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At least 811 records · Page 45Linked to original sources
PubMed1990

Cooperative T1 and T2 effects on contrast using a new driven inversion spin-echo (DISE) MRI pulse sequence.

A pulse sequence is presented for obtaining a single image with combined T1/T2 weighting. T2 relaxation is made to increase intensity, in cooperation with the effect of T1 relaxation, by providing T2 weighting with a 90 degrees-180 degrees-90 degrees driven inversion pulse triplet in an inversion recovery method. Unlike the inversion spin-echo method having a short inversion time (TI), signals in the new driven inversion spin-echo (DISE) method need not be negative and the most T1-sensitive region of the recovery curve can be used. Selecting sensitivity to one relaxation time does not degrade the sensitivity to the other relaxation time. T1 sensitivity is thus extended to longer echo times (TE intervals). T2 sensitivity is extended to longer TI intervals, and the combined T1/T2-weighted technique with intermediate TE and TI has highly cooperative and near-maximal T1 and T2 effects on contrast. Intensity is not multiplicatively degraded by T1 and T2 weighting so that the signal-to-noise of the combined T1/T2-weighted method is high. High intensity and T1 and T2 cooperatively occur for a much wider range of relaxation times, and especially for images heavily weighted to the pathologic intermediate and long T1 and T2 regime.

Brain↗
PubMed1999

Feasibility in the inverse protein folding protocol.

Methods for protein structure (3D)-sequence (1D) compatibility evaluation (threading) have been developed during the past decade. The protocol in which a sequence can recognize its compatible structure in the structural library (i.e., the fold recognition or the forward-folding search) is available for the structure prediction of new proteins. However, the reverse protocol, in which a structure recognizes its homologous sequences among a sequence database, named the inverse-folding search, is a more difficult application. In this study, we have investigated the feasibility of the latter approach. A structural library, composed of about 400 well-resolved structures with mutually dissimilar sequences, was prepared, and 163 of them had remote homologs in the library. We examined whether they could correctly seek their homologs by both forward- and inverse-folding searches. The results showed that the inverse-folding protocol is more effective than the forward-folding protocol, once the reference states of the compatibility functions are appropriately adjusted. This adjustment only slightly affects the ability of the forward-folding search. We noticed that the scoring, in which a given sequence is re-mounted onto a structure according to the 3D-1D alignment determined by the dynamic programming method, is only effective in the forward-folding protocol and not in the inverse-folding protocol. Namely, the inverse-folding search works significantly better with the score given by the 3D-1D alignment per se, rather than that obtained by the re-mounting. The implications of these results are discussed.

Algorithms↗
PubMed1999

[Diagnosis of acute subarachnoid hemorrhage at 1.5 Tesla using proton-density weighted FSE and MRI sequences].

PURPOSE: To evaluate MR imaging at 1.5 Tesla in patients suffering from acute subarachnoid hemorrhage (SAH) using proton-density weighted (PDW) fast spin echo (FSE) and fluid attenuated inversion recovery (FLAIR) sequences. METHODS: 19 patients suffering from acute SAH as diagnosed by CT were studied 6 h to 3 days after hemorrhage. 10 patients without SAH were studied as a control group. The presence of subarachnoid blood as well as possible artifacts was recorded. RESULTS: In all 19 patients subarachnoid hemorrhage was detected on both FLAIR and PDW images (100%). On the FLAIR images, the cerebral ventricles were partially obscured by flow artifacts in 7 of 19 patients, the basal cisterns in 6 of 19 patients. In 4 of these 13 regions blood was diagnosed on both PDW and CT images, while in the other 9 regions both PDW and CT were unremarkable. CONCLUSION: The sensitivity of MRI at 1.5 Tesla in the diagnosis of subarachnoid hemorrhage is comparable to CT. The combination of FLAIR and PDW FSE sequences helps to avoid false-positive results caused by flow artifacts.

Acute Disease↗
PubMedDate not supplied

T1 maps by K-space reduced snapshot-FLASH MRI.

