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PubMed2006

Genetic determinants of capsular serotype K1 of Klebsiella pneumoniae causing primary pyogenic liver abscess.

BACKGROUND: Primary pyogenic liver abscess (PLA) caused by Klebsiella pneumoniae is an emerging infectious disease. Capsular serotype K1 and the magA gene have been reported to be associated with this disease. METHODS: The prevalence of magA was determined by polymerase chain reaction (PCR). The sequences of the magA flanking region were completed by inverse PCR and direct sequencing. Serotyping was performed by double immunodiffusion. Insertion mutations and trans-complementation were used to define the K1 genetic determination region. RESULTS: Thirty-five of 42 strains from patients with PLA were magA positive, whereas only 1 of 32 non-PLA strains was magA positive. All 36 magA-positive strains were serotype K1, and the 38 magA-negative strains were not (36/36 vs. 0/38; P<.0001). Sequencing of the magA flanking region revealed a putative capsular polysaccharide synthesis (cps) region; this region was 25 kb in length and contained 20 open reading frames (ORFs); of these ORFs, 9 were cotranscribed as part of an operon and differed from both MGH78578 and the Chedid strain. Mutation of 4 genes in this region turned the mutant strains anti-K1 negative. Trans-complementation restored the K1 phenotype. CONCLUSIONS: The operon containing magA is responsible for capsular serotype K1 of K. pneumoniae. Several loci in the operon are unique determinants of K1 strains.

Antigens, Bacterial↗
PubMed1993

Cloning and sequence analysis of the dnaK gene region of Lactococcus lactis subsp. lactis.

A 5.4 kb HindIII fragment of Lactococcus lactis subsp. lactis was identified using a homologous dnaK probe generated by PCR and cloned in Escherichia coli. Upstream sequences were generated by inverse PCR. The two cloned fragments partially overlapped, and sequencing of 5915 bp revealed the presence of four open reading frames in the order orf1-grpE-dnaK-orf4. orf1 encodes a 39 kDa protein of unknown function which shows considerable sequence homology with the Orf39 and Orfa proteins of Bacillus subtilis and Clostridium acetobutylicum, respectively. The downstream ORFs showed high homology to the grpE and dnaK genes of other prokaryotes. The DnaK protein has a characteristic 24-amino-acid deletion exhibited by all the known DnaK proteins of Gram-positive species. In many bacteria the dnaK and dnaJ genes are found as part of the same operon. The L. lactis dnaK operon is unusual in that the dnaK gene is followed by a putative transcription terminator and a fourth large ORF which shares no homology with the dnaJ genes of other bacteria but has a small degree of homology with various membrane proteins. Vegetative promoter sequences are found upstream of both orf1 and orf4. A 12 bp inverted repeat is found upstream of the putative promoter of orf1 and an 8 bp inverted repeat is found between this promoter and the orf1 initiation codon. These repeats are thought to be involved in regulation of the heat-shock genes. The DnaK homologue is induced approximately 3-fold on heat shock at 42 degrees C.

Amino Acid Sequence↗
PubMedDate not supplied

Morphology and development of mirror-image doublets of Stylonychia mytilus.

This paper describes the cortical anatomy and development of mirror-image doublets of Stylonychia mytilus, analyzed using the protargol technique. The reversed, or "left-handed" (LH) component of these doublets is a mirror image of the normal or "right handed" (RH) component with regard to the arrangement of cortical structures. The mirror-image patterning is imperfect, however, as the individual ciliary structures of the LH component all are of normal internal asymmetry, and the orientation of membranelles is inverted. Certain structures that would be expected to form near the line of symmetry are absent. During cell division and cortical reorganization, ciliary primordia arise and become arranged in a mirror-image pattern that is more perfect than that exhibited by the mature structures. Deviations from a mirror-image pattern appear at late stages when organelle sets differentiate within ciliary primordia: for example, the membranelle set differentiates within the oral primordium of the LH component in a sequence that is an inversion rather than a mirror image of the corresponding sequence of the RH component. This mixed control of oral development by different cortical "informational systems" accounts for some of the characteristic abnormalities of the mature oral structures of the LH component.

Animals↗
PubMed1996

MR relaxation times in human brain: measurement at 4 T.

