressing the COOH terminus end of the EPR-1 extracellular domain (Ala157-Glu221) did not bind anti-EPR-1 mAbs and did not associate with factor Xa. Mutagenesis of Asn131 or Lys133 in the EPR-1 ligand recognition domain abolished factor Xa binding by 80 +/- 5.5 and 96 +/- 4%, respectively, while mutation of Lys126, Gly128, Asn129, and Asn134 was without effect. A synthetic peptide duplicating the EPR-1 sequence S123PGKPGNQNSKNEPP137 dose dependently inhibited factor V/Va-independent thrombin generation of resting endothelium (IC50 approximately 1 microM), while the adjacent EPR-1 sequence P136PKK-RERERSSHCYP150 was ineffective. These findings demonstrate that EPR-1 contains two spatially distinct functional domains implicated in lymphocyte activation (Met1-Arg60) or factor Xa binding and prothrombin activation (Pro120-Ala154). These interacting sequences may provide a novel potential target for inhibition of factor Xa-dependent vascular cell responses.

Amino Acid Sequence↗

PubMed1995

Cis-regulatory control of the SM50 gene, an early marker of skeletogenic lineage specification in the sea urchin embryo.

The SM50 gene encodes a minor matrix protein of the sea urchin embryo spicule. We carried out a detailed functional analysis of a cis-regulatory region of this gene, extending 440 bp upstream and 120 bp downstream of the transcription start site, that had been shown earlier to confer accurate skeletogenic expression of an injected expression vector. The distal portion of this fragment contains elements controlling amplitude of expression, while the region from -200 to +105 contains spatial control elements that position expression accurately in the skeletogenic lineages of the embryo. A systematic mutagenesis analysis of this region revealed four adjacent regulatory elements, viz two copies of a positively acting sequence (element D) that are positioned just upstream of the transcription start site; an indispensable spatial control element (element C) that is positioned downstream of the start site; and further downstream, a second positively acting sequence (element A). We then constructed a series of synthetic expression constructs. These contained oligonucleotides representing normal and mutated versions of elements D, C, and A, in various combinations. We also changed the promoter of the SM50 gene from a TATA-less to a canonical TATA box form, without any effect on function. Perfect spatial regulation was also produced by a final series of constructs that consisted entirely of heterologous enhancers from the CyIIIa gene, the SV40 early promoter, and synthetic D, C, and A elements. We demonstrate that element C exercises the primary spatial control function of the region we analyzed. We term this a 'locator' element. This differs from conventional 'tissue-specific enhancers' in that while it is essential for expression, it has no transcriptional activity on its own, and it requires other, separable, positive regulatory elements for activity. In the normal configuration these ancillary positive functions are mediated by elements A and D. Only positively acting control elements were observed in the SM50 regulatory domain throughout this analysis.

Animals↗

PubMed1985

Constructing mental representations of objects from successive views.

A three-dimensional analogue of Hochberg's (1968) aperture viewing paradigm, the orthogonal slices task, examined the effects of complexity on processing objects. Ten subjects constructed, transformed, and compared mental representations of Shepard-Metzler (1971) figures varying in the number of component parts; processing time increased with complexity. A second study showed no effects of complexity on processing time when subjects merely judged the equivalence of the patterns used in the first study presented in sequence. Rather, constructed mental representations appear to preserve some of the spatial character of the corresponding objects. This conclusion was strengthened by the results of recognition tasks which showed that discrimination of constructed objects from appropriate distractors is better after subjects do the first (orthogonal slices) task than after they do the second (sequence matching) task.

Adult↗

PubMed1991

The target DNA sequence for resolution of poxvirus replicative intermediates is an active late promoter.