The T1 maps evaluated from k-space reduced Snapshot fast low angle shot (FLASH) images provide high contrast parameter images for tissue characterization in vivo of any body region. An algorithm for computing T1 values that allows a fast and reliable evaluation of T1 maps and yields reproducible values of tissue parameters in MR imaging is presented. The algorithm combined with the Snapshot FLASH inversion recovery imaging sequence permits a precise determination of T1 values, even for T1 times as low as 50 ms. Comparison with a spectroscopical inversion recovery method on identical phantoms demonstrates the accuracy of this technique. With its total acquisition time of approximately 2 s, IR Snapshot FLASH is fast enough to be used in monitoring fast T1 dynamics.

Magnetic Resonance Imaging↗
PubMed2002

Improved efficiency in double-inversion fast spin-echo imaging.

Double-inversion fast spin-echo (FSE) pulse sequences can be designed to provide excellent suppression of blood signal in black-blood MRI. However, because a nonselective inversion is used, these sequences typically have been highly inefficient. In this work it is demonstrated that the efficiency of double-inversion sequences can be greatly improved by a form of interleaving in which all of the slices to be imaged in a single pass are reinverted each time a signal is obtained from any single slice. To date, several studies have demonstrated a high level of blood suppression with these more efficient techniques.

Aged↗
PubMed1997

Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats.

Emery-Dreifuss muscular dystrophy (EMD) is an X-linked disorder characterized by contractures, progressive muscle weakness and cardiomyopathy. The emerin gene, located in human Xq28, is approximately 2 kb in length, is composed of 6 exons and falls within a 219-kb region that has been completely sequenced. Immediately centromeric to emerin is the 26-kb filamin gene (FLN1), composed of 48 exons and encoding the actin-binding protein 280 (refs 7,8). Flanking this 48-kb FLN1/emerin region are two large inverted repeats, each 11.3 kb, that exhibit > 99% sequence identity. The high level of genomic detail in this region allowed us to characterize the first complete emerin gene deletion mutation that also involved a partial duplication of the nearby FLN1 gene. This rearrangement could be explained by mispairing of the large inverted repeats, followed by double recombination among one set of mispaired repeats and internal sequences. Furthermore, our characterization of this rare DNA rearrangement revealed a more common result of the mispairing of these large inverted repeats--recombination contained within the inverted repeats leading to the maintenance of repeat sequence homogeneity and inversion of the 48-kb FLN1/emerin region. The presence of this frequent inversion, found in the heterozygous state in 33% of females, helps to explain the discrepancies observed between the genetic and physical map distances in this region of the X chromosome. It also illustrates the biological insights which can be gleaned by sequencing the human genome.

Adult↗
PubMed1995

Inversions with deletions and duplications.

Complex mutational events, including de novo inversion with deletion and duplication of sequence, have been observed but are difficult to model. We propose that nascent leading-strand misalignment upon the lagging-strand template during DNA replication can result in the inversion of sequence. The positioning of this misalignment and of the realignment of the leading strand back into the leading-strand template will determine if the inversion is accompanied by deletion and duplication of sequence. We suggest that such strand misalignment-realignment events may occur at the replication fork during concurrent DNA replication.

Base Sequence↗
PubMed2004

Relaxation filtered hyperfine spectroscopy (REFINE).

A simple and general applicable method to separate spectrally overlapping hyperfine spectra of two paramagnetic compounds is presented. Overlapping spectral contributions from different paramagnetic species are a common situation in electron paramagnetic resonance (EPR) spectroscopy, resulting in complicate EPR spectra of metal enzymes, organic radicals or in the field of material sciences. On the other hand, the longitudinal relaxation times T1 of these species contributing to the overall EPR signal can vary by several orders of magnitude, depending on the paramagnetic component under study. These differences can be used to selectively study individual species by using an inversion-recovery preparation sequence as a filter. Here, we demonstrate the possibility to separate hyperfine spectra of two spectrally overlapping paramagnetic species by combining an inversion-recovery based relaxation filter together with ESEEM or ENDOR hyperfine spectroscopy (REFINE). The feasibility of the presented method is demonstrated on model compounds and the necessary requirements are discussed.

