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PubMed2001

Subunit assembly and mode of DNA cleavage of the type III restriction endonucleases EcoP1I and EcoP15I.

DNA cleavage by type III restriction endonucleases requires two inversely oriented asymmetric recognition sequences and results from ATP-dependent DNA translocation and collision of two enzyme molecules. Here, we characterized the structure and mode of action of the related EcoP1I and EcoP15I enzymes. Analytical ultracentrifugation and gel quantification revealed a common Res(2)Mod(2) subunit stoichiometry. Single alanine substitutions in the putative nuclease active site of ResP1 and ResP15 abolished DNA but not ATP hydrolysis, whilst a substitution in helicase motif VI abolished both activities. Positively supercoiled DNA substrates containing a pair of inversely oriented recognition sites were cleaved inefficiently, whereas the corresponding relaxed and negatively supercoiled substrates were cleaved efficiently, suggesting that DNA overtwisting impedes the convergence of the translocating enzymes. EcoP1I and EcoP15I could co-operate in DNA cleavage on circular substrate containing several EcoP1I sites inversely oriented to a single EcoP15I site; cleavage occurred predominantly at the EcoP15I site. EcoP15I alone showed nicking activity on these molecules, cutting exclusively the top DNA strand at its recognition site. This activity was dependent on enzyme concentration and local DNA sequence. The EcoP1I nuclease mutant greatly stimulated the EcoP15I nicking activity, while the EcoP1I motif VI mutant did not. Moreover, combining an EcoP15I nuclease mutant with wild-type EcoP1I resulted in cutting the bottom DNA strand at the EcoP15I site. These data suggest that double-strand breaks result from top strand cleavage by a Res subunit proximal to the site of cleavage, whilst bottom strand cleavage is catalysed by a Res subunit supplied in trans by the distal endonuclease in the collision complex.

Adenosine Triphosphatases↗
PubMed2004

Most chloroplast DNA of maize seedlings in linear molecules with defined ends and branched forms.

We used pulsed-field gel electrophoresis, restriction fragment mapping, and fluorescence microscopy of individual DNA molecules to analyze the structure of chloroplast DNA (cpDNA) from shoots of ten to 14 day old maize seedlings. We find that most of the cpDNA is in linear and complex branched forms, with only 3-4% as circles. We find the ends of linear genomic monomers and head-to-tail (h-t) concatemers within inverted repeat sequences (IRs) near probable origins of replication, not at random sites as expected from broken circles. Our results predict two major and three minor populations of linear molecules, each with different ends and putative origins of replication. Our mapping data predict equimolar populations of h-t linear concatemeric molecules differing only in the relative orientation (inversion) of the single copy regions. We show how recombination during replication can produce h-t linear concatemers containing an inversion of single copy sequences that has for 20 years been attributed to recombinational flipping between IRs in a circular chromosome. We propose that replication is initiated predominantly on linear, not circular, DNA, producing multi-genomic branched chromosomes and that most replication involves strand invasion of internal regions by the ends of linear molecules, rather than the generally accepted D-loop-to-theta mechanism. We speculate that if the minor amount of cpDNA in circular form is useful to the plant, its contribution to chloroplast function does not depend on the circularity of these cpDNA molecules.

Chloroplasts↗
PubMed1997

Cloning, expression and activation of a truncated 92-kDa gelatinase minienzyme.