PURPOSE: To determine the values for relaxation times in human brain for magnetic resonance (MR) imaging at 4 T. MATERIALS AND METHODS: T1 measurements were made with a progressive saturation sequence, an implementation of the Look-Locker sequence, and an inversion-recovery (IR) interleaved echo-planar imaging (IEPI) sequence. T2 measurements were made with a standard spin-echo (SE) sequence and an SE IEPI sequence. RESULTS: The T1 measurements yielded values of 1,724 msec +/- 51 for gray matter, 1,043 msec +/- 27 for white matter, and 4,550 msec +/- 800 msec for cerebrospinal fluid. The deep gray matter regions had T1 values of 1,458 +/- 38 (caudate nucleus) and 1,372 +/- 60 (putamen). The T2 measurements yielded results of 63 msec +/- 6.2 for gray matter and 49.8 msec +/- 2.2 for white matter. CONCLUSION: The T1 values measured at 4 T show a higher value than predicted from extrapolation at lower field strengths. The T2 measurements showed a slight decrease in values over those measured at lower-field strength. The gain in signal-to-noise ratio from the higher field strength may be substantially offset by these altered relaxation time values to a degree that is sequence dependent.

Adult↗
PubMed2003

MR imaging of epidermoids at the cerebellopontine angle.

The most common location of intracranial epidermoid is the cerebellopontine angle (CPA). The present study compared the visibility of epidermoid at the CPA in various pulse sequences. Seven patients with epidermoid at the CPA underwent conventional MR imaging (T(1)-, T(2)- and proton density-weighted imaging) as well as diffusion-weighted echo-planar imaging. Fast fluid-attenuated inversion recovery (FLAIR) sequences, magnetization transfer contrast (MTC) sequences, and MR cisternography were employed for selected patients. The signal intensity of the lesions relative to cerebrospinal fluid (CSF), the degree of lesion demarcation and the displacement of surrounding structures were evaluated. Proton density-weighted imaging depicted the lesions as hyper-intense to CSF with clearer delineation than T(1)- and T(2)-weighted imaging. Diffusion-weighted imaging depicted all lesions as strongly hyper-intense relative to CSF and brain tissue. FLAIR sequences depicted the lesions with mixed signal intensities but with poor-to-medium demarcation. MTC imaging increased delineation of the lesions to some degree. MR cisternography depicted the lesions as hypo-intense to CSF and clearly showed the anatomical relation to neighboring nerves and vessels. We concluded that diffusion-weighted imaging could specifically reveal an epidermoid at the CPA as a strongly hyper-intense lesion, and that MR cisternography is mandatory for preoperative planning.

Adolescent↗
PubMed1996

Long time echo STIR sequence magnetic resonance imaging of optic nerves in optic neuritis.

Magnetic resonance images of optic nerves were obtained in 20 patients with acute optic neuritis (ON), and assessed by means of clinical, visual field and visual evoked potential evaluations; the imaging was repeated 1 year later. The results of the conventional Short Tau Inversion Recovery (STIR) sequence obtained using short time echo (STE-STIR: 22 msec) were compared with those of the long time echo sequence (LTE-STIR: 80 msec). The conventional STE-STIR sequence revealed lesions in 57.2% cases of acute ON and in 42.9% of the optic nerves affected by previous ON; the LTE-STIR sequence was diagnostic in 95.2% of acute ON cases and in 85% of patients with previous ON. The calculated length of the optic nerve lesions was significantly longer in the images obtained using the LTE-STIR sequence than in those obtained using conventional STE-STIR sequences.

Adult↗
PubMed1995

Long time echo stir sequence magnetic resonance imaging of optic nerves in optic neuritis.

Magnetic resonance imaging of optic nerves was obtained in 13 patients with acute optic neuritis and in 13 patients with a previous history of optic neuritis (ON), assessed by clinical, visual fields and visual evoked potentials evaluations. Results of the conventional short tau inversion recovery (STIR) sequence obtained with short time echo (STE-STIR: 22 ms) were compared with long time echo (LTE-STIR: 80 ms) sequence. The conventional STE-STIR sequence revealed lesions in 78.5% of acute ON and in 58.8% of optic nerves affected by previous ON. The LTE-STIR sequence was diagnostic in 92.8% of acutely symptomatic nerves, in 94.1% of nerves with previous ON. The calculated length of optic nerve lesions was significantly longer in imaging obtained with the LTE-STIR sequence than with the conventional STE-STIR sequences, both in acute and previous ON.

Adult↗
PubMed1987

Shufflon: multi-inversion of four contiguous DNA segments of plasmid R64 creates seven different open reading frames.

The IncI alpha plasmid R64 was found to bear a highly mobile DNA segment which was designated as a clustered inversion region (J. Bacteriol. 165, 94-100, 1986). The clustered inversion region consists of four DNA segments designated respectively as A, B, C and D which differ in molecular size and restriction sites. The four DNA segments invert independently or in groups resulting in a complex DNA rearrangement. We now show the nucleotide sequence of the clustered inversion region of R64. The present results suggest that the clustered inversion region is a biological switch to select one of seven open reading frames whose primary structures at the region proximal to N-termini are constant while those at the C-terminal region are variable. A name, "Shufflon" was proposed to call this kind of the clustered inversion region.

