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PubMed1982

Long terminal repeat (LTR)-derived recombination of retroviral DNA: sequence analyses of an aberrant clone of baboon endogenous virus DNA which carries an inversion from the LTR to the gag region.

Nucleotide sequences of a cloned proviral DNA of baboon endogenous virus M7 were analyzed, which carried an internal inversion. The inversion of 2.2 kilobase pairs was occurred between the junction of two tandem LTRs and a site locating in the p30 region of the gag gene. The ATAA sequence was a target for recombination generating the inversion, which was duplicated at both ends of the inverted segment. AAA and CA were lost at the 5'- and 3'-ends of the LTRs by the inversion, respectively. On both sides of the target sequence, long AG-rich stretches were detected, which may specify the site of recombination together with the target sequence. The characteristic base changes in the inversion are concluded to result from an illegitimate recombination associated with LTRs, as well as in case of provirus integration into the host cell DNA. We propose and discuss models to explain the processes of recombination to generate both inversion and integration.

Amino Acid Sequence↗
PubMed1996

The iron-containing superoxide dismutase-encoding gene from Chlamydomonas reinhardtii obtained by direct and inverse PCR.

The complete sequence of the Fe2+ -containing superoxide dismutase (Fe-SOD)-encoding gene of Chlamydomonas reinhardtii was determined from genomic DNA by use of the direct (PCR) and inverse PCR (IPCR). It was confirmed by reverse transcription-PCR. Primers employed in the PCR represented oligodeoxyribonucleotides corresponding to conserved amino acid (aa) residues of Fe-SOD. From the sequence of direct PCR product, primers were designed for IPCR. All amplified fragments were cloned and sequenced. Analysis of Fe-SOD reveals that the open reading frame consists of 234 aa which show a high degree of homology to other Fe-SOD. The first 33 aa are predominantly either hydrophobic or basic, and may serve as the signal peptide for this chloroplastic protein. Potential transcription start points and eukaryotic control elements, as well as a polyadenylation site, were identified.

Amino Acid Sequence↗
PubMed1997

Expansion of the IR in the chloroplast genomes of buckwheat species is due to incorporation of an SSC sequence that could be mediated by an inversion.

The chloroplast genomes in buckwheat species contain large inverted repeats which are at least 4 kbp longer than the majority of those in land plants. The length of the buckwheat inverted repeats was attributable to an additional region located adjacent to the borders of the small single-copy region. We have cloned and sequenced a 5. 2-kbp SmaI fragment corresponding to this extra region in the inverted repeats. A homology search revealed that the sequence of the SmaI fragment is highly homologous to one side of the small single-copy region of the inverted repeats in dicot chloroplast DNAs such as tobacco and beechdrops. Interestingly, a 3.7-kbp segment in the middle of the SmaI fragment is inserted in the opposite orientation relative to those of the other dicot species, and 17-bp direct repeats are found located at both the ends of the additional region. These results suggest that expansion of the inverted repeats in buckwheat chloroplast DNA might have been associated with an inversion.

Chloroplasts↗
PubMed1998

Three-dimensional fast fluid attenuated inversion recovery (3D fast FLAIR): a new MRI sequence which increases the detectable cerebral lesion load in multiple sclerosis.

Two-dimensional (2D) fluid attenuated inversion recovery (FLAIR) magnetic resonance imaging is superior to T2 weighted conventional spin echo (CSE), in certain areas of the brain but not in others, in detecting the lesions of multiple sclerosis (MS). The present study evaluates the ability of a recently developed three-dimensional fast FLAIR (3D fast FLAIR) sequence in detecting and quantifying the brain lesions of multiple sclerosis. The lesion volumes measured on the 3D fast FLAIR sequence with 1.5 mm thick slices were compared with those obtained from CSE brain images with 5 mm thick slices. The findings seen in 3D fast FLAIR brain images in 10 normal control subjects are also described. 3D fast FLAIR images showed an overall increase of 34% in lesion volume compared with CSE. The increase was most marked in the periventricular and "discrete" areas of the cerebral hemispheres. Lesion volumes seen in the subcortical areas were similar in both sequences. The CSE images displayed higher lesion volumes in the posterior cranial fossa. It is concluded that 3D fast FLAIR is a promising technique for quantifying cerebral pathology in MS which is not accessible to 2D CSE.