The matrix metalloproteinases (MMPs) are a family of highly homologous zinc-endopeptidases that degrade extracellular matrix components. Human 92-kDa gelatinase (MMP-9) represents one of the MMPs that cleaves native collagen type IV. As a basis for structural investigations, the short form (catalytic domain, amino acid residues 113-450) of the 92-kDa gelatinase cDNA was cloned and expressed in E. coli as a minienzyme. By combination of reverse transcription (RT) and polymerase chain reaction (PCR), the truncated 92-kDa gelatinase-cDNA was amplified from the corresponding mRNA derived from ovarian carcinoma cells. The cDNA fragment obtained was cloned in E. coli and sequenced. With the exception of one nucleotide inversion at position 745 (gt-->tg) the cDNA sequence was identical to the nucleotide sequence of the 92-kDa gelatinase as has been previously reported. The protein was expressed in E. coli using the vector pET-12b. The recombinant protein was stored in inclusion bodies and extracted as a 38 kDa species from the inclusion bodies by solubilization in 8 M urea. The product was purified by affinity chromatography and gel filtration. Amino-terminal sequence analysis confirmed the identity with the catalytic domain of 92-kDa gelatinase. The recombinant protein was refolded in the presence of Ca2+ and Zn2+ and yielded an active minienzyme with gelatinolytic activity. It degrades the native substrate collagen type IV and the synthetic substrate Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 x AcOH like the full-length 92-kDa gelatinase. The catalytic activity could be inhibited by the specific MMP inhibitors TIMP-1 and TIMP-2.

Base Sequence↗
PubMed1998

Cocaine decreases cortical cerebral blood flow but does not obscure regional activation in functional magnetic resonance imaging in human subjects.

The authors used functional magnetic resonance imaging (fMRI) to determine whether acute intravenous (i.v.) cocaine use would change global cerebral blood flow (CBF) or visual stimulation-induced functional activation. They used flow-sensitive alternating inversion recovery (FAIR) scan sequences to measure CBF and blood oxygen level-dependent (BOLD) sensitive T2* scan sequences during visual stimulation to measure neuronal activation before and after cocaine and saline infusions. Cocaine (0.6 mg/kg i.v. over 30 seconds) increased heart rate and mean blood pressure and decreased end tidal carbon dioxide (CO2). All measures returned to baseline by 2 hours, the interinfusion interval, and were unchanged by saline. Flow-sensitive alternating inversion recovery imaging demonstrated that cortical gray matter CBF was unchanged after saline infusion (-2.4 +/- 6.5%) but decreased (-14.1 +/- 8.5%) after cocaine infusion (n = 8, P < 0.01). No decreases were detected in white matter, nor were changes found comparing BOLD signal intensity in cortical gray matter immediately before cocaine infusion with that measured 10 minutes after infusion. Visual stimulation resulted in comparable BOLD signal increases in visual cortex in all conditions (before and after cocaine and saline infusion). Despite a small (14%) but significant decrease in global cortical gray matter CBF after acute cocaine infusion, specific regional increases in BOLD imaging, mediated by neurons, can be measured reliably.

Adult↗
PubMed1994

Localization of a putative human brain sodium channel gene (SCN1A) to chromosome band 2q24.

We have identified four putative human sodium channel gene sequences, 55 bp each, using the polymerase chain reaction (PCR) on total human placental DNA with primers specific for the cDNA sequence of the rat brain sodium channel I alpha (Scn1a) gene. One of these sequences was extended bidirectionally by genomic inverse-PCR to obtain a 1.6-kb fragment. Sequencing of this 1,556-bp fragment showed a 282-bp complete exon, which has 95% and 94% homology at the nucleotide and amino acid levels, respectively, with the rat Scn1a gene. We putatively assign this sequence as belonging to the gene coding the alpha-subunit of a human brain type I sodium channel (SCN1A). PCR on human x rodent somatic cell hybrids with primers derived from SCN1A localized this gene to chromosome 2. Fluorescence in situ hybridization to human metaphase chromosomes sublocalized the gene to chromosome band 2q24.

Base Sequence↗
PubMed2003

Detection of atherosclerotic plaque with Gadofluorine-enhanced magnetic resonance imaging.

