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PubMed2001

A linear-time algorithm for computing inversion distance between signed permutations with an experimental study.

Hannenhalli and Pevzner gave the first polynomial-time algorithm for computing the inversion distance between two signed permutations, as part of the larger task of determining the shortest sequence of inversions needed to transform one permutation into the other. Their algorithm (restricted to distance calculation) proceeds in two stages: in the first stage, the overlap graph induced by the permutation is decomposed into connected components; then, in the second stage, certain graph structures (hurdles and others) are identified. Berman and Hannenhalli avoided the explicit computation of the overlap graph and gave an O(nalpha(n)) algorithm, based on a Union-Find structure, to find its connected components, where alpha is the inverse Ackerman function. Since for all practical purposes alpha(n) is a constant no larger than four, this algorithm has been the fastest practical algorithm to date. In this paper, we present a new linear-time algorithm for computing the connected components, which is more efficient than that of Berman and Hannenhalli in both theory and practice. Our algorithm uses only a stack and is very easy to implement. We give the results of computational experiments over a large range of permutation pairs produced through simulated evolution; our experiments show a speed-up by a factor of 2 to 5 in the computation of the connected components and by a factor of 1.3 to 2 in the overall distance computation.

Algorithms↗
PubMed1998

Activation of the beta-catenin gene by interstitial deletions involving exon 3 in primary colorectal carcinomas without adenomatous polyposis coli mutations.

Among 222 primary colorectal cancers we examined, 58 showed no detectable APC mutations by the protein truncation test. We screened those 58 tumors for somatic mutations in the beta-catenin gene. Although amino acid substitutions in serine or threonine residues in exon 3 had been reported, we found no such mutations; however, in seven tumors, we detected somatic interstitial deletions of 234-760 bp, each of which included all or part of exon 3. Short nucleotide sequences at both ends of each deletion were either identical or complementary, indicating that repeated or inversely repeated sequences were involved in the somatic rearrangements. Reverse transcription-PCR experiments using RNAs isolated from three of these seven tumors detected transcripts that lacked exon 3, in addition to the normal transcript. In one of these cases, we confirmed accumulation of aberrant beta-catenin protein in cytoplasm and nuclei of cancer cells by Western and immunohistochemical analyses. This result suggested that, in the absence of a peptide encoded by exon 3, beta-catenin is stabilized and has a dominant oncogenic effect on colorectal tumorigenesis.

Carcinoma↗
PubMed1988

Magnetic resonance imaging of renal transplants: initial experience.

Magnetic resonance imaging (MRI) was used in 45 renal transplant investigations (38 patients) using a Picker 0.15 T resistive system and a localized surface coil. An attempt was made to define optimal sequences in the evaluation of both normal and pathological transplants. Three sequences were found to be of value; a T1 weighted sequence (IR2180/700/40) to assess corticomedullary differentiation and its loss in acute rejection and acute tubular necrosis, a T2 weighted sequence (SE2000/80) for assessment of renal vessels and disturbances in blood supply, and a STIR (short tau inversion recovery) sequence (IR800/100/40) to define further the distended collecting system in obstruction and the presence of any perirenal collection. Encouraging results have been obtained, particularly in cases of acute rejection. It is suggested that the MRI scan is a useful screening test in cases of clinical doubt and may even obviate biopsy in some cases.

Adult↗
PubMed1987

[Magnetic resonance imaging (MRI) of pituitary adenomas].