Adult↗
PubMed1994

Optic nerve injury demonstrated by MRI with STIR sequences.

We studied nine patients with optic nerve injury associated with closed head trauma by magnetic resonance imaging (MRI) with short inversion time inversion recovery (STIR) sequences on 11 occasions from 4 days to 14 years after the injury: three studies were within 17 days and eight over 4 months to 14 years. MRI revealed abnormal high signal in 10 of the 11 injured nerves. MRI 4 days after the injury showed no abnormality.

Adult↗
PubMed1990

A and T homopolymeric stretches mediate a DNA inversion in Plasmodium falciparum which results in loss of gene expression.

Ring-infected erythrocyte surface antigen-negative isolates of Plasmodium falciparum demonstrate a complex DNA rearrangement with inversion of 5' coding sequences, deletion of upstream and flanking sequences, and healing of the truncated chromosome by telomere addition. An inversion intermediate that results in the telomeric gene structure for RESA has been identified in the pathway. This inversion creates a mitotically stable substrate for the sequence-specific addition of telomere repeats at the deletion breakpoint.

Animals↗
PubMed2003

Magnetic resonance imaging examinations of the spine in patients with ankylosing spondylitis, before and after successful therapy with infliximab: evaluation of a new scoring system.

OBJECTIVE: To evaluate a magnetic resonance imaging (MRI) scoring system for the assessment of spinal inflammation in patients with ankylosing spondylitis (AS) who participated in a randomized, placebo-controlled trial of infliximab, and to examine whether infliximab is also effective for the reduction of MRI-proven spinal inflammation. METHODS: Twenty patients with AS (9 women and 11 men, mean age 40.9 years) were examined at baseline and after 3 months. Nine patients had received infusions of infliximab (5 mg/kg body weight) at weeks 0, 2, and 6, and 11 patients had received placebo. Three MRI sequences and 2 scoring systems were used. Chronic lesions were evaluated by T1-weighted turbo spin-echo (TSE) sequences and were assigned a chronicity score. Active lesions were evaluated either by repetition of T1-weighted TSE sequences after infusion of gadolinium-diethylenetriaminepentaacetic acid (Gd-DTPA) or by short tau inversion recovery (STIR) sequences, and were assigned an activity score. The 40 images were evaluated twice by 2 readers who were blinded to the names of the patients and the dates of the examinations, and were analyzed in relation to the clinical results. RESULTS: Active spinal lesions were detected in 15 of 20 patients (75%); the frequency as determined by STIR was equal in the 2 groups. At baseline, the total MRI scores determined using Gd-DTPA, STIR, and T1 were 112.5, 156, and 253.5, respectively. The interrater variance and intrarater variance were, respectively, 6.4 and 7.7 for the active lesion score as determined by Gd-DTPA, 15.7 and 5.3 for the active lesion score as determined by STIR sequence, and 167.3 and 75.5 for the chronic lesion score as determined by T1 sequence. Based on the means of the scores assigned by the 2 readers, the active lesion score as determined by Gd-DTPA improved by 40% in the infliximab group compared with 6% in the placebo group, the active lesion score as determined by STIR improved by 60% in the infliximab group but deteriorated by 21% in the placebo group, and the chronic lesion score as determined by T1 improved by 7% in the infliximab group but worsened by 35% in the placebo group. Five patients in the infliximab group and 2 in the placebo group were clinical responders. The acute MRI changes correlated with clinical improvement as assessed by the Bath Ankylosing Spondylitis Disease Activity Index. CONCLUSION: This novel MRI scoring system performed well in assessing acute inflammation by using STIR and post-Gd-DTPA sequences. In correlation with clinical improvement in patients with active AS who were treated with infliximab, significant regression of spinal inflammation was shown by using the MRI activity scores.

