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PubMed2002

Structure and chromosomal distribution of human mitochondrial pseudogenes.

Nuclear mitochondrial pseudogenes (Numts) have been found in the genome of many eukaryote species, including humans. Using a BLAST approach, we found 1105 DNA sequences homologous to mitochondrial DNA (mtDNA) in the August 2001 Goldenpath human genome database. We assembled these sequences manually into 286 pseudogenes on the basis of single insertion events and constructed a chromosomal map of these Numts. Some pseudogenes appeared highly modified, containing inversions, deletions, duplications, and displaced sequences. In the case of four randomly selected Numts, we used PCR tests on cells lacking mtDNA to ensure that our technique was free from genome-sequencing artifacts. Furthermore, phylogenetic investigation suggested that one Numt, apparently inserted into the nuclear genome 25-30 million years ago, had been duplicated at least 10 times in various chromosomes during the course of evolution. Thus, these pseudogenes should be very useful in the study of ancient mtDNA and nuclear genome evolution.

Chromosome Mapping↗
PubMed2004

Rényi continuous entropy of DNA sequences.

Entropy measures of DNA sequences estimate their randomness or, inversely, their repeatability. L-block Shannon discrete entropy accounts for the empirical distribution of all length-L words and has convergence problems for finite sequences. A new entropy measure that extends Shannon's formalism is proposed. Renyi's quadratic entropy calculated with Parzen window density estimation method applied to CGR/USM continuous maps of DNA sequences constitute a novel technique to evaluate sequence global randomness without some of the former method drawbacks. The asymptotic behaviour of this new measure was analytically deduced and the calculation of entropies for several synthetic and experimental biological sequences was performed. The results obtained were compared with the distributions of the null model of randomness obtained by simulation. The biological sequences have shown a different p-value according to the kernel resolution of Parzen's method, which might indicate an unknown level of organization of their patterns. This new technique can be very useful in the study of DNA sequence complexity and provide additional tools for DNA entropy estimation. The main MATLAB applications developed and additional material are available at the webpage . Specialized functions can be obtained from the authors.

Animals↗
PubMed1981

Inversions between ribosomal RNA genes of Escherichia coli.

It might be anticipated that the presence of redundant but oppositely oriented sequences in a chromosome could allow inversion of the intervening material through homologous recombination. For example, the ribosomal RNA gene rrnD of Escherichia coli has the opposite orientation fro rrnB and rrnE and is separated from these genes by roughly 20% of the chromosome. Starting with a derivative of Cavalli Hfr, we have constructed mutants that have an inversion of the segment between rrnD and either rrnB or rrnE. These mutants are generally quite viable but do exhibit a slight reduction in growth rate relative to the parental strain. A major line of laboratory E. coli, W3110 and its derivatives, also has an inversion between rrnD and rrnE, probably created directly by a recombinational event between these highly homologous genes.

Crosses, Genetic↗
PubMed1988

Sequence identity between an inverted repeat family of transposable elements in Drosophila and Caenorhabditis.

The Tc1-like transposable elements, originally described in Caenorhabditis elegans, have a much wider phylogenetic distribution than previously thought. In this paper, we demonstrate that Tc1 shares sequence identity in its open reading frame and terminal repeats with a new transposable element Barney (also known as TCb1-Transposon Caenorhabditis briggsae 1). Barney was detected and isolated by Tc1 hybridization from the closely related nematode species, Caenorhabditis briggsae. The conserved open reading frames of Tc1 and Barney share identity with a structurally similar family of elements named HB found in Drosophila melanogaster, after the introduction of 3 small centrally located deletions in HB1. These reading frames would code for proteins with 30% amino acid identity (42% when conservative changes are included). Tc1, Barney and HB1 contain highly conserved blocks of amino acids which are likely to be in the functional domains of the putative transposase.

Amino Acid Sequence↗
PubMed1996

Comparison between conventional and fast spin-echo stir sequences.

