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PubMed1985

Novel rearrangements of herpes simplex virus DNA sequences resulting from duplication of a sequence within the unique region of the L component.

We constructed insertion mutants of herpes simplex virus type 1 that contained a duplication of DNA sequences from the BamHI-L fragment (map units 0.706 to 0.744), which is located in the unique region of the L component (UL) of the herpes simplex virus type 1 genome. The second copy of the BamHI-L sequence was inserted in inverted orientation into the viral thymidine kinase gene (map units 0.30 to 0.32), also located within UL. A significant fraction of the progeny produced by these insertion mutants had genomes with rearranged DNA sequences, presumably resulting from intramolecular or intermolecular recombination between the BamHI-L sequences at the two different genomic locations. The rearranged genomes either had an inversion of the DNA sequence flanked by the duplication or were recombinant molecules in which different regions of the genome had been duplicated and deleted. Genomic rearrangements similar to those described here have been reported previously but only for herpes simplex virus insertion mutants containing an extra copy of the repetitive a sequence. Such rearrangements have not been reported for insertion mutants that contain duplications of herpes simplex virus DNA sequences from largely unique regions of the genome. The implications of these results are discussed.

Base Sequence↗
PubMed2002

Incorporation of realistic delivery limitations into dynamic MLC treatment delivery.

The clinical implementation of IMRT involves the use of a number of complex software-based systems, typically including an inverse planning system, a leaf sequencer, and a computer-controlled treatment delivery system. The inverse planning system determines the desired fluence patterns, the leaf sequencer translates those fluence maps into leaf trajectories, and the control system delivers those trajectories. While verification of intensity-modulated treatment fields has focused primarily on the dosimetric aspects of delivery, accurate delivery of the intended fluence distribution is dependent upon both the leaf sequencer and delivery control systems. Leaf sequencing algorithms typically do not incorporate many control system limitations, and this can lead to discrepancies between planned and delivered sequences. In this work, simple and complex fields were sequenced for the dynamic sliding window technique using different leaf speeds and tolerance settings to identify various limitations of the accelerator control system. This work was conducted on a Varian 2100 EX equipped with a Millennium 120 leaf MLC. The identified limitations were then incorporated into the sequencing algorithm using a limiting leaf velocity (less than the maximum leaf velocity), the leaf position tolerance, and the communications delay in the control system. Collision avoidance in leaf pairs was found to depend on a control system-enforced minimum gap between leaves and led to acceleration effects. By incorporating these effects into the leaf sequencing algorithm, dynamic sliding-window leaf sequences were produced which did not require beam interruptions or dose rate modulations for the parameter values used in calculating the sequence (dose rate, tolerance, leaf speed, and total monitor units). Incorporation of control system limitations into the leaf sequencing algorithm results in IMRT fields that are delivered with the prescribed constant dose rate, require less time to deliver, and have well-defined, calculable transmission dose characteristics.

Acceleration↗
PubMed2004

Effective blood signal suppression using double inversion-recovery and slice reordering for multislice fast spin-echo MRI and its application in simultaneous proton density and T2 weighted imaging.

PURPOSE: To design a multislice double inversion-recovery fast spin-echo (FSE) sequence, with k-space reordered by inversion time at slice position (KRISP) technique, to produce black-blood vessel wall magnetic resonance imaging (MRI). MATERIALS AND METHODS: In this sequence, central k-space sampling for each slice is required at inversion time (TI) of the blood signal. To fill the entire k-space, the peripheral lines are obtained less or greater the TI and using a rotating slice order. Blood flow signal suppression was first evaluated using a phantom. Simulation studies were used to investigate FSE image quality. The final sequence was then applied to the rabbit abdominal aorta MRI at 4.7 T. RESULTS: In the flow phantom study, artifacts from slow-flowing water were substantially reduced by the KRISP technique; residual water spins were dephased by the strong phase-encoding gradient required for peripheral k-space. These dephased spins flowed into the slice plane where the center of k-space was being acquired at the TI of the flowing water signal. Multislice black-blood MR images were successfully obtained in the rabbit abdomen using the sequence with the k-trajectory optimized by the simulation study. CONCLUSION: The KRISP technique was effective both in multislice double inversion-recovery FSE and in blood signal suppression.

Abdomen↗
PubMed1997

Enhancement of Xe-133 ventilation lung scan image acquired after Tc-99m perfusion scan.

