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PubMed1984

Derivation of quantitative information in NMR imaging: a phantom study.

The use of NMR imaging as a quantitative research tool requires insight into the relationship between various imaging techniques and their resultant images. Work was undertaken to elucidate this relationship by using the following procedure. First, a theoretical model of NMR imaging under various pulse sequences was elaborated. Subsequently, a series of inversion recovery and saturation recovery images of a particular object slice was generated by varying the sequence parameters. Finally, pure rho, T1 and T2 images of that slice were obtained by solving the corresponding model equations. This procedure was applied to a test phantom containing tubes with suitable reference substances, including aqueous solutions of agar, manganese chloride and deuterium, and water-fat mixtures. The concentration of various samples was chosen such as to yield rho, T1 and T2 values usually encountered in clinical NMR imaging. Experiments were carried out with a prototype resistive NMR imager with a static magnetic field of 0.14 T, corresponding to a hydrogen proton resonance frequency of 5.9 MHz. For most samples a weighted non-linear regression analysis showed the theoretical model to produce an adequate parametrisation of the data at the 5% significance level, given the number of data points and the experimental accuracy. The quantitative information extracted from the NMR imaging experiments, i.e. rho, T1 and T2, appeared to be in good agreement with the results of conventional methods, including NMR spectroscopy. The clinical efficacy of the proposed methods is currently being investigated.

Humans↗
PubMed2005

Gene conversion and evolution of Xq28 duplicons involved in recurring inversions causing severe hemophilia A.

Inversions breaking the 1041 bp int1h-1 or the 9.5-kb int22h-1 sequence of the F8 gene cause hemophilia A in 1/30,000 males. These inversions are due to homologous recombination between the above sequences and their inverted copies on the same DNA molecule, respectively, int1h-2 and int22h-2 or int22h-3. We find that (1) int1h and int22h duplicated more than 25 million years ago; (2) the identity of the copies (>99%) of these sequences in humans and other primates is due to gene conversion; (3) gene conversion is most frequent in the internal regions of int22h; (4) breakpoints of int22h-related inversions also tend to involve the internal regions of int22h; (5) sequence variations in a sample of human X chromosomes defined eight haplotypes of int22h-1 and 27 of int22h-2 plus int22h-3; (6) the latter two sequences, which lie, respectively, 500 and 600 kb telomeric to int22h-1 are five-fold more identical when in cis than when in trans, thus suggesting that gene conversion may be predominantly intrachromosomal; (7) int1h, int22h, and flanking sequences evolved at a rate of about 0.1% substitutions per million years during the divergence between humans and other primates, except for int1h during the human-chimpanzee divergence, when its rate of evolution was significantly lower. This is reminiscent of the slower evolution of palindrome arms in the male specific regions of the Y chromosome and we propose, as an explanation, that intrachromosomal gene conversion and cosegregation of the duplicated regions favors retention of the ancestral sequence and thus reduces the evolution rate.

Animals↗
PubMed1997

Cellular recombination pathways and viral terminal repeat hairpin structures are sufficient for adeno-associated virus integration in vivo and in vitro.