MRI of 20 patients, 17-82 years old, with pituitary adenomas confirmed histopathologically, and 30 normal patients without pituitary dysfunction were reviewed. The studies were performed with a 0.5 Tesla MR scanner with a slice thickness of 10 mm. Inversion recovery sequences were employed as T 1-weighted examination, with repetition time (TR) of 2100-2500 msec, an inversion time (TI) of 600 msec and an echo time (TE) of 40 msec. The T 2-weighted examination had a TR of 1800-2500 msec and a TE of 120 msec. T 1-weighted images were obtained in all cases and T 2-weighted images in 14 cases. Spin echo images with a TR of 600-1000 msec and a TE of 40 msec (SE 40/600-1000) were also obtained in 14 cases. On T 1-weighted images, 20 adenomas were classified into six groups, according to their signal intensities; marked low intensity (1), low intensity (1), isointensity (11), high intensity (3), marked high intensity (1) and mixed intensity (3). On T 2-weighted images, 14 adenomas were classified into five groups; low intensity (1), isointensity (2), high intensity (4), marked high intensity (6) and mixed intensity (1). On SE 40/600-1000 images, 14 adenomas were also classified into four groups; low intensity (8), high intensity (2) and mixed intensity (3). Two adenomas with recent intratumoral hemorrhage had marked high intensity on both T1 and T2-weighted images. SE 40/600-1000 images were useful in evaluating the size and the extent of the visual pathway was best appreciated on IR images. Comparison between normal and involved cavernous sinus by adenomas was made.

Adenoma↗
PubMed2001

Chromosomal integration of transduced recombinant baculovirus DNA in mammalian cells.

Our group and others have recently demonstrated the ability of recombinant baculoviruses to transduce mammalian cells at high frequency. To further characterize the use of baculovirus as a mammalian gene delivery system, we examined the status of transduced DNA stably maintained in Chinese hamster ovary (CHO) cells. Four independent clones carrying two introduced markers, the genes for neomycin resistance (Neo) and green fluorescent protein (GFP), were selected. PCR analysis, Southern blotting, and DNA sequencing showed that discrete portions of the 148-kb baculovirus DNA were present as single-copy fragments ranging in size from 5 to 18 kb. Integration into the CHO cell genome was confirmed by fluorescent in situ hybridization (FISH) analysis. For one clone, the left and right viral/chromosomal junctions were determined by DNA sequencing of inverse PCR products. Similarly, for a different clone, the left viral/chromosomal junction was determined; however, the right junction sequence revealed the joining to another viral fragment by a short homology (microhomology), a hallmark of illegitimate recombination. The random viral breakpoints and the lack of homology between the virus and flanking chromosomal sequences are also suggestive of an illegitimate integration mechanism. To examine the long-term stability of reporter gene expression, all four clones were grown continuously for 36 passages in either the presence or absence of selection for Neo. Periodic assays over a 5-month period showed no loss of GFP expression for at least two of the clones. This report represents the first detailed analysis of baculovirus integrants within mammalian cells. The potential advantages of the baculovirus system for the stable integration of genetic material into mammalian genomes are discussed.

Animals↗
PubMed2004

Neovascularization of bone marrow in patients with diffuse multiple myeloma: a correlative study of magnetic resonance imaging and histopathologic findings.

BACKGROUND: The goal of the current study was to assess the correlation between bone marrow histology and contrast enhancement in infiltrative diffuse myeloma. METHODS: Forty-four patients with homogeneous diffuse infiltration of bone marrow by multiple myeloma were examined using magnetic resonance imaging of the spine. The sequence protocol included T1-weighted spin-echo (pre- and post-gadolinium dimeglumine administration) and short-inversion time inversion recovery sequences. The percent increase in signal after intravenous gadolinium administration was calculated in bone marrow from patients with myeloma and from a control group of 86 patients who did not have bone marrow disease. Grade of infiltration with plasma cells, fat cell content, and hematopoietic marrow content were evaluated via histologic assessment of bone marrow, and microvessel density was evaluated via anti-CD34-positive immunostaining. RESULTS: Increased microvessel density was observed in association with increasing plasma cell content (Kruskall-Wallis test: P < 0.0001). Contrast enhancement increased in a stepwise manner according to grade of microvessel density (Mann-Whitney U test: P < 0.05 and P < 0.001 for increases from low to intermediate and intermediate to high grade) and was significantly higher in patients with myeloma compared with control patients (Mann-Whitney U test: P < 0.001). A significant correlation also was found between histologic extent of tumor infiltration and contrast enhancement (Mann-Whitney U test: P < 0.0001). The mean level of contrast enhancement was 18% in the control group, 26% in patients with low-grade infiltration, 49% in patients with intermediate-grade infiltration, and 90% in patients with high-grade infiltration. In addition, fat cell content was found to be inversely correlated with contrast enhancement (chi-square test: P < 0.01). CONCLUSIONS: As a consequence of increased microvessel density, decreased fat cell content, and increased cellularity, the presence of diffuse bone marrow infiltration in patients with multiple myeloma can be verified using gadolinium-enhanced magnetic resonance imaging.