The linear double-stranded genomes of poxviruses such as Shope fibroma virus (SFV) replicate autonomously within the cytoplasm of infected cells, and it is believed that all of the replication functions are virally encoded. During DNA replication the incompletely base-paired terminal hairpin loops of the viral genome transiently exist in the form of inverted repeat replicative intermediates. These inverted repeat structures form the target for telomere resolution events that include sequence-specific cleavage and directed strand exchange to form the hairpin termini of progeny virus genomes. The terminal sequence domain which forms the telomere resolution target (TRT) shares considerable sequence similarity with viral late promoters. In this study we demonstrate that the TRT of SFV is capable of functioning as a strong viral promoter late in infection. A spectrum of TRT mutations affects telomere resolution and late transcription in a strictly concordant fashion, suggesting that the two activities may be inextricably linked. Further support for this concept comes from the demonstration that a late SFV promoter sequence designated cryptic TRT, which differs substantially from the native TRT in terms of sequence, can support telomere resolution when placed in the correct spatial context. The proposed model for telomere resolution invokes directed unwinding of the TRT double helix by a transcription initiation complex and processing of the resulting secondary structure by viral late-gene products.

Animals↗

PubMed1997

Developmental analysis and subcellular localization of the murine homologue of ELL.

The ELL gene was first identified by its involvement with MLL in the translocation (11;19)(q23;p13.1) in acute myeloid leukemia. To date, nine other MLL partner genes have been cloned, but their precise functions have yet to be determined. To characterize the functions of ELL further, we have cloned the murine homologue of ELL and have found that the gene is highly conserved at the nucleotide and amino acid level. The open reading frame of the murine homologue contains 602 aa, slightly smaller than the 621 aa in the human gene. With Northern blot analysis, a 3.4-kb transcript is detected in all tissues examined with greatest levels of expression in the liver. Unlike human ELL, only a single transcript can be detected with either murine coding sequence or 3' untranslated region probes. To examine the spatial and temporal pattern of expression in murine development, in situ hybridization studies were performed with sense and antisense riboprobes from the 3' untranslated region of murine Ell. Ell is expressed diffusely by embryonic day 7.5 (E7.5). In addition, high levels of expression can be detected in maternally derived decidual tissue. At E14.5, Ell is expressed diffusely throughout the embryo. However by E16.5, specific expression in the liver and gastrointestinal tract becomes prominent and remains so in both neonates and adults. To determine the subcellular localization of ELL, we developed a polyclonal antiserum to ELL that was used for immunofluorescence studies in COS-7, HeLa, NIH 3T3, and A7r5 cells. The ELL protein was localized to the nucleus but excluded from nucleoli in all cell lines examined. Recently, the gene product of ELL was found to function as an RNA polymerase II elongation factor, an activity that is consistent with our immunofluorescence data. Thus, these studies extend our understanding of the normal functions of ELL and provide additional insight into its aberrant function when fused to MLL in acute myeloid leukemia.

Acute Disease↗

PubMed2001

Atrophy of Müller glia and photoreceptor cells in chick retina misexpressing cNSCL2.

PURPOSE: To investigate whether and how the basic helix-loop-helix (bHLH) gene cNSCL2 is involved in retinal development. METHODS: cNSCL2, the chick homologue of human NSCL2, was isolated and sequenced. In situ hybridization was used to examine its spatial and temporal expression pattern in the retina. Replication-competent retrovirus RCAS was used to drive cNSCL2 misexpression in the developing chick retina, and the effect of the misexpression was analyzed. RESULTS: Expression of cNSCL2 in the retina was restricted. Its mRNA was detected in amacrine and horizontal cells, but not in photoreceptor, bipolar, or ganglion cells. Retroviral-driven misexpression of cNSCL2 in the developing chick retina resulted in missing photoreceptor cells and gross deficits in the outer nuclear layer (ONL). These deficits were probably not because of decreased photoreceptor production, in that the ONL appeared normal in early developmental stages. TUNEL+ cells were detected in the ONL, indicating that photoreceptor cells underwent apoptosis in retinas misexpressing cNSCL2. Müller glial cells were far fewer in the experimental retina than in the control, indicating that cNSCL2 also caused Müller glia atrophy. The onset of Müller glia disappearance preceded that of photoreceptor degeneration. CONCLUSIONS: Expression of cNSCL2 in the chick retina was restricted to amacrine and horizontal cells. Misexpression of cNSCL2 caused severe retinal degeneration, and photoreceptor cells and Müller glia were particularly affected.