PURPOSE: To evaluate the common characteristics and differences in contrast behavior of short-TI-inversion-recovery (STIR) and short-TI-inversion-recovery fast spin-echo (TurboSTIR) sequences. MATERIAL AND METHODS: Phantoms doped with increasing doses of Gd-DTPA and a pork-fat phantom were used to evaluate the dependence of the STIR and TurboSTIR signals on the T1 relaxation time. Clinical TurboSTIR images were obtained from 30 patients with musculoskeletal abnormalities and compared to conventional STIR images in 15 cases and to postcontrast TurboSTIR images in another 15 cases. RESULTS: In the phantom measurements, a significantly shorter inversion time (TI) was needed to achieve fat suppression on TurboSTIR images, and, with an identical number of signal averages, contrast-to-noise ratios were lower on TurboSTIR images. These differences between STIR and TurboSTIR can be attributed to the contribution of stimulated echoes to overall TurboSTIR signal and can be compensated by a shorter TI and a higher number of signal averages for TurboSTIR, respectively. With these adaptations, clinical TurboSTIR and STIR images showed an identical contrast behavior with fat suppression and a high sensitivity to pathological lesions but TurboSTIR saved a significant amount of scan time and reduced some types of artifacts. Contrast uptake impaired lesion conspicuity on TurboSTIR images. CONCLUSION: TurboSTIR sequences should replace conventional STIR sequences and should be performed before contrast administration.

Adolescent↗
PubMed1991

Double-step and inverse polymerase chain reaction for sensitive detection and cloning of T cell receptor variable region sequences.

We have developed a sensitive and rapid method for detection and cloning of cDNA amplified by double-step and inverse polymerase chain reaction (PCR) techniques. The blunt-ended double-strand cDNA libraries were circularized with T4 ligase and subsequently amplified by double-step PCR with two sets of primers of outward orientation (at amounts of 1-10 pmol in the first step and 100 pmol in the second step) which hybridize with the known region of the target DNA. This method is useful for analysis of the repertoires of TCR or immunoglobulins, in particular TCR alpha-chains, which are encoded by a single known constant region gene and greater than 100 unknown variable and joining region gene segments. By using this method, we detected at least 10(4) copies of TCR alpha-chain transcripts in the original samples which are equivalent to 10(3) T cells. The use of 1-10 ng of cytoplasmic RNA allowed us to make approximately 10(3) independent TCR alpha-chain libraries and to determine the sequence of unknown TCR alpha-chain cDNA by this method. We also show the frequency of a TCR alpha-chain usage in naive spleen and tumor-infiltrating lymphocytes.

Animals↗
PubMed1995

A PCR-based strategy for rapid mapping of hepadnavirus integrated sequences in hepatocellular carcinomas.

A methodology based on polymerase chain reaction (PCR) and restriction analysis for rapid mapping of woodchuck hepatitis virus (WHV) integrations in hepatocellular carcinoma (HCC) tissues is described. Conventional PCR with viral primer pairs is not suitable for mapping WHV-integrated regions because the presence of minimum amounts of non-integrated (PCR amplifiable) WHV genome and replicative intermediates cannot be excluded. The first relevant part of the strategy is the identification of the cellular sequences flanking the WHV integration in order to select one (or more) integration-specific primer. The cellular flanking sequence can be rapidly obtained by means of inverse-PCR amplification of the viral/cellular junction and sequencing of the product. Mapping of the integrated regions is carried out by fixed flanking primer PCR (FFP-PCR) using the cellular primer as a 'fixed' primer in PCR association with each of an available set of WHV primers. Amplification of episomal WHV sequences is thus avoided. PCR products can also undergo restriction analysis. PCR-positive viral primers and specific WHV restriction sites are assembled into a map, based on the size and restriction pattern of the PCR products. The results of WHV integration mapping in a woodchuck HCC are described.

Animals↗
PubMed2002

Analysis of an inactivated Lg-FLO1 gene present in bottom-fermenting yeast.

During the course of investigating a flocculation-related gene of a bottom-fermenting yeast, we identified a new Lg-FLO1 homologue which contains the N-terminal domain of the Lg-FLO1 gene. The results of the partial DNA sequence analysis of the amplified product obtained by inverse-PCR suggested that the homologue contains a sequence present in the YIL169c (chr. IX of Saccharomyces cerevisiae). Southern blot analyses using the VTH1, HXT12, SDL1 and UBP7 genes as probes for chr. IX strongly indicated that an approximately 20-kb region from the YIL169c ORF to the left telomere in chr. IX translocated to the Lg-FLO1 ORF region in chr. VIII of bottom-fermenting yeast. This translocation might convert a flocculent cell to a non-flocculent one.

Journal Article↗
PubMed1989

Liver metastases: detection with MR imaging at 0.5 and 1.5 T.