Adipocytes↗
PubMed1999

[Object analysis of cervical lymph nodes using MRI turbo-STIR sequence in cases of head and neck tumors].

Diagnosis of cervical lymph nodes from head and neck tumors was studied using MRI turbo-STIR (short TI inversion recovery) sequence and conventional MRI sequence in 15 patients. After the MRI examination, 10 of the 15 patients underwent radical neck dissections. The detection of cervical lymph nodes with the conventional MRI was not clear. However, MRI turbo-STIR depicted clear cervical lymph node margins by selectively suppressing fat signals. Thus, the accuracy of diagnosis of cervical lymph nodes by the turbo-STIR was higher than by conventional MRI. On the other hand, differential diagnosis between metastatic and non-metastatic lymph nodes remains difficult only by turbo-STIR. These findings suggest that MRI turbo-STIR sequence is more useful in the detection of cervical lymph nodes than the conventional MRI methods.

Aged↗
PubMed2006

[MR coronary angiography with MS-325, a blood pool contrast agent: comparison of an inversion recovery steady-state free precession with an inversion recovery fast low angle shot sequence in volunteers].

PURPOSE: To compare the signal-to-noise and contrast-to-noise ratio as well as the image quality of 3D inversion recovery steady-state free precession (IR-SSFP) and 3D inversion recovery fast low angle shot (IR-FLASH) sequences for contrast-enhanced breath-hold MRCA. MATERIALS AND METHODS: 24 healthy volunteers (10 female, 14 male, mean age 29.8 +/- 6.1 years) were involved in this study. All examinations were performed on a 1.5 T MR scanner (Magnetom Sonata, Siemens, Germany) after injection of 0.05 mmol/kg body weight MS-325 (EPIX Pharmaceuticals, Cambridge, MA and Schering AG, Berlin, Germany). MRCA was performed using IR-SSFP (TR 3.8 ms, TE 1.6 ms, FA 65 degrees , 35 phase encoded steps, bandwidth 540 Hz/pixel, slice thickness 1.5 mm, in-plane resolution 1.2 x 0.9 - 1.4 x 1.0 mm) and IR-FLASH (TR 3.8 ms, TE 1.6 ms, FA 25 degrees , bandwidth 490 Hz/pixel, slice thickness 1.5 mm, in-plane resolution 1.2 x 0.9 - 1.4 x 1.0 mm) sequences. For all scans the inversion time was set to null the signal intensity of the myocardium. Signal-to-noise ratio (SNR) as well as contrast-to-noise ratio (CNR) measurements (blood versus myocardium) were performed. The image quality was assessed based on a 5-point scale ranging from 1 (excellent) to 5 (non-diagnostic) by two radiologists in consensus. RESULTS: The mean signal-to-noise ratio of blood (27.7 +/- 4.7 vs. 22.6 +/- 4.9, P < 0.0001) and the contrast-to-noise ratio (21.0 +/- 4.3 vs. 15.8 +/- 4.3, P < 0.0001) showed significantly higher values for IR-SSFP sequences. The mean image quality scores were significantly higher for SSFP (3.6 +/- 0.7) than FLASH (2.8 +/- 0.9) sequences (P < 0.05). CONCLUSION: IR-SSFP sequences show a considerable overall improvement in image quality compared to IR-FLASH sequences for MRCA after injection of a gadolinium-based blood pool contrast agent.