Base Sequence↗
PubMed2006

Endonuclease G: a role for the enzyme in recombination and cellular proliferation.

Our earlier studies had suggested that endonuclease G (EndoG), a member of the evolutionarily conserved DNA/RNA nonspecific betabetaalpha-Me-finger nuclease family, functioned in the a sequence-mediated segment inversion observed during herpes simplex virus 1 replication. To test this hypothesis, we used RNA interference to reduce the level of EndoG in mammalian cells in culture. Reduction of EndoG produced a small but statistically significant decrease in a sequence-mediated recombination, suggesting that EndoG does play a role in this process. We also observed that reduction in the level of EndoG resulted in a deficiency in cell proliferation. Cells with a reduced level of EndoG also showed changes in cell distribution in the cell cycle, producing a pattern characteristic of cells that have been arrested in the G(2) phase. These findings suggest that EndoG is required for normal cellular proliferation.

Animals↗
PubMed2004

A novel cis-acting element facilitates minus-strand DNA synthesis during reverse transcription of the hepatitis B virus genome.

Hepadnaviruses replicate through reverse transcription of an RNA pregenome, resulting in a relaxed circular DNA genome. The first 3 or 4 nucleotides (nt) of minus-strand DNA are synthesized by the use of a bulge in a stem-loop structure near the 5' end of the pregenome as a template. This primer is then transferred to a complementary UUCA motif, termed an acceptor, within DR1* near the 3' end of the viral pregenome via 4-nt homology, and it resumes minus-strand DNA synthesis: this process is termed minus-strand transfer or primer translocation. Aside from the sequence identity of the donor and acceptor, little is known about the sequence elements contributing to minus-strand transfer. Here we report a novel cis-acting element, termed the beta5 region (28 nt in length), located 20 nt upstream of DR1*, that facilitates minus-strand DNA synthesis. The deletion or inversion of the sequence including the beta5 region diminished minus-strand DNA synthesis initiated at DR1*. Furthermore, the insertion of the beta5 region into its own position in a mutant in which the sequences including the beta5 region were replaced restored minus-strand DNA synthesis at DR1*. We speculate that the beta5 region facilitates minus-strand transfer, possibly by bringing the acceptor site in proximity to the donor site via base pairing or by interacting with protein factors involved in this process.

Cell Line, Tumor↗
PubMed1986

Liver metastases: detection by phase-contrast MR imaging.

Forty patients with biopsy-proved metastatic liver cancers were studied by magnetic resonance (MR) imaging using one or more conventional (in-phase) pulse sequences and a corresponding phase-contrast (opposed-phase) pulse sequence. Pulse-sequence performance was quantitated by measuring signal-difference-to-noise (SD/N) ratios between cancerous tissue and liver. The SD/N performance of T2-weighted spin-echo (SE) pulse sequences improved when used with the phase-contrast technique. SE 2,000/30 opposed-phase images showed improved (P less than .001) SD/N in 72% of patients over in-phase images. The SD/N of T1-weighted SE or inversion recovery pulse sequences deteriorated when used with the phase-contrast technique. Changes in measured SD/N correlated well with image appearance and actual lesion detectability in individual cases. Phase-contrast imaging should be employed routinely when T2-weighted SE pulse sequences are relied on to detect liver cancer.

Humans↗
PubMed1998

Quantification of gadolinium-DTPA concentrations for different inversion times using an IR-turbo flash pulse sequence: a study on optimizing multislice perfusion imaging.

The purpose of this study was to optimize an inversion-recovery (IR) turbo fast low-angle shot (FLASH) for multislice imaging by evaluating the accuracy of calculated the relaxation-rate (R1) for different inversion times (TI). This is important for tracer kinetic modeling because it requires a system responding linearly to input. R1 are linearly related to changes in the concentration of gadolinium (Gd)-diethylenetriaminepentaacetic acid (DTPA), and R1 is a parameter that can be derived from the magnetic resonance (MR) signal. The accuracy of calculated R1 using an IR turbo fast low-angle shot was evaluated in phantoms and for increasing TIs using spectroscopically measured R1 values as reference. Signal curves, obtained in vivo after a bolus injection of Gd-DTPA, were used in an analytical computer program to study the effect of different TI-values on accurate calculation of R1. Results show that TIeff should be <200 ms to measure the bolus-passage of Gd-DTPA in blood accurately, whereas the myocardial response can be measured correctly for TIeff < 870 ms at 1.5 T. The initial slope of the myocardial signal enhancement curve becomes steeper for larger TI values, whereas the calculated R1 curves were similar, indicating that these curves, rather than signal curves, are more suitable even for qualitative perfusion evaluation. It is concluded that the results can be incorporated in a multislice IR turbo fast low-angle shot using the first slice (with a short TI) for assessment of both the arterial input function and the tissue response and the second slice in another position for assessment of the tissue response alone.