Allyl Compounds↗
PubMed1984

Genomic structure and possible retroviral origin of the chicken CR1 repetitive DNA sequence family.

We have analyzed the sequence and structure of three CR1 family repetitive elements found in the region adjoining the 3' end of a chicken calmodulin gene. Members of this family are approximately equal to 300 base pairs long and are dispersed throughout the chicken genome. The present data, when taken together with that from four CR1s sequenced previously, reveal that the CR1 family has an overall structure possessing several features associated with the long terminal repeats of avian retroviruses. This finding implies that a retroviral mechanism may be responsible for the dispersion of CR1 sequences throughout the chicken genome. The seven different CR1 repeats that have been analyzed exist at defined locations in the chicken genome relative to nearby structural genes. A directional polarity has been assigned to the CR1 family based upon limited sequence homology to mammalian Alu-type sequences. Interestingly, whether present in 5' - or 3'-flanking DNA, the CR1 sequences have an inverse orientation such that they all "point toward" the nearby structural genes. This is consistent with the previously proposed concept that chicken CR1 sequences may be involved in defining the boundaries of active chromosomal domains of gene expression.

Animals↗
PubMed1996

Kinematic analysis of eyelid movements in patients recovering from unilateral facial nerve palsy.

We assessed eyelid function by subjective clinical examination and quantitative means in patients recovering from facial nerve palsy. Electromagnetic search coil techniques were used to record the concurrent movements of the two eyelids to study alterations in blink main sequence (peak velocity versus amplitude) relationships and interocular differences in eyelid kinematics. After onset of unilateral palsy, the paresis of eyelid closure showed varying degrees of recovery. Adaptive increases in blink main sequence slope contributed to maximizing closure of the paretic eyelid. However, blink adaptation mechanisms must operate bilaterally, as there also was evidence of altered main sequence slope in the nonparetic eyelid. In general, main sequence slope was inversely related to the level of eyelid paresis. The highest indices of blink adaptation were in those patients with moderate paresis, and main sequence slope was decreased in those patients with increasing degrees of recovery. The assessment of eyelid function with search coil techniques provides a sensitive means of monitoring disease and treatment course. Data also aid understanding of adaptive gain control in the neural control of blink in health and disease.

Adaptation, Physiological↗
PubMed2006

[A method using long primers for cloning the upstream sequence of delta-6 fatty acid desaturases gene of Thamnidium elegans by nested inverse PCR].

Thamnidium elegans is a kind of phycomycete that produces essential unsaturated fatty acids, particularly y-linolenic acid. In this process, delta6-Fatty acid desaturase (D6D) plays a key role due to its enzymatic properties that catalyze the delta6 site dehydrogenation of precursor linoleic acid (18:2delta(9, 12) n-6) and a-linolenic acid (18:3delta(9, 12, 15) n-3). This reaction is the first and rate-limiting step of highly unsaturated fatty acids (HUFA) synthesis pathways. After we have isolated and cloned the gene coding delta6-fatty acid desaturase from Thamnidium elegans As3.2806 (GenBank accession number DQ099380), our interest focuses on the promotion and regulation of the gene transcription. To achieve this aim, we designed long primers and used nested inverse PCR to amplify DNA flanking sequences. First, genome of Thamnidium elegans was extracted and digested with restriction enzymes EcoR I and Kpn I , respectively. Then we ligated the digested DNA with T4 ligase at low concentration which is propitious for linear DNA to joint intromolecule. According to the sequence of delta6-fatty acid desaturase gene of Thamnidium elegans, we designed a couple of 35nt long inverse primers and two couples of shorter inverse primers for inverse PCR. Three rounds of PCR reactions were performed. In the primary reaction, the ligated DNA was used as a template, and the product was used as the template of the secondary reaction, the tertiary reaction was achieved in the same way. After all the three rounds of reactions, we got a nice product about 4 kb from the EcoR I digested sample, in which a 1.3kb 5' upstream sequence (GenBank accession number DQ309425) of delta6-fatty acid desaturase gene containing several putative regulatory elements including TATA. box, FSE-2, AP-1 sites, CCAAT cis-element site and STRE-binding site was derived after sequencing. All of these implied intensely that this 1.3kb fragment is a condition-regulated promoter. It is the first report about Thamnidium elegans detla6-fatty acid desaturase gene promoter. The procedure described here is a rapid and simple method and particularly useful to isolate flanking sequences from fungal genome. box, FSE-2, AP-1 sites, CCAAT cis-element site and STRE-binding site was derived after sequencing. All of these implied intensely that this 1.3 kb fragment is a condition-regulated promoter. It is the first report about Thamnidium elegans delta6-fatty acid desaturase gene promoter. The procedure described here is a rapid and simple method and particularly useful to isolate flanking sequences from fungal genome.