Adult↗
PubMed2006

Magnetic resonance angiography, function and viability evaluation in patients with Kawasaki disease.

OBJECTIVES: We evaluated the ability of magnetic resonance imaging to perform a noninvasive assessment of coronary arteries, function and viability in one examination in a population with Kawasaki disease. BACKGROUND: Magnetic resonance angiography (MRA) can identify coronary abnormalities in patients with Kawasaki disease (KD). Contrast enhanced cardiovascular magnetic resonance (CeCMR) is the current gold standard for scar detection. Steady-state, free precession (SSFP) cine is a reliable technique to evaluate myocardial function and wall motion. METHODS: Twenty patients with KD aged 7-12 yrs, were examined. Coronary MRA was performed using a 1.5 T system with two ECG-triggered pulse sequences. CeCMR images were acquired 15 minutes after the i.v. injection of 0.1 mmol/kg Gd-DTPA using an inversion recovery sequence. SSFP cines were acquired using 6-mm short-axis slices from the atrioventricular ring to the apex. RESULTS: Aneurysms of the coronary arteries were identified in 7 patients and coronary ectasia was present in the remaining 12 patients while 1 patient had both. Transmural anterior-apical scar was detected by ceCMR in two cases, while small inferior necrosis was identified in another 2 cases. Left ventricular function was deteriorated only in the two patients with antero-apical infarction. The presence of myocardial infarction was detected in the territory supplied by the involved coronary artery. CONCLUSION: In Kawasaki disease MRA, SSFP cine and ceCMR are able to perform noninvasive coronary artery evaluation, function and infarct detection in a single study.

Child↗
PubMed1994

Characteristics of magnetic resonance sequences used for imaging silicone gel, saline, and gel-saline implants at low field strengths.

RATIONALE AND OBJECTIVES: Low-field magnetic resonance imaging (MRI) evaluation of breast implants is described, with emphasis on the capabilities provided by different imaging sequences. METHODS: Open architecture MR images using a .064-T permanent magnet and three-dimensional Fourier transform and inversion recovery sequences were obtained. A breast coil was designed and built for this project. Symptomatic and asymptomatic patients with silicone, saline-silicone and saline implants, and phantoms were part of this study. Phase images were used to differentiate protons in silicone, water, and fat. RESULTS AND CONCLUSIONS: Low-field MRI permitted differentiation of silicone, water, and fat. Implant anatomy and surrounding pathology could be imaged and identified.

Adult↗
PubMed1999

The W(sh), W(57), and Ph Kit expression mutations define tissue-specific control elements located between -23 and -154 kb upstream of Kit.

The Kit and PDGFRa receptor tyrosine kinases are encoded in close proximity at the murine white spotting (W) and patch (Ph) loci. Whereas W mutations affect hematopoiesis, melanogenesis, and gametogenesis, the Ph mutation affects melanogenesis and causes early lethality in homozygotes. The W(sh), W(57), and Ph mutations diminish Kit expression in certain cell types such as mast cells and enhance it in others. The W(sh), W(57), and Ph mutations arose from deletions and inversions affecting sequences in between the Kit and PDGFRa genes. We have determined the precise location of the breakpoint of the W(sh) inversion and the endpoints of the W(57) deletion upstream of the Kit transcription start site and examined the effect of these mutations on Kit expression in mast cells and hematopoietic stem cells and lineage progenitors. Our results indicate that positive elements controlling Kit expression in mast cells mapping in between -23 and -154 kb from the transcription start site can be dissociated from negative elements controlling Kit misexpression during embryonic development in the vicinity of the PDGFRa gene. In addition, we have identified two clusters of hypersensitive sites in mast cells at -23 -28 kb and -147 -154 kb from the Kit gene transcription start site. Analysis of these hypersensitive sites in mutant mast cells indicates a role for HS4-6 in Kit expression in mast cells. These findings provide a molecular basis for the phenotype of these Kit expression mutations and they provide insight into the complex mechanisms governing the regulation of Kit expression.