BACKGROUND: The purpose of this study was to visualize atherosclerotic plaques independently of luminal narrowing using T1-weighted contrast-enhanced MRI. METHODS AND RESULTS: Eight Watanabe heritable hyperlipidemic (WHHL) rabbits, aged 9 to 18 months, and 8 age-matched controls (New Zealand White rabbits) underwent MRI of the aortic arch before and up to 48 hours after injection of 100 micromol/kg Gadofluorine (Schering AG). Additionally, 8 WHHL rabbits were examined with Magnevist (Schering AG). A half-Fourier acquisition single-shot turbo-spin-echo (HASTE) sequence and a T1-weighted inversion-recovery turbo fast, low-angle shot sequence were used for data acquisition. Immediately after the MR examination, the animals were killed, the aorta was stained with Sudan red, and ex vivo imaging of the stained aortic specimens was performed. Additionally, gadolinium concentrations in plaque (Sudan-positive) and normal (Sudan-negative) aortic wall segments were measured. Plain MR imaging revealed no plaques in the aortic arch in either animal group. Enhancement occurred in the aortic wall of all WHHL rabbits examined with Gadofluorine but not in the vessel wall of animals examined with Magnevist and the control group. Sudan red staining demonstrated multiple plaques in the aortic arch of all WHHL rabbits. Ex vivo imaging demonstrated that the area of hyperenhancement matched the area of plaques stained with Sudan red. The gadolinium concentration was 7+/-5 nmol/g for normal aortic wall of the control group and 368+/-30 nmol/g for aortic wall with plaque in WHHL. CONCLUSIONS: Gadofluorine enhances the imaging of atherosclerotic plaques and enables improved plaque detection of even nonstenotic lesions that are not visible on unenhanced MRI.

Animals↗
PubMed1991

Reciprocal hybrid joints demonstrate successive V-J rearrangements on the same chromosome in the human TCR gamma locus.

Novel variable (V)--joining (J) gene rearrangements are described in the human T cell receptor gamma locus, in which, on the one hand, the V3 variable gene is joined to the heptamer--nonamer recombination signals of the J1 segment and, on the other hand, the J1 segment is joined to the V3 recombination signals through head-to-head fusion. These recombination products, or hybrid joints, have been originated through an inversion of 47 kb DNA. Interestingly the inverted DNA stretch contains a normal V9-J9 rearrangement. These findings are the first direct demonstration that successive rearrangements occur, on the same chromosome, in the human T cell receptor gamma locus, and suggest that the chronology of the joining events plays a role in the ontogeny of T cells and their differentiation in gamma/delta + and alpha/beta + lineages.

Amino Acid Sequence↗
PubMed2001

In search of a 9q13 latent centromere in 9qh polymorphic inversions.

In search of a 9q13 latent centromere in 9qh polymorphic inversions: The presence of alphoid sequences in 9q13 has prompted the suggestion that such a region could harbor a latent centromere which under certain circumstances may appear as a neocentromere. We tested this hypothesis by means of FISH with a centromere 9-specific alphoid probe in lymphocyte metaphases from 13 unrelated individuals with a 9qh polymorphic inversion. Since all inverted chromosomes had the alphoid signal onto the primary constriction, it was not possible to identify any neocentromere . We believe, however, that the number of cases was not enough to conclude that all the polymorphic inversions of chromosome 9 are genuine.

Base Sequence↗
PubMed2002

Aberrant transposition of a Tc1-mariner element, impala, in the fungus Fusarium oxysporum.

We previously determined that the impalaD transposable element of Fusarium oxysporum was able to mobilize a non autonomous copy of impala ( niaD::imp::hph), inserted in the niaD gene encoding nitrate reductase. Generally, mobilization results in the recovery of Nia(+) revertants at low frequency. In the course of this study, we recovered a transformant that gave rise to Nia(+) revertants at a high rate. These revertants displayed atypical phenotypes and showed a niaD hybridization pattern different from that in more typical revertants. Molecular analysis of the structure of the transformant and atypical revertants indicated that (i) in the transformant, two copies of impala, one defective and one active, were inserted at the same genomic locus in a head-to-head orientation; and (ii) all the revertants analyzed presented the same chromosomal rearrangement, an inversion resulting in the replacement of the niaD promoter by a new sequence containing a cryptic promoter. We also frequently observed additional DNA rearrangements (deletion or inversion) in these revertants. The sequences at the rearrangement junctions indicated the occurrence of a transposition event that used the ITRs (Inverted Terminal Repeats) of separate transposons arranged in direct orientation. These features can be interpreted as the consequences of an aberrant transposition process. Such a process may account for the rearrangements observed in some genomic regions containing multiple transposon ends, and could serve as a mechanism for the generation of genetic diversity.