Base Sequence↗
PubMed1982

Clinical NMR imaging of the brain: 140 cases.

Cranial nuclear magnetic resonance (NMR) scans were performed on 13 healthy volunteers and 140 patients with a broad spectrum of neurologic disease and compared with x-ray computed tomography (CT) scans. The NMR scans included a variety of sequences reflecting proton density, blood flow, T1, and T2 as well as transverse, sagittal, and coronal images. White matter, gray matter, and cerebrospinal fluid were clearly distinguished in the normal brain with inversion-recovery (IR) sequences, and normal progressive myelination was demonstrated in infants and children. Acute hemorrhages displayed short T1 values, but other pathologic processes such as infarction, infection, demyelination, edema, and malignancy were associated with long T1 values. Cysts had very long T1 values (about that of cerebrospinal fluid). Spin-echo (SE) sequences showed increased values of T2 in a variety of conditions and highlighted lesions against the relatively featureless background of the remaining brain. With inversion-recovery scans, different stages of infarction were recognized in the hemispheres. NMR was more useful than CT in demonstrating brainstem infarction. The white matter lesions in demyelinating diseases were well demonstrated with NMR scans. Many more lesions were observed in multiple sclerosis with NMR than with CT. Benign tumors were well seen and usually had shorter T1 values than malignant tumors. Mass effects from tumors were generally better demonstrated with NMR than with CT, including more subtle mass effects such as displacement of the external capsule. Abnormalities were seen in diseases of the basal ganglia, including marked atrophy of the head of the caudate nucleus in Huntington chorea. Advantages of NMR imaging include the high level of gray-white matter contrast, lack of bone artifact, variety of possible sequences, transverse, sagittal, and coronal imaging, sensitivity to pathologic change, and lack of known hazard. Disadvantages include lack of bone detail, limited spatial resolution, lack of contrast agents, and cost. Promising directions for future clinical research include developmental neurology, tissue characterization with T1 and T2, assessment of blood flow, and the development of contrast agents. Much more detailed evaluation will be required, but NMR seems to be a potentially important addition to existing techniques of neurologic diagnosis.

Adolescent↗
PubMed1990

The role of the STIR sequence in magnetic resonance imaging examination of bone tumours.