Animals↗
PubMed1997

The white gene of the tephritid fruit fly Bactrocera tryoni is characterized by a long untranslated 5' leader and a 12kb first intron.

A 300 bp fragment from exon 6 of the white gene of Bactrocera tryoni was used to screen a B. tryoni genomic library. One positive (approximately 14 kb) insert contained exons 2-6 of white by nucleotide and amino acid sequence similarity to the white genes of D. melanogaster (O'Hare et al., 1984; Pepling & Mount, 1990). Lucilia cuprina (Garcia et al., 1996). Ceratitis capitata (Zwiebel et al., 1995) and Anopheles gambiae (Besansky et al., 1995). A white 5' cDNA fragment containing exons 1, 2 and part of exon 3 was amplified, cloned and sequenced. An inverse PCR fragment of genomic DNA was generated, containing the exon 1 coding region plus approximately 2.1 kb of upstream sequence, encompassing the putative promoter of the gene. Exon 1 was found to be 728 bp long, encoding the first twenty-five amino acids. The full length of intron 1 was shown to be 12 kb (amplified using long PCR protocols), up to 3 times the length of the longest white intron 1 isolated to date.

ATP-Binding Cassette Transporters↗
PubMed1995

Gene conversion during vector insertion in embryonic stem cells.

Recombination of an insertion vector into its chromosomal homologue is a conservative event in that both the chromosomal and the vector sequences are preserved. However, gene conversion may accompany homologous recombination of an insertion vector. To examine gene conversion in more detail we have determined the targeting frequencies and the structure of the recombinant alleles generated with a series of vectors which target the hprt gene in embryonic stem cells. We demonstrate that gene conversion of the introduced mutation does not significantly limit homologous recombination and that gene conversion occurs without a sequence specific bias for five different mutations. The frequency of the loss of a vector mutation and the gain of a chromosomal sequence is inversely proportional to the distance between the vector mutation and the double-strand break. The loss of a chromosomal sequence and the gain of a vector mutation occurs at a low frequency.

Alleles↗
PubMed1992

Fat suppression in magnetic resonance imaging at low field strength using binomial pulse sequences.

The use of binomial pulse sequences for fat suppression in MRI at low field strength (0.15 T) was investigated. Both spin-echo and inversion-recovery sequences were used and images obtained of the limbs, head and neck, and pelvis of volunteers and patients. Good fat suppression was seen particularly in small fields of view. Despite technical problems, chemical shift selective techniques can be applied at low field strength.

Adipose Tissue↗
PubMed2003

Identification and characterization of a novel gene disrupted by a pericentric inversion inv(4)(p13.1q21.1) in a family with cleft lip.

Cleft lip with or without cleft palate is a common birth defect affecting 1 in every 700 live births. Several genetic loci are believed to be involved in the pathogenesis of syndromic and non-syndromic clefting. We identified a pericentric inversion of chromosome 4, inv(4)(p13q21) that segregates with cleft lip in a two-generation family. By using a combination of fluorescence in situ hybridization, yeast artificial chromosome, bacterial artificial chromosome contig mapping, and database searching we mapped and sequenced the inversion breakpoint region. The pericentric inversion disrupts a gene (ACOD4) on chromosome 4q21 that codes for a novel acyl-CoA desaturase enzyme. The 3.0 kb human ACOD4 cDNA spans approximately 170 kb and is composed of five exons of ACOD4. The inversion breakpoint is located in the second exon. The 3.0 kb mRNA is expressed at high level in fetal brain; a lower expression level was found in fetal kidney. No expression of ACOD4 was detected in fetal lung or liver or in adult tissues. The five exons code for a protein of 330 amino acids, with a predicted molecular weight of 37.5 kDa. The protein is highly similar to acyl-CoA desaturases from Drosophila melanogaster to Homo sapiens. The catalytically essential histidine clusters and the potential transmembrane domains are well conserved.