Base Sequence↗
PubMed2000

Translation during cold adaptation does not involve mRNA-rRNA base pairing through the downstream box.

The downstream box (DB) has been proposed to enhance translation of several mRNAs and to be a key element controlling the expression of cold-shocked mRNAs. However, the proposal that the DB exerts its effects through a base pairing interaction with the complementary anti-downstream box (antiDB) sequence (nt 1469-1483) located in the penultimate stem (helix 44) of 16S rRNA remains controversial. The existence of this interaction during initiation of protein synthesis under cold-shock conditions has been investigated in the present work using an Escherichia coli strain whose ribosomes lack the potential to base pair with mRNA because of a 12 bp inversion of the antiDB sequence in helix 44. Our results show that this strain is capable of cold acclimation, withstands cold shock, and its ribosomes translate mRNAs that contain or lack DB sequences with similar efficiency, comparable to that of the wild type. The structure of helix 44 in 30S ribosomal subunits from cells grown at 37 degrees C and from cells subjected to cold shock was also analyzed by binding a 32P-labeled oligonucleotide complementary to the antiDB region and by chemical probing with DMS and kethoxal. Both approaches clearly indicate that this region is in a double-stranded conformation and therefore not available for base pairing with mRNA.

Adaptation, Physiological↗
PubMed2002

Femur: MR imaging-guided radio-frequency ablation in a porcine model-feasibility study.

PURPOSE: To determine the feasibility of magnetic resonance (MR) imaging-guided and -monitored radio-frequency (RF) ablation of bone. MATERIALS AND METHODS: Seven femurs were treated in five pigs with use of a 0.2-T open MR imager. An 11-gauge bone marrow needle was percutaneously inserted into the distal femur metaphysis with MR fluoroscopy (fast imaging with steady-state precession, or FISP, sequences) to introduce an RF electrode into the bone with further image guidance. Thermal ablation was performed for 10 minutes (90 degrees C +/- 2 [mean +/- SD]). MR follow-up was performed immediately after ablation and again at 7 and 14 days after the procedure (with contrast material-enhanced T1-weighted, T2-weighted, and fast short inversion time inversion-recovery, or STIR, sequences). The animals were sacrificed at day 14. The femurs were sliced, decalcified, and stained. Image analysis was performed to measure lesion diameter and contrast-to-noise ratio (CNR) and to evaluate complications. RESULTS: Technical success was obtained in all animals. The lesion diameter perpendicular to the electrode was 15.4 mm +/- 2.7. No significant complications were noted. The thermal lesions displayed low signal intensity with a sharp rim of high signal intensity. T2-weighted images demonstrated the highest CNR and the lowest error in predicting the lesion size immediately after ablation (2.7 mm +/- 1.3). Contrast-enhanced T1-weighted images demonstrated the highest accuracy at day 14 (1.0 mm +/- 1.0). CONCLUSION: RF ablation of bone with MR imaging as the sole imaging modality is feasible and allows monitoring of the ablation.

Animals↗
PubMed2001

Disruption of the bipartite imprinting center in a family with Angelman syndrome.

Imprinting in 15q11-q13 is controlled by a bipartite imprinting center (IC), which maps to the SNURF-SNRPN locus. Deletions of the exon 1 region impair the establishment or maintenance of the paternal imprint and can cause Prader-Willi syndrome (PWS). Deletions of a region 35 kb upstream of exon 1 impair maternal imprinting and can cause Angelman syndrome (AS). So far, in all affected sibs with an imprinting defect, an inherited IC deletion was identified. We report on two sibs with AS who do not have an IC deletion but instead have a 1-1.5 Mb inversion separating the two IC elements. The inversion is transmitted silently through the male germline but impairs maternal imprinting after transmission through the female germline. Our findings suggest that the close proximity and/or the correct orientation of the two IC elements are/is necessary for the establishment of a maternal imprint.