In nuclear medicine, the match and mismatch between the images of lung perfusion and ventilation provide an important criterion to diagnose pulmonary embolism. Usually, for imaging clarity, the ventilation scan using 133Xe is performed before the perfusion scan using 99mTc. But the inverse order is preferred clinically, since (i) if the perfusion image is normal, there is no need to do the ventilation scan, and (ii) if the perfusion image is abnormal, the ventilation image can be obtained by focusing on the perfusion abnormalities. However, the quality of the ventilation image is reduced if the ventilation scan is performed after the perfusion scan, because the 140 keV photons emitted from 99mTc will scatter into the acquisition window of 133Xe (81 keV). The purpose of this study is to apply image processing techniques to reduce the scattering effect of 99mTc to get a better 133Xe ventilation image. First, an image sequence in the preferred inverse order is simulated using the images acquired in the normal order. Image processing techniques are used to find an optimized way to reduce the scattering background in the ventilation image. Second, a real image sequence is acquired in the inverse order. An improved ventilation image is then obtained by applying image processing techniques to this image sequence.

Humans↗
PubMed1999

Molecular population genetics of the rp49 gene region in different chromosomal inversions of Drosophila subobscura.

Nucleotide variation at the ribosomal protein 49 (rp49) gene region has been studied in 75 lines of Drosophila subobscura belonging to four chromosomal arrangements (Ost, O3+4, O3+4+8, and O3+4+23). The location of the rp49 gene region within the inversion loop differs among heterokaryotypes: it is very close to one of the breakpoints in heterozygotes involving Ost chromosomes, while it is in a more central position in all other heterokaryotypes. The distribution of nucleotide polymorphism in the different arrangements is consistent with a monophyletic origin of the inversions. The data also provide evidence that gene conversion and possibly double crossover are involved in shuffling nucleotide variation among gene arrangements. The analyses reveal that the level of genetic exchange is higher when the region is located in a more central position of the inverted fragment than when it is close to the breakpoints. The pairwise difference distributions as well as the negative values of Tajima's and Fu and Li's statistics further support the hypothesis that nucleotide variation within chromosomal arrangements still reflects expansion after the origin of the inversions. Under the expansion model, we have estimated the time of origin of the studied inversions.

Animals↗
PubMed2003

An in silico exploration of the neutral network in protein sequence space.

Designating amino-acid sequences that fold into a common main-chain structure as "neutral sequences" for the structure, regardless of their function or stability, we investigated the distribution of neutral sequences in protein sequence space. For four distinct target structures (alpha, beta,alpha/beta and alpha+beta types) with the same chain length of 108, we generated the respective neutral sequences by using the inverse folding technique with a knowledge-based potential function. We assumed that neutral sequences for a protein structure have Z scores higher than or equal to fixed thresholds, where thresholds are defined as the Z score for the corresponding native sequence (case 1) or much greater Z score (case 2). An exploring walk simulation suggested that the neutral sequences mapped into the sequence space were connected with each other through straight neutral paths and formed an inherent neutral network over the sequence space. Through another exploring walk simulation, we investigated contiguous regions between or among the neutral networks for the distinct protein structures and obtained the following results. The closest approach distance between the two neutral networks ranged from 5 to 29 on the Hamming distance scale, showing a linear increase against the threshold values. The sequences located at the "interchange" regions between the two neutral networks have intermediate sequence-profile-scores for both corresponding structures. Introducing a "ball" in the sequence space that contains at least one neutral sequence for each of the four structures, we found that the minimal radius of the ball that is centered at an arbitrary position ranged from 35 to 50, while the minimal radius of the ball that is centered at a certain special position ranged from 20 to 30, in the Hamming distance scale. The relatively small Hamming distances (5-30) may support an evolution mechanism by transferring from a network for a structure to another network for a more beneficial structure via the interchange regions.

Amino Acid Sequence↗
PubMed1994

Analysis of the Anopheles gambiae genome using RAPD markers.

RAPD analysis technique is used as a rapid and reliable tool for genome analysis in the malaria vector Anopheles gambiae. Using more than eighty different commercially available primers we identified more than sixty different DNA segments that were differentially amplified in different strains of An. gambiae s.s. and An. arabiensis. An estimate of the cytogenetic position of these markers is provided by their hybridization to divisional dot-blot filters. Potentially useful RAPD markers can be cytogenetically mapped with more precision by in situ hybridization and, as they segregate as dominant markers in a Mendelian fashion, they can also be genetically mapped relative to other genes or rearrangements. Finally, we identified markers for their potential use in the identification of different mosquito strains.

Animals↗
PubMed2004

Myocardial infarction: optimization of inversion times at delayed contrast-enhanced MR imaging.