Animals↗

PubMed2000

Improved peripheral MRA using multi-velocity-encoding phase contrast-enhanced MRA techniques.

Phase contrast MR angiography (PC-MRA) depends on phase shifts caused by blood flow. Generally, PC sequences employ one VENC (velocity-encoding) value for each encoded spatial direction to optimize the signal in major vessels during peak systolic flow. We compared a mono-(30) with a multi-(20/30/45) VENC-PC-MRA technique in 10 patients with peripheral arterial occlusive disease. In all patients, the multi-VENC-PC sequence enhanced the vascular signal in vessels with very different flow velocities in one measurement. Large fields-of-view can be measured in a relatively short examination time to obtain an overview of the peripheral arterial system of the patient when contrast-enhanced MRA is not possible.

Arterial Occlusive Diseases↗

PubMed1999

Detection of homonuclear decoupled in vivo proton NMR spectra using constant time chemical shift encoding: CT-PRESS.

A new pulse sequence, termed CT-PRESS, is presented, which allows the detection of in vivo 1H NMR spectra with effective homonuclear decoupling. A PRESS sequence with a short echo-time TE, used for spatial localization, is supplemented by an additional 180 degrees pulse. The temporal position of this 180 degree pulse is shifted within a series of experiments, while the time interval between signal excitation and detection is kept constant. CT-PRESS is a two-dimensional (2D) spectroscopic experiment as far as data acquisition and processing are concerned, although only diagonal signals are generated in the 2D spectrum. However, since the principle of constant time chemical shift encoding is used in the t1 domain, effective homonuclear decoupling is obtained by projecting the 2D spectrum onto the corresponding f1 axis. Thus, good spectral resolution and high signal-to-noise ratio are obtained. The main advantage, as compared to localized 2D J-resolved MRS, is that optimized experiments can be performed for coupled resonances of interest by choosing the sequence parameters dependent on the type of multiplets, the J-coupling constants and T2. Major fields of application will be parametric studies on coupled resonances, (e.g., T1, diffusion behavior or magnetization transfer) and/or the detection of spatial and temporal changes of metabolites with coupled spin systes.

Animals↗

PubMed1993

Six members of the mouse forkhead gene family are developmentally regulated.

The 110-aa forkhead domain defines a class of transcription factors that have been shown to be developmentally regulated in Drosophila melanogaster and Xenopus laevis. The forkhead domain is necessary and sufficient for target DNA binding as shown for the rat hepatic nuclear factor 3 (HNF3) gene family. We have cloned six forkhead gene family members from a mouse genomic library in addition to the mouse equivalents of the genes for HNF3 alpha, -beta, and -gamma. The six genes, termed fkh-1 to fkh-6, share a high degree of similarity with the Drosophila forkhead gene, having 57-67% amino acid identity within the forkhead domain. fkh-1 seems to be the mammalian homologue of the Drosophila FD1 gene, as the sequences are 86% identical. fkh-1 to fkh-6 show distinct spatial patterns of expression in adult tissues and are expressed during embryogenesis.

Amino Acid Sequence↗

PubMed2001

Quantitative evaluation of the lactate signal loss and its spatial dependence in press localized (1)H NMR spectroscopy.