Sixty patients with primary bone tumours were evaluated with magnetic resonance imaging (MRI) at 0.5 T with both conventional spin-echo (SE) and short inversion time inversion recovery (STIR) sequences. The results have been reviewed in order to evaluate the accuracy of STIR and conventional SE sequences in the detection of tumours, the definition of intramedullary extent and soft-tissue involvement. The intraosseous neoplastic extent has been compared with macroslides of surgical specimens in 24 cases. The role of the STIR sequence in detection of recurrences in the post-surgical follow-up was also evaluated. The STIR sequence, designed to suppress signal from fat, also enhances the signal from tissue with long T1 and T2 relaxation times, such as neoplastic and inflammatory tissue. The STIR sequence with T1 of 120-130 ms in all cases suppressed the high signal from fatty bone marrow, giving a clear depiction of tumour extent, in both its intramedullary and soft-tissue components, and is superior to conventional SE images. The high sensitivity (100% of our cases) of this technique is counterbalanced by its lack of specificity: on STIR sequences both tumour and peritumorous oedema give an increase of signal intensity, limiting assessment of tumour extent. Peritumoral oedema, only present in our series in malignant neoplasms, may however be differentiated on the basis of the configuration of the abnormal areas, and by comparing STIR images with short repetition time/echo time sequence results.

Adolescent↗
PubMed2001

Molecular characterization of a cryptic plasmid from Campylobacter jejuni.

Campylobacter jejuni is a leading bacterial cause of human enterocolitis. Molecular genetic characterization of this pathogen has been hampered by the lack of genetic tools that are functional in this organism. Cloning vectors commonly used in other organisms usually do not replicate within C. jejuni. To develop a system for functional analysis of C. jejuni genes, a small plasmid (pCJ01) identified in a poultry isolate of C. jejuni was sequenced and characterized in this study. By using inverse PCR, the full sequence of pCJ01 was amplified and subsequently determined. Results indicate that pCJ01 is a circular molecule of 3212 bp, with a G + C content of 33.5%. A typical plasmid replication origin with iteron sequences is identified upstream of the DNA sequences encoding replication initiation proteins. Four open reading frames (ORFs) are present in pCJ01. ORF1 and ORF2 share high homology with the putative RepA and RepB proteins, respectively, of known C. coli plasmids. ORF3 and ORF4, of unknown function, do not exhibit homology with any sequences deposited in the GenBank database. Hydropathy analysis predicts that ORF3 and ORF4 contain multiple stretches of hydrophobic amino acids, suggesting that they may encode transmembrane proteins. Since pCJ01 is a small plasmid and can be readily prepared from C. jejuni, it may be modified for use in molecular characterization of C. jejuni virulence genes.

Base Sequence↗
PubMed1998

Chromosomal arm replacement generates a high level of intraspecific polymorphism in the terminal inverted repeats of the linear chromosomal DNA of Streptomyces ambofaciens.

The chromosomal DNA of the bacteria Streptomyces ambofaciens DSM40697 is an 8-Mb linear molecule that ends in terminal inverted repeats (TIRs) of 210 kb. The sequences of the TIRs are highly variable between the different linear replicons of Streptomyces (plasmids or chromosomes). Two spontaneous mutant strains harboring TIRs of 480 and 850 kb were isolated. The TIR polymorphism seen is a result of the deletion of one chromosomal end and its replacement by 480 or 850 kb of sequence identical to the end of the undeleted chromosomal arm. Analysis of the wild-type sequences involved in these rearrangements revealed that a recombination event took place between the two copies of a duplicated DNA sequence. Each copy was mapped to one chromosomal arm, outside of the TIR, and encoded a putative alternative sigma factor. The two ORFs, designated hasR and hasL, were found to be 99% similar at the nucleotide level. The sequence of the chimeric regions generated by the recombination showed that the chromosomal structure of the mutant strains resulted from homologous recombination events between the two copies. We suggest that this mechanism of chromosomal arm replacement contributes to the rapid evolutionary diversification of the sequences of the TIR in Streptomyces.

Amino Acid Sequence↗
PubMed1997

Tn916 transposition in Haemophilus influenzae Rd: preferential insertion into noncoding DNA.