Adult↗
PubMed2003

Cloning and characterisation of a glucoamylase gene (GlaM) from the dimorphic zygomycete Mucor circinelloides.

This article reports a novel strategy for the cloning of glucoamylase genes using conserved sequences and semi-nested PCR and its application in cloning the GlaM glucoamylase gene and cDNA from the dimorphic zygomycete Mucor circinelloides. The deduced 609-amino-acid enzyme (including signal peptide) is 63% identical to the Rhizopus oryzae raw starch-degrading glucoamylase and is the third glucoamylase reported to have the putative starch-binding domain placed N-terminally. The C-terminal catalytic domain is separated from the starch-binding domain by a serine/threonine-rich linker. An alignment of the cloned gene and cDNA sequences showed that the gene contains three introns. The transcriptional start site and the site of polyadenylation were defined by primer extension and 3'RACE, respectively. The atypical Kozak sequence is identical to the one used in R. oryzae in positions -1 to -4. Northern slot blots revealed that glucoamylase transcription is induced during growth on starch and repressed by glucose. In silico analysis of the 1.9-kb promoter sequence cloned by inverse PCR revealed the presence of several putative regulatory elements, most notably a 19-bp sequence containing six overlapping copies of the Saccharomyces cerevisiae Nrg1p binding sequence.

Amino Acid Sequence↗
PubMed2006

Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.

With the goal of solving the whole-cell problem with Escherichia coli K-12 as a model cell, highly accurate genomes were determined for two closely related K-12 strains, MG1655 and W3110. Completion of the W3110 genome and comparison with the MG1655 genome revealed differences at 267 sites, including 251 sites with short, mostly single-nucleotide, insertions or deletions (indels) or base substitutions (totaling 358 nucleotides), in addition to 13 sites with an insertion sequence element or defective prophage in only one strain and two sites for the W3110 inversion. Direct DNA sequencing of PCR products for the 251 regions with short indel and base disparities revealed that only eight sites are true differences. The other 243 discrepancies were due to errors in the original MG1655 sequence, including 79 frameshifts, one amino-acid residue deletion, five amino-acid residue insertions, 73 missense, and 17 silent changes within coding regions. Errors in the original MG1655 sequence (<1 per 13,000 bases) were mostly within portions sequenced with out-dated technology based on radioactive chemistry.

Base Sequence↗
PubMed2001

[MR-morphological changes of the metacarpophalangeal joints in patients with rheumatoid arthritis: Comparison of early and chronical stages].

UNLABELLED: MR-morphological changes of the metacarpophalangeal joints in patients with rheumatoid arthritis: Comparison of early and chronical stages. PURPOSE: Evaluation of MRI findings in the metacarpophalangeal (MCP) joints in patients with early (eRA) and chronical rheumatoid arthritis (cRA). MATERIAL AND METHODS: In 22 RA patients (9 with disease duration </= 1.5 years = eRA) the dominant hands were examined by MRI in coronal T(2) weighted turbo-spin-echo (TSE). T(1) weighted spin-echo (SE) sequences before and after injection of Gd-DTPA and fat-suppressed short tau inversion recovery (STIR) sequences, followed by miniarthroscopy (MA) of the MCP II joint after an interval of 24 hours. MRI and MA findings were assessed using standardised semiquantitative items of synovial and bony pathologies and a statistical comparison between eRA and cRA patients was performed. RESULTS: In MRI synovial proliferation was detected in 13/13 cRA and 8/9 eRA patients. It was statistically not significant; the degree of synovial proliferation was however lower in the eRA group. All eRA patients with synovial changes showed enhancement after administration of contrast medium, a marker which correlated with the clinical activity. In 2/13 cRA patients no uptake of contrast medium was evident. Bony erosions and strongly narrowing joint space correlated with disease duration and were documented significantly rarer in the eRA patients (1/9, 2/9) than in the cRA patients (9/13, 10/13). CONCLUSION: In RA patients, MRI of the metacarpophalangeal joints can detect specific pathological changes which are observed significantly more often in either early or chronic stages and which are associated with disease activity and duration.