Localized (1)H NMR spectroscopy using the 90 degrees -t(1)-180 degrees -t(1)+t(2)-180 degrees -t(2)-Acq. PRESS sequence can lead to a signal loss for the lactate doublet compared with signals from uncoupled nuclei which is dependent on the choice of t(1) and t(2). The most striking signal loss of up to 78% of the total signal occurs with the symmetrical PRESS sequence (t(1)=t(2)) at an echo time of 2/J (approximately 290 ms). Calculations have shown that this signal loss is related to the pulse angle distributions produced by the two refocusing pulses which leads to the creation of single quantum polarization transfer (PT) as well as to not directly observable states (NDOS) of the lactate AX(3) spin system: zero- and multiple-quantum coherences, and longitudinal spin orders. In addition, the chemical shift dependent voxel displacement (VOD) leads to further signal loss. By calculating the density operator for various of the echo times TE=n/J, n=1, 2, 3,..., we calculated quantitatively the contributions of these effects to the signal loss as well as their spatial distribution. A maximum signal loss of 75% can be expected from theory for the symmetrical PRESS sequence and TE=2/J for Hamming filtered sinc pulses, whereby 47% are due to the creation of NDOS and up to 28% arise from PT. Taking also the VOD effect into account (2 mT/m slice selection gradients, 20-mm slices) leads to 54% signal loss from NDOS and up to 24% from PT, leading to a maximum signal loss of 78%. Using RE-BURP pulses with their more rectangular pulse angle distributions reduces the maximum signal loss to 44%. Experiments at 1.5 T using a lactate solution demonstrated a maximum lactate signal loss for sinc pulses of 82% (52% NDOS, 30% PT) at TE=290 ms using the symmetrical PRESS sequence. The great signal loss and its spatial distribution is of importance for investigations using a symmetrical PRESS sequence at TE=2/J.

Acetic Acid↗

PubMed2005

Time-resolved contrast-enhanced three-dimensional magnetic resonance angiography of the chest: combination of parallel imaging with view sharing (TREAT).

RATIONALE AND OBJECTIVES: In view sharing, some parts of k-space are updated more often than others, leading to an effective shortening of the total acquisition time. Undersampling of high-frequency k-space data, however, can result in artifacts at the edges of blood vessels, especially during the rapid signal intensity changes. The objective of this study was to evaluate a new time-resolved echo-shared angiographic technique (TREAT) combining parallel imaging with view sharing. First, the presence of artifacts arising from different temporal interpolation schemes was evaluated in simulations of the point spread function. Second, the image quality and presence of artifacts of time-resolved parallel three-dimensional magnetic resonance angiography (3D MRA) of the chest, acquired with and without view sharing, was assessed in a clinical study of patients with cardiovascular or pulmonary disease. MATERIALS AND METHODS: Using parameters from a time-resolved parallel 3D MRA sequence without view sharing (parallel MRA), giving a 33% increase in spatial resolution, our simulations have revealed that k-space segmentation in 3 regions provides acceptable artifacts. Thirty-six consecutive patients (mean age, 50 +/- 16 years; 15 females, 22 males) were examined in a clinical study with TREAT. The image data were compared with that of a group of 31 consecutive patients (mean age, 46 +/- 19 years; 12 females, 19 males) examined with a conventional time-resolved parallel MRA sequence without view sharing (parallel MRA). The image quality and presence of artifacts was assessed in a blind comparison by 2 radiologists in consensus using MPR and MIP reconstructions. Furthermore, the peak SNR of the pulmonary artery and aorta was compared between both MRA sequences. RESULTS: The image quality of TREAT was rated significantly higher than that of the parallel MRA sequence without view sharing: depending on the orientation of MPR and MIP reconstructions, an excellent image quality was found in 69-89% with TREAT and in 45-71% with the parallel MRA protocol without view sharing, respectively. The presence of artifacts was equal with both sequences. CONCLUSION: View sharing can be successfully combined with other acceleration techniques, such as parallel imaging. TREAT allows the assessment of the thoracic vasculature with a high temporal and spatial resolution.

Cardiovascular Diseases↗

PubMed1996

Lineage-specific regulation of the neural differentiation gene MASH1.