Nineteen patients with known liver metastases were examined with two magnetic resonance (MR) pulse sequences at 0.5 T and three pulse sequences at 1.5 T. In addition, the patients were studied with computed tomography (CT) enhanced with ethiodized oil emulsion-13 (EOE-13). At 0.5 T a spin-echo (SE) 300/22 (repetition time/echo time, msec) sequence prospectively demonstrated 92.4% of the detectable liver metastases, while an SE 2,000/80 sequence showed 52.1% of the lesions. At 1.5 T, an SE 300/25 sequence depicted 68.3% and an SE 2,000/80 sequence 71.6%, while the more T1-weighted inversion recovery (IR) 2,000/600 (repetition time/inversion time, msec) sequence demonstrated 89.5% of the lesions. EOE-13 CT scans depicted 93.3%. These findings suggest that T1-weighted imaging is as successful at demonstrating liver metastases at 1.5 T with an IR 2,000/600 sequence as at 0.5 T with an SE 300/22 sequence. At both field strengths, MR imaging of the liver is comparable to state-of-the-art CT.

Humans↗
PubMed1994

Identification of a novel first exon in the human dystrophin gene and of a new promoter located more than 500 kb upstream of the nearest known promoter.

The dystrophin gene, which is mutated in patients with Duchenne and Becker muscular dystrophies, is the largest known human gene. Five alternative promoters have been characterized until now. Here we show that a novel dystrophin isoform with a different first exon can be produced through transcription initiation at a previously unidentified alternative promoter. The case study presented is that of a patient with Duchenne muscular dystrophy who had a deletion extending from the 5' end of the dystrophin gene to exon 2, including all promoters previously mapped in the 5' part of the gene. Transcripts from lymphoblastoid cells were found to contain sequences corresponding to exon 3, indicating the presence of new promoter upstream of this exon. The nucleotide sequence of amplified cDNA corresponding to the 5' end of the new transcript indicated that the 5' end of exon 3 was extended by 9 codons, only the last (most 3') of which codes for methionine. The genomic nucleotide sequence upstream from the new exon, as determined using inverse polymerase chain reaction, revealed the presence of sequences similar to a TATA box, an octamer motif and an MEF-2 element. The identified promoter/exon did not map to intron 2, as might have been expected, but to a position more than 500 kb upstream of the most 5' of the previously identified promoters, thereby adding 500 kb to the dystrophin gene. The sequence of part of the new promoter region is very similar to that of certain medium reiteration frequency repetitive sequences. These findings may help us understand the molecular evolution of the dystrophin gene.

Amino Acid Sequence↗
PubMed1999

Analysis of cystic intracranial lesions performed with fluid-attenuated inversion recovery MR imaging.

BACKGROUND AND PURPOSE: T1-, T2-, and proton density (PD)-weighted sequences are used to characterize the content of cystic intracranial lesions. Fluid-attenuated inversion recovery (FLAIR) MR sequences produce T2-weighted images with water signal saturation. Therefore, we attempted to verify whether FLAIR, as compared with conventional techniques, improves the distinction between intracranial cysts with a free water-like content versus those filled with a non-free water-like substance and, consequently, aids in the identification of these lesions as either neoplastic/inflammatory or maldevelopmental/porencephalic. METHODS: Forty-five cystic intracranial lesions were studied using T1-weighted, T2-weighted, FLAIR, and PD-weighted sequences. By means of clustering analysis of the ratio in signal intensity between the cystic intracranial lesions and CSF, the intracranial lesions were classified as filled with a free water-like content or with a non-free water-like substance. The results were compared with their true content as evaluated either histologically or on the basis of clinical, neuroradiologic, and follow-up features (necrotic material, 13 cases; accumulation of intercellular proteinaceous/myxoid material, eight cases; keratin, five cases; CSF, 19 cases). Cystic intracranial lesions were divided into two clinical groups, neoplastic/inflammatory and maldevelopmental/porencephalic, to evaluate the level of accuracy of each MR technique. The difference in absolute value signal intensity between CSF and cystic intracranial lesion content was calculated on FLAIR and PD-weighted images. RESULTS: PD-weighted and FLAIR sequences, unlike T1- and T2-weighted sequences, accurately depicted all cystic intracranial lesions containing necrotic or myxoid/proteinaceous intercellular material (non-free water-like) and most CSF-containing cystic intracranial lesions (free water-like). All imaging techniques inaccurately showed some of the keratin-containing cystic intracranial lesions and pineal cysts. The overall error rate was 22% for T1-weighted, 27% for T2-weighted, 9% for FLAIR, and 13% for PD-weighted sequences. The signal intensity difference between CSF and cystic intracranial lesion content was higher with FLAIR imaging. CONCLUSIONS: FLAIR imaging depicts far more accurately the content of cystic intracranial lesions and better reveals the distinction between maldevelopmental/porencephalic and neoplastic/inflammatory lesions than do conventional sequences. FLAIR has the added advantage of a higher signal intensity difference between cystic intracranial lesions and CSF.