Seventeen patients underwent magnetic resonance (MR) imaging for myocardial viability with a protocol approved by the institutional review board and gave written informed consent. Breath-hold cine inversion-recovery segmented k-space true fast imaging with steady-state precession sequence, referred to as inversion time (TI) mapping, was performed to determine optimal TI for myocardial infarction inversion-recovery imaging. From TI mapping, optimal TI was 180-315 msec 10-15 minutes after administration of 0.15 mmol/kg of gadolinium-based contrast material. At that optimal TI, relative signal intensity of infarcted myocardium compared with uninfarcted myocardium was maximal (mean +/- standard deviation, 297.8% +/- 86.5), whereas signal-to-noise ratio of uninfarcted myocardium was minimal (4.5 +/- 1.2). When applied to conventional myocardial infarction inversion-recovery imaging, optimal TI resulted in nulling of signal intensity of uninfarcted myocardium in all patients and in excellent conspicuity of infarcted myocardium in all nine patients with visible infarction.

Adult↗
PubMed1994

Noninvasive measurement of renal hemodynamic functions using gadolinium enhanced magnetic resonance imaging.

A technique for the assessment of single kidney hemodynamic functions utilizing a novel MR pulse sequence in conjunction with MR contrast material administration is described. Renal extraction fraction (EF) is derived by measuring the concentration of the incoming contrast agent in the renal artery and the outgoing concentration in the renal vein. The glomerular filtration rate (GFR) can then be determined by the product of EF and renal plasma flow. A modified inversion recovery MR pulse sequence is used to measure the T1 of moving blood. This pulse sequence uses a spatially nonselective inversion pulse. A series of small flip angle detection pulses are then used to monitor the recovery of longitudinal spin magnetization in an image plane intersecting the renal vessels. The recovery rate is measured in each vessel and the T1 of blood determined. These T1 measurements are then used to determine the ratio of contrast concentration in the renal arteries and veins. Blood flow measurements can be obtained simultaneously with T1 measurements by inserting flow-encoding magnetic field gradients into the pulse sequence. Preliminary results in human volunteers suggest the feasibility of noninvasively determining hemodynamic functions with magnetic resonance.

Algorithms↗
PubMed2003

MR colonography with fecal tagging: comparison between 2D turbo FLASH and 3D FLASH sequences.

The objective of this study was to compare inversion recovery turbo 2D fast low-angle shot (FLASH) and 3D FLASH sequences for fecal-tagged MR colonography studies. Fifteen consecutive patients with indications for colonoscopy underwent MR colonography with fecal tagging. An inversion recovery turbo-FLASH sequence was applied and compared in terms of artifacts presence, efficiency for masking residual stool, and colonic wall conspicuity with a fat-saturated 3D FLASH sequence. Both sequences were acquired following administration of paramagnetic contrast agent. Contrast-to-noise ratio and relative contrast between colonic wall and lumen were calculated and compared for both sequences. Turbo 2D FLASH provided fewer artifacts, higher efficiency for masking the residual stool, and colonic wall conspicuity equivalent to 3D FLASH. An inversion time of 10 ms provided homogeneously low signal intensity of the colonic lumen. Contrast to noise between colonic wall and lumen was significantly higher in the 3D FLASH images, whereas differences in relative contrast were not statistically significant. An optimized inversion-recovery 2D turbo-FLASH sequence provides better fecal tagging results and should be added to the 3D FLASH sequence when designing dark-lumen MR colonography examination protocols.

Barium Sulfate↗
PubMed2002

The Chapel Hill hemophilia A dog colony exhibits a factor VIII gene inversion.

In the Chapel Hill colony of factor VIII-deficient dogs, abnormal sequence (ch8, for canine hemophilia 8, GenBank no. ) follows exons 1-22 in the factor VIII transcript in place of exons 23-26. The canine hemophilia 8 locus (ch8) sequence was found in a 140-kb normal dog genomic DNA bacterial artificial chromosome (BAC) clone that was completely outside the factor VIII gene, but not in BAC clones containing the factor VIII gene. The BAC clone that contained ch8 also contained a homologue of F8A (factor 8 associated) sequence, which participates in a common inversion that causes severe hemophilia A in humans. Fluorescence in situ hybridization analysis indicated that exons 1-26 normally proceed sequentially from telomere to centromere at Xq28, and ch8 is telomeric to the factor VIII gene. The appearance of an "upstream" genomic sequence element (ch8) at the end of the aberrant factor VIII transcript suggested that an inversion of genomic DNA replaced factor VIII exons 22-26 with ch8. The F8A sequence appeared also in overlapping normal BAC clones containing factor VIII sequence. We hypothesized that homologous recombination between copies of canine F8A inside and outside the factor VIII gene had occurred, as in human hemophilia A. High-resolution fluorescent in situ hybridization on hemophilia A dog DNA revealed a pattern consistent with this inversion mechanism. We also identified a HindIII restriction fragment length polymorphism of F8A fragments that distinguished hemophilia A, carrier, and normal dogs' DNA. The Chapel Hill hemophilia A dog colony therefore replicates the factor VIII gene inversion commonly seen in humans with severe hemophilia A.