The human parvovirus adeno-associated virus (AAV) is unique in its ability to target viral integration to a specific site on chromosome 19 (ch-19). Recombinant AAV (rAAV) vectors retain the ability to integrate but have apparently lost this ability to target. In this report, we characterize the terminal-repeat-mediated integration for wild-type (wt), rAAV, and in vitro systems to gain a better understanding of these differences. Cell lines latent for either wt or rAAV were characterized by a variety of techniques, including PCR, Southern hybridization, and fluorescence in situ hybridization analysis. More than 40 AAV-rAAV integration junctions were cloned, sequenced, and then subjected to comparison and analysis. In both immortalized and normal diploid human cells, wt AAV targeted integration to ch-19. Integrated provirus structures consisted of head-to-tail tandem arrays with the majority of the junction sequences involving the AAV inverted terminal repeats (ITRs). No complete viral ITRs were directly observed. In some examples, the AAV p5 promoter sequence was found to be fused at the virus-cell junction. Data from dot blot analysis of PCR products were consistent with the occurrence of inversions of genomic and/or viral DNA sequences at the wt integration site. Unlike wt provirus junctions, rAAV provirus junctions mapped to a subset of non-ch-19 sequences. Southern analysis supported the integration of proviruses from two independent cell lines at the same locus on ch-2. In addition, provirus terminal repeat sequences existed in both the flip and flop orientations, with microhomology evident at the junctions. In all cases with the exception of the ITRs, the vector integrated intact. rAAV junction sequence data were consistent with the occurrence of genomic rearrangement by deletion and/or rearrangement-translocation at the integration locus. Finally, junctions formed in an in vitro system between several AAV substrates and the ch-19 target site were isolated and characterized. Linear AAV substrates typically utilized the end of the virus DNA substrate as the point of integration, whereas products derived from AAV terminal repeat hairpin structures in the presence or absence of Rep protein resembled AAV-ch-19 junctions generated in vivo. These results describing wt AAV, rAAV, and in vitro integration junctions suggest that the viral integration event itself is mediated by terminal repeat hairpin structures via nonviral cellular recombination pathways, with specificity for ch-19 in vivo requiring additional viral components. These studies should have an important impact on the use of rAAV vectors in human gene therapy.

Base Sequence↗
PubMed2002

[ISSR markers and their applications in plant genetics].

Recently, inter-simple sequence repeat (ISSR) markers have emerged as an alternative system with reliability and advantages of microsatellites (SSR). The technique involves amplification of genomic segments flanked by inversely oriented and closely spaced microsatellite sequences by a single primer or a pair of primers based on SSRs anchored 5' or 3' with 1-4 purine or pyramidine residues. The sequences of repeats and anchor nucleates are arbitrarily selected. Coupled with the separation of amplification products on a polyacrylamide or agarose gels,ISSR amplification can reveal a much larger number of fragments per primer than RAPD. It is concluded that ISSR technique provides a quick, reliable and highly informative system for DNA fingerprinting.ISSR markers are inherited in Mendelin mode and segregated as dominant markers. This technique has been widely used in the studies of cultivar identification, genetic mapping, gene tagging,genetic diversity, evolution and molecular ecology.

English Abstract↗
PubMed1997

The hsd loci of Mycoplasma pulmonis: organization, rearrangements and expression of genes.

Two paralogous, site-specific invertible loci, designated hsd1 and hsd2 (host specificity determinant), have been identified in the Mycoplasma pulmonis genome. They encode putative type I restriction and modification (R-M) systems with maximum sequence homology to the type IC family, which includes EcoR124II and EcoDXXI. Each locus encodes an endonuclease subunit (HsdR), a methylase subunit (HsdM) and two DNA specificity subunits (HsdS). The gene organization at each locus is such that hsdR and hsdM are flanked by two hsdS genes. Within each locus, one of the hsdS genes, hsdR and hsdM, is encoded in tandem by the same DNA strand, while the second hsdS gene is encoded by the complementary strand but without overlap with the other three hsd genes. The hsdR and hsdM sequences of one locus are almost identical to their counterparts in the other. The four hsdS genes (two per locus) are highly homologous at their 5' ends and also share sequence similarities in the 3' ends of their corresponding coding regions. Owing to the disposition of and sequence similarities among the hsdS genes, they form inverted repeats at each locus. Analysis by polymerase chain reaction (PCR) has shown that both loci behave as site-specific DNA invertible elements with multiple inversion sites, termed 'vipareetus', occurring within the hsdS genes. The inversions lead to a reassortment of hsdS sequences, generating an array of recombinant genes that probably encode S subunits possessing alternative DNA-binding specificities. Sequence information obtained from the analysis of hsd2 transcripts by 5' RACE (rapid amplification of cDNA ends) indicates that inversion induces the transcription of alternative hsdS genes by the relocation of coding sequences downstream of a promoter and ribosome-binding site (RBS) situated at one end of each locus.