Adult↗
PubMed2005

Improved accuracy and consistency in T1 measurement of flowing blood by using inversion recovery GE-EPI.

Problems associated with techniques currently used to measure the T1 of flowing blood are evaluated and a method to improve the consistency and repeatability of measurements is presented. Similar to some currently used techniques, the pulse sequence employs a nonselective adiabatic inversion pulse followed by a series of ECG-gated gradient echo EPI (echo planar imaging) images to obtain images where the blood (fluid) signal exhibits a T1-dependent inversion recovery signal from which the spin lattice relaxation constant (T1) of the flowing fluid can be measured. The new method combines curve fitting with a measure of the curve null point to acquire more accurate and consistent T1 values. Simulation and experimental results show that this combined fitting-nulling method is more stable and consistent in measuring the T1 of flowing fluid. The feasibility of temperature measurement of a flowing fluid based on the temperature dependence of the T1 of water protons is shown in this paper. ECG gating is used to reduce the effects of cyclic intensity changes for measurement of T1 in pulsatile flowing blood.

Blood Flow Velocity↗
PubMed2007

Small hepatic lesions found on single-phase helical CT in patients with malignancy: diagnostic capability of breath-hold, multisection fluid-attenuated inversion-recovery (FLAIR) MR imaging using a half-fourier acquisition single-shot turbo spin-echo (HASTE) sequence.

PURPOSE: To evaluate the diagnostic capability of breath-hold, multisection fluid-attenuated inversion-recovery (FLAIR) imaging using a half-Fourier acquisition single-shot turbo spin-echo (HASTE) sequence in combination with T2-weighted fast spin-echo (FSE) magnetic resonance (MR) sequences for small hepatic lesions found on CT in patients with malignancy. MATERIALS AND METHODS: This study included 48 patients with extrahepatic malignancy who underwent both CT and MR examinations. There were a total of 112 small hepatic lesions (73 cysts and 39 liver metastases, <2 cm in diameter) that showed low attenuation on enhanced CT. Three radiologists independently reviewed the CT and MR (FLAIR-HASTE and T2-weighted FSE) images and assigned a confidence level to their evaluation (cyst or metastasis) on a five-point scale. RESULTS: All three reviewers were significantly better able (P < 0.05) to differentiate small hepatic cyst from liver metastasis with combined FLAIR-HASTE and T2-weighted FSE images (Az values = 0.997-0.999) than with CT (0.917-0.932). The mean values of sensitivity, specificity, and accuracy were significantly higher (P < 0.001) for T2-weighted FSE with FLAIR-HASTE (96.6%, 96.8%, and 96.7%, respectively) than for CT (76.9%, 61.6%, and 67.3%, respectively). A confident diagnosis was rendered in 12 of 112 lesions (10.7%) on the basis of CT, and this rate increased to 83 of 112 (74.1%) on the basis of T2-weighted FSE and FLAIR-HASTE imaging. CONCLUSION: FLAIR-HASTE is considered to be an effective sequence for differentiating hepatic cysts from liver metastases without the use of a contrast agent. With FLAIR-HASTE one can confidently diagnose small hepatic lesions found on CT in patients with a malignancy.

Adolescent↗
PubMedDate not supplied

3D MPRAGE evaluation of the internal auditory canals.

A heavily T1-weighted three-dimensional (3D) gradient echo sequence utilizing a 180 degrees inversion pulse has become available for clinical use, called magnetization prepared rapid acquisition gradient echo (MPRAGE). With the appropriate choice of repetition time, echo time, flip angle, and inversion time (TI), T1-weighted imaging can be performed with excellent anatomic detail and a good signal-to-noise ratio. We performed an initial evaluation of this sequence for detection of abnormalities of the internal auditory canals compared with conventional spin echo (SE) imaging. Fifteen men and 15 women were evaluated. Diagnoses included normal (n = 15 patients), acoustic neuromas (n = 7 tumors in 4 patients), cerebellopontine angle meningiomas (n = 3), postoperative for acoustic neuroma without residual tumor (n = 2), postoperative with evidence of residual tumor (n = 3), glomus jugulare (n = 1), Bell palsy (n = 1), and vestibular enhancement of probable viral etiology (n = 1). The 3D MPRAGE study consisted of 128 coronal partitions, (10/4/1), 10 degrees flip angle, 130 x 256 matrix, 2 mm slice thickness. TI time of 350 ms, 1 s recovery time, and 5.43 min examination time. All enhancing lesions identified on the conventional SE T1-weighted imaging were also identified on the MPRAGE imaging. No diagnostic difference existed between the MPRAGE and conventional SE sequences when pathology was present, but the MPRAGE sequence did have poorer resolution in the axial reformats related to the 130 x 256 in-plane matrix. While not currently able to replace conventional two-dimensional SE imaging, 3D MPRAGE may provide a valuable adjunct to the routine imaging protocol. This technique could replace the coronal T1-weighted SE sequence and provide excellent gray-white differentiation and many contiguous thin sections without a great increase in overall examination time.