Mash1 is a transcription factor required during embryogenesis for the development of multiple neural lineages. It is expressed in restricted domains at specific stages in the developing central and peripheral nervous systems and in the developing olfactory epithelium. We have investigated the regulation of Mash1 expression during embryogenesis using transgenic mice containing Mash1/lacZ reporter constructs. Cis-acting regulatory elements controlling Mash1 expression in the central nervous system are located within an 8-kb sequence upstream of the Mash1 coding region. This 8-kb sequence does not contain elements directing expression to the peripheral nervous system, olfactory epithelium, or retina. Sequences outside this 8 kb but within 36 kb of the Mash1 locus contain elements responsible for expression in the autonomic division of the peripheral nervous system. However, transgene expression in embryos containing the 36-kb sequence was never detected in the olfactory epithelium and retina. Thus, regulatory elements driving expression in these lineages may be at even greater distances from the Mash1 coding region. These data provide evidence for complex regulation of Mash1 expression in which multiple lineage-specific cis-acting regulatory regions span greater than 36 kb of the Mash1 locus. Further characterization of these regions will facilitate the study of factors that regulate the temporal and spatial expression of Mash1 during development. In addition, the regulatory sequences identified here can direct expression of heterologous genes to developing neural lineages that normally express Mash1, thus providing an important tool for examining the function of candidate regulatory genes in mammalian nervous system development.

Animals↗

PubMed1999

Redefining the functional organization of working memory processes within human lateral prefrontal cortex.

It is widely held that the frontal cortex plays a critical part in certain aspects of spatial and non-spatial working memory. One unresolved issue is whether there are functionally distinct subdivisions of the lateral frontal cortex that subserve different aspects of working memory. The present study used positron emission tomography (PET) to demonstrate that working memory processes within the human mid-dorsolateral and mid-ventrolateral frontal regions are organized according to the type of processing required rather than according to the nature (i.e. spatial or non-spatial), of the information being processed, as has been widely assumed. Two spatial working memory tasks were used which varied in the extent to which they required different executive processes. During a 'spatial span' task that required the subject to hold a sequence of five previously remembered locations in working memory a significant change in blood-flow was observed in the right mid-ventrolateral frontal cortex, but not in the anatomically and cytoarchitectonically distinct mid-dorsolateral frontal-lobe region. By contrast, during a '2-back' task that required the subject to continually update and manipulate an ongoing sequence of locations within working memory, significant blood flow increases were observed in both mid-ventrolateral and mid-dorsolateral frontal regions. When the two working memory tasks were compared directly, the one that emphasized manipulation of information within working memory yielded significantly greater activity in the right mid-dorsolateral frontal cortex only. This dissociation provides unambiguous evidence that the mid-dorsolateral and mid-ventrolateral frontal cortical areas make distinct functional contributions to spatial working memory and corresponds with a fractionation of working memory processes in psychological terms.

Adult↗

PubMed2004

Cognitive map formation through sequence encoding by theta phase precession.

The rodent hippocampus has been thought to represent the spatial environment as a cognitive map. The associative connections in the hippocampus imply that a neural entity represents the map as a geometrical network of hippocampal cells in terms of a chart. According to recent experimental observations, the cells fire successively relative to the theta oscillation of the local field potential, called theta phase precession, when the animal is running. This observation suggests the learning of temporal sequences with asymmetric connections in the hippocampus, but it also gives rather inconsistent implications on the formation of the chart that should consist of symmetric connections for space coding. In this study, we hypothesize that the chart is generated with theta phase coding through the integration of asymmetric connections. Our computer experiments use a hippocampal network model to demonstrate that a geometrical network is formed through running experiences in a few minutes. Asymmetric connections are found to remain and distribute heterogeneously in the network. The obtained network exhibits the spatial localization of activities at each instance as the chart does and their propagation that represents behavioral motions with multidirectional properties. We conclude that theta phase precession and the Hebbian rule with a time delay can provide the neural principles for learning the cognitive map.

Algorithms↗