Amino Acid Sequence↗
PubMed1994

Binding of T and T analogs to CG base pairs in antiparallel triplexes.

The goal of this study was to address antiparallel triplex formation at duplex targets that do not conform to a strict oligopurine.oligopyrimidine motif. We focused on the ability of natural bases and base analogs incorporated into oligonucleotide third strands to bind to so-called CG inversions. These are sites where a cytosine base is present in an otherwise purine-rich strand of a duplex target. Using a 26-base-triplet test system, we found that of the standard bases, only thymine (T) shows substantial binding to CG inversions. This is quantitatively similar to the report of Beal and Dervan [Science (1991), 251, 1360-1363]. Binding to CG inversions was only slightly weaker than binding to AT base pairs. Binding of T to CG inversions was also evaluated in two other sequences, with qualitatively similar results. Six different analogs of thymine were also tested for binding to CG inversions and AT base pairs. Significant changes in affinity were observed. In particular, 5-fluoro-2'-deoxyuridine was found to increase affinity for CG inversions as well as for AT base pairs. Studies with oligonucleotides containing pyridin-2-one or pyridin-4-one suggest that thymine O4 plays a critical role in the T.CG interaction. Possible models to account for these observations are discussed.

Base Composition↗
PubMed1989

Site-specific recombinations between direct and inverted res sites of Tn2501.

The resolvase gene and the putative res site of Tn2501 are not closely related to any of the previously described resolution functions. In view of this divergence, we designed genetic experiments to confirm the localization of the res site. We analyzed the activity of the Tn2501-encoded resolvase on substrates containing either directly or invertedly repeated res sites. These experiments confirm the localization of the res site that was predicted from nucleotide sequence data and show that the Tn2501 resolvase promotes site-specific inversions in vivo.

Base Sequence↗
PubMed1987

The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias.

Genes sequences from Escherichia coli, Salmonella typhimurium, and other members of the Enterobacteriaceae show a negative correlation between the degree of synonymous-codon usage bias and the rate of nucleotide substitution at synonymous sites. In particular, very highly expressed genes have very biased codon usage and accumulate synonymous substitutions very slowly. In contrast, there is little correlation between the degree of codon bias and the rate of protein evolution. It is concluded that both the rate of synonymous substitution and the degree of codon usage bias largely reflect the intensity of selection at the translational level. Because of the high variability among genes in rates of synonymous substitution, separate molecular clocks of synonymous substitution might be required for different genes.

Biological Evolution↗
PubMed1992

3'-UTR-dependent deadenylation by the yeast poly(A) nuclease.

Poly(A) tail removal is the first step in the degradation pathway for some mRNAs. The purified poly(A)-binding protein (PAB)-dependent poly(A) nuclease (PAN) from yeast removes mRNA poly(A) tails in vitro by a process similar to that observed in vivo. The exonucleolytic PAN degrades poly(A) and RNA bound by PAB, and can be activated by spermidine to degrade poly(A) in the absence of PAB. The shortening of the poly(A) tail down to 10-25 nucleotides and the terminal deadenylation of this short adenine tract are kinetically distinct reactions. Poly(A) shortening rates are stimulated by the yeast a-mating factor (MFA2) RNA 3' UTR sequence, and this occurs by switching PAN from a distributive to a more processive enzyme. Terminal deadenylation rates are also stimulated to different extents by various RNAs. Inversion of the MFA2 3' UTR sequence completely inhibits the terminal deadenylation reaction owing to the presence of an inhibitory element 70 nucleotides from the poly(A) tail. Other sequence elements inserted at a similar distance from the poly(A) tail also interfere with the reaction. These data suggest that the two phases of poly(A) degradation can be regulated by mRNA sequences, and they provide a mechanistic description of how this regulation could occur in vivo.