Angelman Syndrome↗
PubMed1994

Physical map of mouse chromosome 17 in the region relevant for positional cloning of the Hybrid sterility 1 gene.

Hybrid sterility 1 (Hst1) is the major gene responsible for sterility of male hybrids between Mus musculus and certain laboratory strains. Thus, Hst1 is of importance in studying both postreproductive isolation of closely related species and male fertility. It has been mapped to mouse chromosome 17 in the region corresponding to the third inversion of the t haplotypes. The aim of the present study was to construct a physical map of the Hst1 region as the first step in an effort to clone the gene. Three yeast artificial chromosome (YAC) libraries (Princeton, Whitehead, and ICRF) were screened with polymerase chain reaction (PCR) oligonucleotide primers and DNA probes specific for loci previously mapped into the region of the third inversion. The isolated YAC clones were restriction mapped and arranged into contigs. Sixteen YAC clones were arranged into a single contig encompassing a region approximately 2000 kb long based on restriction mapping of highly overlapping but independently derived YAC clones. Five new loci in the region of the third inversion were mapped and the order and approximate physical distances of 12 loci established in this contig. The Hst1 gene maps approximately 0.2 cM proximal to the D17Ph1 locus encompassed by the YAC contig. Since the contig extends at least 1200 kb proximal to D17Ph1, it should contain the Hst1 gene.

Animals↗
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↗
PubMedDate not supplied

Clinical use of the partial saturation and saturation recovery sequences in MR imaging.

The partial saturation (PS) (90 degree-data collection) and saturation recovery (SR) [(90 degree-dephase)n-90 degree-data collection] sequences are described. The early data collection of the PS sequence is of value in demonstrating tissues with a short T2 such as articular cartilage and the annulus fibrosus. The PS sequence also highlights flow and this may provide specific information in vascular lesions. Appropriate choice of echo time enables chemical shift effects to be seen in normal tissues such as breast and bone marrow as well as a variety of diseases such as bone marrow infiltration, pancreatitis, and fatty infiltration of the liver in which there is mixed lipid and water. The SR sequence can be used to control flow effects as well as to calculate values of T1. Although PS and SR sequences display less T1 and T2 dependent contrast than conventional highly T1 and T2 dependent inversion recovery and spin echo sequences, they may still be of clinical value when the mechanism of contrast formation is change in proton density, chemical shift effects, flow effects, or detection of short T2 tissue components.

Abdomen↗
PubMed2004

Evaluation of patellar chondromalacia with MR: comparison between T2-weighted FSE SPIR and GE MTC.

PURPOSE: To compare two different MR sequences to tissue signal suppression in the study of patellar cartilage abnormalities. MATERIALS AND METHODS: We examined 26 patients with magnetic resonance (MR) imaging: sequences included spectral presaturation with inversion recovery (SPIR), with fat suppression and T2-weighted images, magnetization transfer contrast (MTC) sequences, T1-weighted and T2-weighted spin-echo sequences. All patients underwent conventional knee arthroscopy and in all patients a hyaline cartilage lesion was assessed in three articular zones: the patellar medial facet, the lateral facet and the patellar crista. Was assessed 78 articular facets. The lesions were classified using a standard arthroscopic grading system adapted to MR imaging: normal cartilage that corresponds to the grade 0 according to the Noyes grading system, low grade lesions that correspond to the grade I e IIa and high grade lesions that correspond to grades IIb and III. The arthroscopic results were compared with MR images. We assessed the MR diagnostic accuracy, sensitivity, specificity and MR positive predictive value and negative predictive value of the two sequences taking into consideration total lesions, and high-grade and low grade lesions separately. RESULTS: Twenty-four low grade lesions (16 grade I e 8 grade IIa) and 18 high grade lesions (10 grade IIb e 8 grade III) were diagnosed by arthroscopy. Regarding low grade and high-grade lesions together, the accuracy was 77% for MTC sequences and 90% for SPIR sequences. In identifying low-grade lesions, the sensitivity was 88% for SPIR sequence and 42% for MTC sequences. Specificity for the detection of all lesions was 89% for the SPIR sequences and 94% for the MTC sequences. The SPIR sequence visualised water content abnormalities in degenerating cartilage, which are representative of low-grade lesions. The sensitivity of the sequence enabled us to obtain improved contrast for detecting cartilage surface irregularities. The MTC sequences allowed us to grade high-grade lesions susceptible to surgery and small cartilage defects in the presence of joint fluid. The MTC sequences were insufficient in the diagnosis of early stages of chondromalacia because the suppression of the signal of bonded water reduced the contrast among areas of articular cartilage with different water content. For this reason cartilage oedema and early superficial fibrillation were not identified. CONCLUSIONS: In our experience the SPIR sequence proved superior to the MTC sequence in the identification of low grade lesions of the patellar cartilage. The overall value of such sequences in the study of articular pathology also needs to be assessed in the others sites where the articular cartilage is thinner and surfaces more curvilinear.