Adult↗
PubMed1978

Dose-dependent preferential binding of polycyclic aromatic hydrocarbons to reiterated DNA of murine skin cells in culture.

The distribution of active metabolites of polycyclic aromatic hydrocarbons bound to reiterated or unique regions of murine DNA has been studied by a DNA-DNA renaturation technique. Murine skin cells were exposed to different doses of radioactive polycyclic aromatic hydrocarbons for 24 hr; then the hydrocarbon-labeled DNA was isolated, fragmented, and denatured. Renaturation kinetics and thermal stabilities of DNA-DNA duplexes were studied. At high carcinogen doses, polycyclic aromatic hydrocarbon adducts seem to be distributed equally among the DNA of all reiteration frequencies. At low carcinogen doses, however, a dose-dependent preferential binding to reiterated DNA sequences occurs. An inverse linear relationship appears to exist between the enrichment of hydrocarbon adducts in reiterated DNA sequences and the logarithm of the amount of total hydrocarbon bound to DNA.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed2004

[Basic evaluation of a new technique, tailored contrast truck-fluid-attenuated driven inversion-recovery (TACT-FLADIR), to attenuate the signals of both cerebrospinal fluid and inflow artifacts].

The aim of the present study was to evaluate the new tailored contrast truck-fluid-attenuated driven inversion-recovery (TACT-FLADIR) sequence. Technically, this sequence uses a nonselectively driven inversion (DI) pulse as the inversion pulse. The DI pulse has two parameters, number of refocus pulses (NR) and preparation time (TP). Using normal volunteers, we optimized NR and TP to measure signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) of gray matter (GM) and white matter (WM), and to obtain CSF inflow artifacts. TACT-FLADIR was compared with conventional FLAIR using volunteers and patients. Among the optimized parameters, SNR and CNR were dependent on TP, and inflow artifacts were reduced by increasing NR. In brain imaging, TACT-FLADIR provided improvement in both SNR and CNR compared with conventional imaging with suppressed CSF signal and saturated flow artifacts.

Adult↗
PubMed1997

The site-specific recombinase encoded by pinD in Shigella dysenteriae is due to the presence of a defective Mu prophage.

The DNA inversion systems are made up of an invertible DNA segment and a site-specific recombinase gene. Five systems are known in prokaryotes: the Salmonella typhimurium H segment and hin gene (H-hin), phage Mu G-gin, phage P1 C-cin, Escherichia coli e14 P-pin, and Shigella sonnei B-pinB systems. In this report a site-specific recombinase (pinD) gene of Shigella dysenteriae was cloned and sequenced. pinD mediated inversion of five known segments at the same extent in E. coli. Although one inv sequence was identified, no invertible region was detected in a cloned fragment. The predicted amino acid sequences of PinD and three ORFs showed high homology to those of Gin and its flanking gene products. An ORF homologous to Mom of Mu conserved a functional activity to modify intracellular plasmid DNA. Southern analysis showed that the cloned fragment contains two homologous regions corresponding to the left and right ends of the Mu genome. Together these results indicated that the pinD gene in S. dysenteriae is derived from a Mu-like prophage.

Amino Acid Sequence↗
PubMed2000

Diagnostic value of the fast-FLAIR sequence in MR imaging of intracranial tumors.

The aim of this study was to quantify imaging characteristics of fast fluid-attenuated inversion recovery (FLAIR) sequence in brain tumors compared with T1-postcontrast- and T2-sequences. Fast-FLAIR-, T2 fast spin echo (FSE)-, and T1 SE postcontrast images of 74 patients with intracranial neoplasms were analyzed. Four neuroradiologists rated signal intensity and inhomogeneity of the tumor, rendering of cystic parts, demarcation of the tumor vs brain, of the tumor vs edema and of brain vs edema, as well as the presence of motion and of other artifacts. Data analysis was performed for histologically proven astrocytomas, glioblastomas, and meningiomas, for tumors with poor contrast enhancement, and for all patients pooled. Only for tumors with poor contrast enhancement (n = 12) did fast FLAIR provide additional information about the lesion. In these cases, signal intensity, demarcation of the tumor vs brain, and differentiation of the tumor vs edema were best using fast FLAIR. In all cases, rendering of the tumor's inner structure was poor. For all other tumor types, fast FLAIR did not give clinically relevant information, the only exception being a better demarcation of the edema from brain tissue. Artifacts rarely interfered with evaluation of fast-FLAIR images. Thus, fast FLAIR cannot replace T2-weighted series. It provides additional information only in tumors with poor contrast enhancement. It is helpful for defining the exact extent of the edema of any tumor but gives little information about their inner structure.