Base Sequence↗
PubMed1986

Pulse sequence extrapolation with MR image synthesis.

Previous reports have presented validation studies of magnetic resonance (MR) image synthesis in which multiple spin-echo (MSE) source data were used to generate spin-echo images for various echo times and repetition times (TRs). A new method-"pulse sequence extrapolation" -synthesizes images for pulse sequences different from that of the acquisition. MSE data acquired in a time equivalent to a TR of 2,000 msec can be used to generate inversion-recovery (IR) images for arbitrarily chosen TI inversion times. Other combinations of pulse sequences were also studied, and synthetic images were compared visually and quantitatively to directly acquired images with corresponding parameters. Synthetic IR signals of the brain parenchyma consistently matched directly acquired signals to within 6%, with respect to the full magnetization signal. The noise level of synthetic signals was generally no more than twice that of direct acquisition signals, as predicted. This method can achieve selective fat suppression and enhancement in IR imaging.

Biophysical Phenomena↗
PubMedDate not supplied

Incremental flip angle snapshot FLASH MRI of hepatic lesions: improvement of signal-to-noise and contrast.

Incremental flip angle (IFA) snapshot fast low angle shot (FLASH) is a new modification of inversion recovery snapshot FLASH MR imaging. The method changes the flip angle incrementally from low to high during data acquisition and was applied in the evaluation of 16 focal hepatic lesions in 10 patients. Sequence comparisons were performed with a fixed flip angle inversion recovery snapshot FLASH sequence (standard), a T1- and T2-weighted spin-echo (SE) sequence, and a T1-weighted breath-hold FLASH sequence. Whereas snapshot FLASH images in both pulse sequences were free from physiological motion artifacts, SE and FLASH images showed respiratory artifacts in some patients. Quantitative analysis of IFA snapshot FLASH images at low hepatic and low lesion signal revealed both superior lesion-liver signal-difference-to-noise ratio (SD/N) and superior contrast compared with standard snapshot FLASH without additional artifacts. Unless motion artifacts were evident, SE and FLASH images showed a higher anatomic resolution but lower SD/N and lower contrast than IFA snapshot images. Because of its superior SD/N and contrast, IFA snapshot FLASH will likely widen the application of fast MR imaging techniques.

Humans↗
PubMed1999

Atomic Structures of Oxygen-associated Defects in Sintered Aluminum Nitride Ceramics.

: Convergent-beam electron diffraction and Z-contrast imaging are used to study oxygen-associated defects, flat inversion domain boundaries, dislocations, and interfaces in sintered AlN ceramics. The structures of these defects are directly derived from atomic-resolution Z-contrast images. The flat inversion domain boundaries contain a single Al-O octahedral layer and have a stacking sequence of.bAaB-bAc-CaAc., where -cAb- indicates the single octahedral layer. The expansion at the flat inversion domain boundaries is measured to be 0.06 (+/-0.02) nm. The interfaces between 2H- and polytypoid-AlN are found to be also inversion domain boundaries but their stacking sequence differs from that of the flat inversion domain boundaries.

Journal Article↗
PubMed1994

Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization.

The chromosomes of Arabidopsis thaliana and Brassica oleracea have been extensively rearranged since the divergence of these species; however, conserved regions are evident. Eleven regions of conserved organization were detected, ranging from 3.7 to 49.6 cM in A. thaliana, spanning 158.2 cM (24.6%) of the A. thaliana genome, and 245 cM (29.9%) of the B. oleracea genome. At least 17 translocations and 9 inversions distinguish the genomes of A. thaliana and B. oleracea. In one case B. oleracea homoeologs show a common marker order, which is distinguished from the A. thaliana order by a rearrangement, indicating that the lineages of A. thaliana and B. oleracea diverged prior to chromosomal duplication in the Brassica lineage (for at least this chromosome). Some chromosomal segments in B. oleracea appear to be triplicated, indicating the need for reevaluation of a classical model for Brassica chromosome evolution by duplication. The distribution of duplicated loci mapped for about 13% of the DNA probes studied in A. thaliana suggests that ancient duplications may also have occurred in Arabidopsis. The degree of chromosomal divergence between A. thaliana and B. oleracea appears greater than that found in other confamilial species for which comparative maps are available.