Cerebellopontine Angle↗
PubMed2004

Comparison of the navicular region of newborn foals and adult horses by magnetic resonance imaging.

Magnetic resonance imaging (MRI) was tested for evaluation of the soft tissue structures of the equine digit in 16 limbs, derived from three adult warmblood horses and two newborn warmblood foals. The following measuring sequences were used in sagittal, transversal and coronal planes: spin echo, gradient echo, inversion recovery. The images were made with a 1.5 Tesla Siemens scanner in a CP-Helmholtz circular coil. To compare the visualization of the same tissue structures in adult and in newborn cases the limbs were imaged with the routinely used MRI sequences that are used for mature tissues. In newborn foals the bursa podotrochlearis could not be determined with the used sequences. For both the adult and newborn limbs the most visualization of the same tissue structures including the fluid spaces and growth plates were taken by the inversion recovery sequence. T2 sequence was very informative in adult cases but moderately in newborn foals.

Animals↗
PubMed2006

Breakpoint cloning and haplotype analysis indicate a single origin of the common Inv(10)(p11.2q21.2) mutation among northern Europeans.

The pericentric inv(10)(p11.2q21.2) mutation has been frequently identified in cytogenetic laboratories, is phenotypically silent, and is considered to be a polymorphic variant. Cloning and sequencing of the junction fragments on 10p11 and 10q21 revealed that neither inversion breakpoint directly involved any genes or repetitive sequences, although both breakpoint regions contain a number of repeats. All 20 apparently unrelated inv(10) families in our study had identical breakpoints, and detailed haplotype analysis showed that the inversions were identical by descent. Thus, although considered a common variant, inv(10)(p11.2q21.2) has a single ancestral founder among northern Europeans.

Base Sequence↗
PubMed1987

MR sequence parameter optimization: an algorithmic approach.

The MR pulsing sequence is often described by terms such as spatial resolution, signal-to-noise, coverage, acquisition time, and contrast. These might be considered "secondary" parameters because they are not set directly but are instead specified indirectly by setting the "primary" parameters: field of view; projections (phase-encoded or readout); slice thickness and gap; number of excitations; and the sequence parameter times--repetition, echo delay, and inversion. Together, the primary and secondary parameters specify the MR pulsing sequence. Many of these parameters are interrelated such that setting one parameter indirectly affects another. Parameter specification is thus an iterative procedure that involves compromises to achieve an optimum relative to some predefined criteria. In this article, we examine the interrelationships between the primary and secondary parameters that specify the spin-echo pulsing sequence and suggest an algorithmic approach for selecting the best sequence parameters.

Algorithms↗
PubMed1986

Magnetic resonance imaging of the retroperitoneum.

The results of magnetic resonance imaging (MRI) examinations in 50 patients with histological or clinical diagnoses of retroperitoneal disorders and 20 normal volunteers are presented. An increase in relaxation time (T1) was recognised in most pathological conditions except for four liposarcomas and one adrenal cortical neoplasm and one metastatic lesion of the same gland. Inversion recovery (IR) provided the best tissue contrast, enabling the detection of small lesions. Flow-dependent sequences and sagittal imaging planes were particularly helpful in the evaluation of aortic aneurysms. Ferric ammonium citrate used as an oral paramagnetic contrast agent and a short T1 inversion recovery sequence gave encouraging initial results in recognising bowel loops. Gadolinium-DTPA injected intravenously provided tumour enhancement, indicating vascular perfusion and demarcating tumour margins. An attempt to eliminate motion artefacts was carried out in 15 volunteers and six patients either by a new software system (respiratory ordered phase encoding) or by using short T1 inversion-recovery to suppress the high signal from fat. The same pulse sequence results were useful in demonstrating subcutaneous fistulous tracts by eliminating the adjacent fat. The actual role of MRI in the investigation of the retroperitoneum in view of current technical developments is discussed.

Abscess↗