Contrast Media↗
PubMed1990

A human immunoglobulin kappa orphon without sequence defects may be the product of a pericentric inversion.

The VK gene segments that have been transposed from the kappa locus on the short arm of chromosome 2 at 2p11-12 to other chromosomal sites are called orphons. The 18 VK orphons sequenced up to now carry defects and are to be considered pseudogenes. We now describe the VKI gene segment V108 whose sequence is without any defects and which was localized to the long arm of chromosome 2 at 2q12-14 by in situ hybridization. The V108 region may have been transposed from the short to the long arm of chromosome 2 by a pericentric inversion. Possible reasons for the conservation of its sequence are discussed. In spite of its bona fide sequence V108 is considered to be an unlikely candidate for a VK-JK rearrangement and subsequent functional expression.

Amino Acid Sequence↗
PubMed1993

Application of a mixed imaging sequence for MR imaging characterization of human breast disease.

Single slice MR images were obtained from 9 normal breasts, 17 breasts with benign tumors, and 11 breasts with malignant tumors using an interleaved (mixed) spin echo (SE) inversion-recovery (IR) imaging sequence. SE and IR MR images were synthesized with variable repetition, echo and inversion times from the mixed sequence data. These images were used to qualitatively evaluate the contrast possibilities available when imaging the breast with MR imaging. Proton T1 and T2 relaxation times were determined for normal breast tissues and malignant and benign breast tumors from pure T1 and T2 images calculated using the mixed sequence data. The mean T1 value in benign tumors of 1,049.02 +/- 40.31 was found to be significantly longer (p < 0.0001) than the mean value of malignant tumors (876.09 +/- 27.83) and normal tissues (795.64 +/- 21.12). The value of T2 in benign tumors (89.15 +/- 8.33) was significantly longer (p < 0.01) than the value of T2 in normal tissues (62.82 +/- 4.06). The mixed sequence can be applied to improve image contrast between malignant tumors, benign tumors, and normal tissues of the breast and can potentially differentiate between these tissues in vivo.

Breast Diseases↗
PubMed1997

Zinc(II) tolerance in Escherichia coli K-12: evidence that the zntA gene (o732) encodes a cation transport ATPase.

A transposon (Tn 10dCam) insertion mutant of Escherichia coli K-12 was isolated that exhibited hypersensitivity to zinc(II) and cadmium(II) and, to a lesser extent, cobalt(II) and nickel (II). The mutated gene, located between 75.5 and 76.2 min on the chromosome, is named zntA (for Zn(II) transport or tolerance). The metal-sensitive phenotype was complemented by a genomic DNA clone mapping at 3677.90-3684.60 kb on the physical map. Insertion of a kanamycin resistance (KnR) cassette at a SalI site in a subcloned fragment generated a plasmid that partially complemented the zinc(II)-sensitive phenotype. DNA sequence analysis revealed that the KnR cassette was located within the putative promoter region of an ORF (o732 or yhhO) predicted to encode a protein of 732 amino acids, similar to cation transport P-type ATPases in the Cpx-type family. Inverse PCR and sequence analysis revealed that the Tn 10dCam element was located within o732 in the genome of the zinc(II)-sensitive mutant. The zntA mutant had elevated amounts of intracellular and cell surface-bound Zn(II), consistent with the view that zntA+ encodes a zinc(II) efflux protein. Exposure of the zntA mutant to cobalt(II) and cadmium(II) also resulted in elevated levels of intracellular and cell surface-bound metal ions.

Adenosine Triphosphatases↗
PubMed1995

High resolution neuroimaging at 4.1T.

In this article we report on acquisition of high resolution 512 x 512 images at 4.1T using an inversion recovery gradient-echo sequence and a volume head coil developed for high field applications. The Ti values for cerebral white and grey matter were measured to be 834 and 1282 ms, respectively. The partial saturation inversion recovery sequence (Tir 800 ms and TR 2500 ms) provided excellent contrast-to-noise for white to grey matter. Consequently, the images consistently visualized the thalamic nuclear groups, hippocampal fine structure, as well as small draining vessels of the white matter.

Brain↗