Amino Acid Sequence↗
PubMed1985

Site-specific DNA inversion is enhanced by a DNA sequence element in cis.

A segment of the bacteriophage P1 genome, called the C segment, can be inverted by site-specific recombination; the two different orientations of the invertible segment confer different host ranges to the phage. Inversion is catalyzed by the product of the cin gene which is adjacent to one of the crossover sites flanking the C segment. The Cin-catalyzed recombination can be measured in trans by using tester plasmids in which inversion switches on antibiotic-resistance genes. We show here that an additional sequence, distinct from the two crossover sites, is needed in cis for efficient inversion. This sequence is part of the cin structural gene and stimulates recombination more than 100-fold. We have localized the major enhancer sequence on a 72-base-pair fragment and found its activity to be largely independent of the orientation or position of the sequence with respect to the crossover sites.

Journal Article↗
PubMed2001

MRI of the wrist and finger joints in inflammatory joint diseases at 1-year interval: MRI features to predict bone erosions.

The aim of this study was to assess the ability of MRI determined synovial volumes and bone marrow oedema to predict progressions in bone erosions after 1 year in patients with different types of inflammatory joint diseases. Eighty-four patients underwent MRI, laboratory and clinical examination at baseline and 1 year later. Magnetic resonance imaging of the wrist and finger joints was performed in 22 patients with rheumatoid arthritis less than 3 years (group 1) who fulfilled the American College of Rheumatology (ACR) criteria for rheumatoid arthritis, 18 patients with reactive arthritis or psoriatic arthritis (group 2), 22 patients with more than 3 years duration of rheumatoid arthritis, who fulfilled the ACR criteria for rheumatoid arthritis (group 3), and 20 patients with arthralgia (group 4). The volume of the synovial membrane was outlined manually before and after gadodiamide injection on the T1-weighted sequences in the finger joints. Bones with marrow oedema were summed up in the wrist and fingers on short-tau inversion recovery sequences. These MRI features was compared with the number of bone erosions 1 year later. The MR images were scored independently under masked conditions. The synovial volumes in the finger joints assessed on pre-contrast images was highly predictive of bone erosions 1 year later in patients with rheumatoid arthritis (groups 1 and 3). The strongest individual predictor of bone erosions at 1-year follow-up was bone marrow oedema, if present at the wrist at baseline. Bone erosions on baseline MRI were in few cases reversible at follow-up MRI. The total synovial volume in the finger joints, and the presence of bone oedema in the wrist bones, seems to be predictive for the number of bone erosions 1 year later and may be used in screening. The importance of very early bone changes on MRI and the importance of the reversibility of these findings remain to be clarified.

Arthritis, Psoriatic↗
PubMed2003

Sequence differentiation associated with an inversion on the neo-X chromosome of Drosophila americana.

Sex chromosomes originate from pairs of autosomes that acquire controlling genes in the sex-determining cascade. Universal mechanisms apparently influence the evolution of sex chromosomes, because this chromosomal pair is characteristically heteromorphic in a broad range of organisms. To examine the pattern of initial differentiation between sex chromosomes, sequence analyses were performed on a pair of newly formed sex chromosomes in Drosophila americana. This species has neo-sex chromosomes as a result of a centromeric fusion between the X chromosome and an autosome. Sequences were analyzed from the Alcohol dehydrogenase (Adh), big brain (bib), and timeless (tim) gene regions, which represent separate positions along this pair of neo-sex chromosomes. In the northwestern range of the species, the bib and Adh regions exhibit significant sequence differentiation for neo-X chromosomes relative to neo-Y chromosomes from the same geographic region and other chromosomal populations of D. americana. Furthermore, a nucleotide site defining a common haplotype in bib is shown to be associated with a paracentric inversion [In(4)ab] on the neo-X chromosome, and this inversion suppresses recombination between neo-X and neo-Y chromosomes. These observations are consistent with the inversion acting as a recombination modifier that suppresses exchange between these neo-sex chromosomes, as predicted by models of sex chromosome evolution.

Animals↗