Amino Acid Sequence↗
PubMed1984

[Dietary fiber and OGTT: blood sugar variations after administration of a new purified glucomannane].

After having stressed the importance of fibres in the nutritional field, pointing out the inverse relationship between vegetal fibres consumption in various populations and diffusion of many diseases of the so-called "industrialized" societies (such as obesity, diabetes, dyslipidemias, atherosclerosis, cholelithiasis, cancer of the colon, etc.), the Authors report their experiment on a new experimental product based on glucomannane purified (PRL). The present study was carried out on 24 obese subjects (5 males and 19 females). The patients, normoglycemics in their basic condition, were submitted to OGTT with 75 g of glucose in the morning before eating and were subdivided into two groups, the first (Group A) characterized by the sequence OGTT + placebo; after a few days, by another OGTT + experimental product; the second characterized by the inverse sequence. Four tablets (glucomannane purified 5,2 g) and four tablets of placebo was the posology employed. The evaluation of the possible action of the product in reducing or slowing down the intestinal absorption of glucose was the aim of the research. The results obtained show that the administration of the product under study has led to a sharp decrease of the average glycemic values with variations per cent ranging from 13% to 16% in Group A, from 10% to 11% in Group B and from 7% to 12% in the two groups considered on the whole. In conclusion, the Authors wish an increased diffusion of dietary fibres and particularly of the glucomannanes in all those dysmetabolic forms having at their bases an unbalanced, hypercaloric alimentation, rich in refined aliments and poor in fibres.

Blood Glucose↗
PubMed2003

Transient oscillations under strongly mismatched Hartmann-Hahn conditions.

Based on the standard 2D Polarization inversion experiment, a new pulse sequence (PI-TAPF) is proposed. It represents a combination of Polarization Inversion and TAPF (time averaged precession frequency) sequences. The depolarization period consists of phase-alternating intervals of different duration in the I channel. The pulse sequence yields transient oscillations under the strongly mismatched HH conditions where the required power for the dilute spins is reduced by a factor of 5. Experimental results recorded for a sample of ferrocene powder are well reproduced by numerical simulations.

Algorithms↗
PubMed2005

[Comparison of a T1-weighted inversion-recovery-, gradient-echo- and spin-echo sequence for imaging of the brain at 3.0 Tesla].

PURPOSE: The increased T1 relaxation times at 3.0 Tesla lead to a reduced T1 contrast, requiring adaptation of imaging protocols for high magnetic fields. This prospective study assesses the performance of three techniques for T1-weighted imaging (T1w) at 3.0 T with regard to gray-white differentiation and contrast-to-noise-ratio (CNR). MATERIALS AND METHODS: Thirty-one patients were examined at a 3.0 T system with axial T1 w inversion recovery (IR), spin-echo (SE) and gradient echo (GE) sequences and after contrast enhancement (CE) with CE-SE and CE-GE sequences. For qualitative analysis, the images were ranked with regard to artifacts, gray-white differentiation, image noise and overall diagnostic quality. For quantitative analysis, the CNR was calculated, and cortex and basal ganglia were compared with the white matter. RESULTS: In the qualitative analysis, IR was judged superior to SE and GE for gray-white differentiation, image noise and overall diagnostic quality, but inferior to the GE sequence with regard to artifacts. CE-GE proved superior to CE-SE in all categories. In the quantitative analysis, CNR of the basal ganglia was highest for IR, followed by GE and SE. For the CNR of the cortex, no significant difference was found between IR (16.9) and GE (15.4) but both were superior to the SE (9.4). The CNR of the cortex was significantly higher for CE-GE compared to CE-SE (12.7 vs. 7.6, p < 0.001), but the CNR of the basal ganglia was not significantly different. CONCLUSION: For unenhanced T1 w imaging at 3.0 T, the IR technique is, despite increased artifacts, the method of choice due to its superior gray-white differentiation and best overall image quality. For CE-studies, GE sequences are recommended. For cerebral imaging, SE sequences give unsatisfactory results at 3.0 T.