Adolescent↗
PubMedDate not supplied

[FLAIR MR sequence in the diagnosis and follow-up of low-grade astrocytomas].

AIM: To evaluate the sensitivity of fluid-attenuated inversion recovery (FLAIR) sequence in the diagnosis and follow-up of the patients with low-grade astrocytomas compared with T2-weighted (T2W) sequence. METHODS: Twenty-four patients with biopsy-confirmed low-grade astrocytoma (age range, 15-66 years) underwent T1-weighted (T1W), T2W and FLAIR imaging with a superconducting unit 1.0 T. FLAIR images were qualitatively evaluated by comparison with T2W images by the three experienced neuroradiologists. To evaluate the diagnostic value of FLAIR, the neuroradiologists individually assessed the possibilities of the detection of lesions, as well as the possibilities of the differentiation of tumor from the surrounding edema on FLAIR vs. T2W images. Every examiner ranked FLAIR sequence vs. T2W in three degrees: worse, equal and better. RESULTS: The comparison of FLAIR with T2W spin-echo (SE) images with regard to the detection of the lesions showed that 82.8% of FLAIR studies were superior, 17.2% were of similar diagnostic value, and none was inferior to the T2W images. The comparison of images with regard to the differentiation of tumor boundaries vs. surrounding edema showed that 92.5% of FLAIR studies were superior, 7.5% were of similar diagnostic value, and none was inferior to the T2W images. CONCLUSION: Our results were similar to the previous studies' results concerning the advantages of FLAIR sequence in the diagnosis of low grade astrocytomas over T2W sequence. FLAIR was better at showing different tumor components, and at distinguishing CSF from the cystic component, and the postoperative cavity, compared with T2W images. Our conclusion was that FLAIR could be routinely used in the evaluation and follow-up of low-grade astrocytomas.

Adolescent↗
PubMed2002

Improved recognition of native-like protein structures using a family of designed sequences.

The goal of the inverse protein folding problem is to identify amino acid sequences that stabilize a given target protein conformation. Methods that attempt to solve this problem have proven useful for protein sequence design. Here we show that the same methods can provide valuable information for protein fold recognition and for ab initio protein structure prediction. We present a measure of the compatibility of a test sequence with a target model structure, based on computational protein design. The model structure is used as input to design a family of low free energy sequences, and these sequences are compared with the test sequence by using a metric in sequence space based on nearest-neighbor connectivity. We find that this measure is able to recognize the native fold of a myoglobin sequence among different globin folds. It is also powerful enough to recognize near-native protein structures among non-native models.

Amino Acid Sequence↗
PubMed1992

Magnetic resonance imaging. Diverse appearances of uveal malignant melanomas.

Fifteen patients with uveal malignant melanomas were studied by magnetic resonance imaging. The magnetic resonance imaging appearances varied from those that have been reported previously to be characteristic of these tumors. In our series, malignant melanomas were of high signal on the T1 sequence and of variable but usually also of high signal on the T2 and Short Tau Inversion Recovery (STIR) sequences, a signal combination rarely described before. We postulate that magnetic resonance imaging appearances may be dependent on variations in histologic factors and on the type and field strength of the scanner used. It is widely believed that the paramagnetic melanin in malignant melanomas gives these tumors characteristic magnetic resonance imaging appearances, but our finding of diverse magnetic resonance imaging appearances for proved malignant melanomas suggests that this may not always be the case. We advise caution in diagnosing malignant melanomas from magnetic resonance imaging appearances alone.

Adult↗