The availability of completely sequenced genomes has created an opportunity for high throughput mutational studies. Using the conjugative transposon Tn916, a pilot project was initiated to determine the efficiency of gene disruption in the first completely sequenced bacterium, Haemophilus influenzae Rd strain KW20. DNA was isolated from Tn916-mutagenized cells, and the point of transposon insertion was determined by inverse PCR, DNA sequencing, and mapping to the wild-type genome sequence. Analysis of the insertion sites at the nucleotide level demonstrated a biased pattern of insertion into regions rich in stretches of A's and T's. Although Tn916 integrated at multiple dispersed positions throughout the chromosome, 9 of 10 insertion events occurred in noncoding, intergenic DNA. It was determined that the intergenic DNA was over 5% more A + T-rich than that of protein coding sequences. This suggests that A + T-rich sequences similar to the Tn916 insertion site would be more likely to reside in the intergenic DNA. In an effort to identify other likely sites for transposon integration, a hidden Markov model of the consensus target insertion site was derived from the Tn916-H. influenzae junction fragments and searched against the entire genome. Eighty percent of the 30 highest-scoring predicted Tn916 target sites were from intergenic, nonprotein-coding regions of the genome. These data support the hypothesis that Tn916 has a marked preference for insertion into noncoding DNA for H. influenzae, suggesting that this mobile element has evolved to minimize disruption of host cell function on integration.

Base Sequence↗
PubMed2002

Radiologic differentiation of intracranial epidermoids from arachnoid cysts.

OBJECTIVE: Intracranial epidermoids (cholesteatomas) mimic arachnoid cysts in their radiologic characteristics, especially in the cerebellopontine angle. It is essential to differentiate the two conditions because they warrant different therapeutic interventions. The objective of this study is to elucidate the different radiologic characteristics of the conditions. STUDY DESIGN AND SETTING: This was a retrospective study of 4 patients referred for a differential diagnosis and management of intracranial cystic lesions to the Departments of Neurotology/Neurosurgery and Neuroradiology in a tertiary referral university hospital. PATIENTS: Four patients of different age groups with cystic intracranial lesions, diagnosed epidermoid or arachnoid cysts, were chosen. A retrospective analysis of their case charts, radiologic and surgical interventions, and follow-up records was undertaken. METHODS: The imaging techniques used included computerized tomographic scans, magnetic resonance imaging (MRI) with T1, T2, proton-density, and gadolinium-enhanced T1 images. In addition, special MRI sequences were used that included fluid-attenuated inversion recovery and echo planar diffusion scanning. All the patients underwent an audiovestibular evaluation. RESULTS: Both lesions are characteristically well demarcated and have a homogeneous low density, similar to cerebrospinal fluid on computerized tomographic scan, showing no contrast enhancement. On MRI, epidermoids and arachnoid cysts usually appear hypointense on T1-weighted images and hyperintense on T2-weighted images. On fluid-attenuated inversion recovery, an arachnoid cyst tends to follow cerebrospinal fluid intensity, whereas an epidermoid becomes hyperintense. There are occasions when an epidermoid may appear as a low-intensity lesion on fluid-attenuated inversion recovery. This dilemma is resolved with the use of echo planar diffusion scanning, on which an epidermoid remains bright. CONCLUSION: The authors recommend the use of fluid-attenuated inversion recovery and diffusion sequence MRI when definitive radiologic diagnosis of cystic intracranial lesions becomes difficult with routine computerized tomographic scanning and MRI.

Adult↗
PubMed2003

rRNA antitermination functions with heat shock promoters.

Transcription antitermination in the rRNA operons of Escherichia coli requires a unique nucleic acid sequence that serves as a signal for modification of the elongating RNA polymerase, making it resistant to Rho-dependent termination. We examined the antitermination ability of RNA polymerase elongation complexes that had initiated at three different heat shock promoters, dnaK, groE, and clpB, and then transcribed the antitermination sequence to read through a Rho-dependent terminator. Terminator bypass comparable to that seen with sigma(70) promoters was obtained. Lack of or inversion of the sequence abolished terminator readthrough. We conclude that RNA polymerase that uses sigma(32) to initiate transcription can adopt a conformation similar to that of sigma(70)-containing RNA polymerase, enabling it to interact with auxiliary modifying proteins and bypass Rho-dependent terminators.

Bacterial Proteins↗