Brain↗
PubMed1992

The basis for the mechanistic bias for deletional over inversional V(D)J recombination.

V(D)J recombination between recognition sites in the genome is characterized by certain biases. At some loci, proximal sites undergo recombination substantially more frequently than distal ones. The joining of DH/JH is an example of this. Because the DH element bears signal sequences on each side, inversion would be expected as often as deletion in DH/JH recombination. However, the markedly favored outcome is deletion, entailing utilization of the closer recombination site. One model proposed to explain these biases is the tracking model in which the recombinase tracks from one site to the other. Here, we have directly tested for various types of tracking in V(D)J recombination and have found no indication that it occurs. In addition, we have created DH-JH minilocus substrates for analysis of the basis for the preference for deletion. We find that we can reproduce the deletional bias for the system. Moreover, by flipping the orientation of the D segment, we can reverse the bias such that the frequency of inversions can exceed the number of deletions. These results indicate (1) that there is no intrinsic topological preference in this reaction, and (2) that the sequence of the signal and coding ends determines the bias.

Antibody Diversity↗
PubMed2003

A novel IS element, IS621, of the IS110/IS492 family transposes to a specific site in repetitive extragenic palindromic sequences in Escherichia coli.

An Escherichia coli strain, ECOR28, was found to have insertions of an identical sequence (1,279 bp in length) at 10 loci in its genome. This insertion sequence (named IS621) has one large open reading frame encoding a putative protein that is 326 amino acids in length. A computer-aided homology search using the DNA sequence as the query revealed that IS621 was homologous to the piv genes, encoding pilin gene invertase (PIV). A homology search using the amino acid sequence of the putative protein encoded by IS621 as the query revealed that the protein also has partial homology to transposases encoded by the IS110/IS492 family elements, which were known to have partial homology to PIV. This indicates that IS621 belongs to the IS110/IS492 family but is most closely related to the piv genes. In fact, a phylogenetic tree constructed on the basis of amino acid sequences of PIV proteins and transposases revealed that IS621 belongs to the piv gene group, which is distinct from the IS110/IS492 family elements, which form several groups. PIV proteins and transposases encoded by the IS110/IS492 family elements, including IS621, have four acidic amino acid residues, which are conserved at positions in their N-terminal regions. These residues may constitute a tetrad D-E(or D)-D-D motif as the catalytic center. Interestingly, IS621 was inserted at specific sites within repetitive extragenic palindromic (REP) sequences at 10 loci in the ECOR28 genome. IS621 may not recognize the entire REP sequence in transposition, but it recognizes a 15-bp sequence conserved in the REP sequences around the target site. There are several elements belonging to the IS110/IS492 family that also transpose to specific sites in the repeated sequences, as does IS621. IS621 does not have terminal inverted repeats like most of the IS110/IS492 family elements. The terminal sequences of IS621 have homology with the 26-bp inverted repeat sequences of pilin gene inversion sites that are recognized and used for inversion of pilin genes by PIV. This suggests that IS621 initiates transposition through recognition of their terminal regions and cleavage at the ends by a mechanism similar to that used for PIV to promote inversion at the pilin gene inversion sites.

Amino Acid Sequence↗
PubMed2004

The small chromosomes of Trypanosoma brucei involved in antigenic variation are constructed around repetitive palindromes.

Most eukaryotic genomes contain large regions of satellite DNA. These arrays are often associated with essential chromosomal functions, but remain largely absent from genome projects because of difficulties in cloning and sequence assembly. The numerous small chromosomes of the parasite Trypanosoma brucei fall into this category, yet are critical to understanding the genome because of their role in antigenic variation. Their relatively small size, however, makes them particularly amenable to physical mapping. We have produced fine-resolution maps of 17 complete minichromosomes and partial maps of two larger intermediate-sized chromosomes. This revealed a canonical structure shared by both chromosomal classes based around a large central core of 177-bp repeats. Around the core are variable-length genic regions, the lengths of which define chromosomal class. We show the core region to be a repetitive palindrome with a single inversion point common to all the chromosomes of both classes, suggesting a mechanism of genesis for these chromosomes. Moreover, palindromy appears to be a feature of (peri)centromeres in other species that can be easily overlooked. We propose that sequence inversion is one of the higher-order sequence motifs that confer chromosomal stability.

Animals↗