Adolescent↗
PubMed2006

In vivo measurement of the apparent diffusion coefficient in normal and malignant prostatic tissue using thin-slice echo-planar imaging.

PURPOSE: Diffusion is a physical process based on the random movement of water molecules, known as Brownian movement. Diffusion-weighted imaging (DWI) is a magnetic resonance imaging (MRI) technique that provides information on such biophysical properties of tissues as density, cell organisation and microstructure, which influence the diffusion of water molecules. The aim of this study was to evaluate the ability of MRI to obtain information on the diffusion of water molecules in normal and malignant prostate tissues. MATERIALS AND METHODS: Ten volunteers and 19 patients with prostate lesions diagnosed by transrectal ultrasound (TRUS) were enrolled in our study. Morphological imaging was obtained with T2-weighted turbo spin-echo (TSE) sequences with and without fat suppression [spectral presaturation with inversion recovery (SPIR)] and an axial dynamic T1-weighted SPIR fast-field echo (FFE) sequence during intravenous administration of contrast material. DWI was obtained with a high-spatial-resolution single-shot spin-echo echo planar imaging (EPI) inversion recovery (IR) sequence. The apparent diffusion coefficient (ADC) maps were analysed by positioning an 8-pixel region of interest (ROI) over different zones of the prostate, and the focal lesion when present. The tumour was confirmed by a TRUS-guided needle biopsy taken within 1 month of the MRI examination. RESULTS: The mean ADC value of the central zones (1,512.07+/-124.85x10(-3) mm2/s) was significantly lower than the mean ADC of the peripheral zones (1,984.11+/-226.23x10(-3) mm2/s) (p<0.01). The mean ADC value of tumours (958.97+/-168.98x10(-3) mm2/s) was significantly lower than the mean values of normal peripheral zones (p<0.01). CONCLUSIONS: Our preliminary results indicate that DWI is useful for characterising tissue in the different regions of the prostate gland and in distinguishing normal from cancerous tissues, given its ability to detect early changes in the structural organisation of prostate tissue.

Adult↗
PubMed2003

Differences in definity and optison microbubble destruction rates at a similar mechanical index with different real-time perfusion systems.

The purpose of this study was to determine microbubble responses to different pulse sequence schemes that exist on low mechanical index (MI) real-time perfusion imaging systems using either intravenous albumin-coated (Optison) or lipid-encapsulated (Definity) microbubbles. A tissue-mimicking phantom was created that permitted insonation of microbubbles at 3 cm (near field) and 9 cm (far field) from the diagnostic transducer face. Differences in effluent microbubble concentration were measured after they passed through vessels being insonified with pulse sequence schemes that transmitted alternating polarity (pulse inversion Doppler), alternating amplitude (power modulation), or both (contrast pulse sequencing) at a similar MI, frame rate, and transmit frequency. Normalized contrast signal intensity within a recirculating chamber was also measured in the near and far field. Pulse inversion Doppler produced less initial normalized contrast signal intensity and greater destruction rates than amplitude varying pulse sequence schemes like power modulation or contrast pulse sequencing at both the 0.1- and 0.2-MI settings. These differences indicate that the same MI setting on different real-time perfusion imaging techniques will produce different microbubble responses.

Albumins↗