Arabidopsis↗
PubMed1990

Characterization of chicken octamer-binding proteins demonstrates that POU domain-containing homeobox transcription factors have been highly conserved during vertebrate evolution.

The DNA sequence motif ATTTGCAT (octamer) or its inverse complement has been identified as an evolutionarily conserved element in the promoter region of immunoglobulin genes. Two major DNA-binding proteins that bind in a sequence-specific manner to the octamer DNA sequence have been identified in mammalian species--a ubiquitously expressed protein (Oct-1) and a lymphoid-specific protein (Oct-2). During characterization of the promoter region of the chicken immunoglobulin light chain gene, we identified two homologous octamer-binding proteins in chicken B cells. When the cloning of the human gene for Oct-2 revealed it to be a member of a distinct family of homeobox genes, we sought to determine if the human Oct-2 cDNA could be used to identify homologous chicken homeobox genes. Using a human Oct-2 homeobox-specific DNA probe, we were able to identify 6-10 homeobox-containing genes in the chicken genome, demonstrating that the Oct-2-related subfamily of homeobox genes exists in avian species. Low-stringency screening of a chicken embryonic cDNA library allowed us to clone one of these genes. DNA sequence analysis revealed it to be the chicken homologue of the human Oct-1 gene. The predicted protein sequence of the chicken Oct-1 gene demonstrated that the gene for Oct-1 has been highly conserved during vertebrate evolution with an overall 96% amino acid sequence identity between the chicken and human proteins. The previously described POU domain (termed POU for its presence in the Pit-1, Oct-1/Oct-2, and Unc-86 genes) and homeobox domain are 100% conserved between the two protein products. Together, our data show that the POU-containing subfamily of homeobox genes have been highly conserved during vertebrate evolution, apparently as a result of selection for their DNA-binding and transcriptional regulatory properties.

Amino Acid Sequence↗
PubMed1986

Dynamic spin-echo MRI of liver cancer using Gadolinium-DTPA: animal investigation.

An animal model of liver cancer was used to demonstrate that with a fast MRI technique, Gadolinium-DTPA increases tumor-liver contrast. A spin-echo pulse sequence with short repetition (TR) and echo-delay (TE) times (TR 250/TE 15/Excitations 1) has a scan time of 0.6 min, which allows early dynamic postcontrast infusion imaging. This is necessary to capture peak compartmental differences when an extracellular contrast agent such as Gadolinium-DTPA is used. This short TR/short TE pulse sequence also increases T1-dependent tissue contrast over the traditional (inversion recovery or spin echo) T1-weighted pulse sequences. Our studies suggest a significant potential for improved detection of liver metastases with Gadolinium-DTPA-enhanced liver MRI.

Adenocarcinoma↗
PubMed1999

Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms.

The analysis of transgene silencing effects in plants and other eukaryotic organisms has revealed novel mechanisms of epigenetic regulation that are based on recognition of nucleic acid sequence homology. These homology-dependent gene silencing phenomena are characterized by an inverse relationship between copy number of a particular sequence and expression levels. Depending on whether promoter regions or transcribed sequences are repeated, silencing occurs at the transcriptional or post-transcriptional level, respectively. Different silencing effects involving DNA-DNA or RNA-DNA associations in the nucleus, and RNA-RNA interactions in the cytoplasm appear to reflect distinct host defense responses to parasitic sequences, including transposable elements (TEs), viroids and RNA viruses. Natural epigenetic phenomena that resemble transgene silencing effects often involve endogenous genes comprising recognizable TE sequences or rearrangements generated by TEs and can thus be interpreted in terms of host defense systems. A genome defense that inactivates TEs by methylation might have been recruited during evolution to regulate the transcription of plant and vertebrate genes that contain remnants of TE insertions in promoter regions.

DNA Methylation↗
PubMed2006

Phase-sensitive inversion recovery (PSIR) single-shot TrueFISP for assessment of myocardial infarction at 3 tesla.

PURPOSE: The aim of the current study was to show if contrast-to-noise ratio (CNR) could be improved without loss of diagnostic accuracy if a phase-sensitive inversion recovery (PSIR) single-shot TrueFISP sequence is used at 3.0 T instead of 1.5 T. MATERIAL AND METHODS: Ten patients with myocardial infarction were examined on a 1.5 T magnetic resonance (MR) system (Avanto, Siemens Medical Systems) and at a 3.0 T MR system. Imaging delayed contrast enhancement was started 10 minutes after application of contrast material. A phase-sensitive inversion recovery (PSIR) single-shot TrueFISP sequence was used at 1.5 and 3.0 T and compared with a segmented IR turboFLASH sequence at 1.5 T, which served as the reference method. Infarct volumes and CNR of infarction and normal myocardium were compared with the reference method. RESULTS: The PSIR Single-Shot TrueFISP technique allows for imaging nine slices during a single breathhold without adaptation of the inversion time. The mean value of CNR between infarction and normal myocardium was 5.9 at 1.5 T and 12.2 at 3.0 T (magnitude images). The CNR mean value of the reference method was 8.4. The CNR mean value at 3.0 T was significantly (P = 0.03) higher than the mean value of the reference method. The correlation coefficients of the infarct volumes, determined with the PSIR single-shot TrueFISP technique at 1.5 T and at 3.0 T and compared with the reference method, were r = 0.96 (P = 0.001) and r = 0.99 (P = 0.0001). CONCLUSION: The use of PSIR single-shot TrueFISP at 3.0 T allows for accurate detection and assessment of myocardial infarction. CNR is significantly higher at 3.0 T compared with 1.5 T. The PSIR single-shot technique at 3.0 T provides a higher CNR than the segmented reference technique at 1.5 T.

Adult↗
PubMed2002

Magnetic resonance imaging of myocardial fibrosis in hypertrophic cardiomyopathy.

Myocardial fibrosis can occur in patients who have hypertrophic cardiomyopathy in the absence of epicardial coronary disease. In such patients, myocardial fibrosis has been linked to a poorer prognosis than in those without fibrosis. Gadolinium-DTPA delayed-enhancement magnetic resonance imaging (de-MRI) accurately identifies regions of myocardial fibrosis. We used de-MRI to screen for myocardial fibrosis in 8 patients with nonobstructive hypertrophic cardiomyopathy that had been diagnosed by 2-dimensional echocardiography. After localization of the heart and acquisition of electrocardiographically gated cine images, gadolinium-DTPA (0.2 mmol/kg) was administered to the patient. Fifteen minutes later, de-MRI images were obtained using a T1-weighted, inversion-recovery fast, low-angle shot sequence. Images were gated to end-diastole and obtained during a single breath-hold. The inversion time was modified iteratively to obtain maximal nulling of the signal from the ventricular myocardium. Regions of myocardium with abnormally high signals (>300% of remote normal myocardium) were designated as fibrotic. Eight patients with hypertrophic cardiomyopathy underwent de-MRI. The mean age was 52 years, the mean left ventricular mass was 201 grams, and the mean ejection fraction was 0.68. In the 6 patients with recent clinical deterioration, de-MRI showed clearly delineated areas of myocardial fibrosis; no such areas were seen in the 2 asymptomatic patients. We conclude that patients with symptomatic hypertrophic cardiomyopathy display regions of abnormal signal intensity on de-MRI that likely represent fibrosis. This technique may provide useful information in the evaluation of such patients and warrants further study.

Adult↗