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At least 937 records · Page 52Linked to original sources
PubMed2003

An intraspecific linkage map of the chickpea ( Cicer arietinum L.) genome based on sequence tagged microsatellite site and resistance gene analog markers.

An intraspecific linkage map of the chickpea genome based on STMS as anchor markers, was established using an F(2) population of chickpea cultivars with contrasting disease reactions to Ascochyta rabiei (Pass.) Lab. At a LOD-score of 2.0 and a maximum recombination distance of 20 cM, 51 out of 54 chickpea-STMS markers (94.4%), three ISSR markers (100%) and 12 RGA markers (57.1%) were mapped into eight linkage groups. The chickpea-derived STMS markers were distributed throughout the genome, while the RGA markers clustered with the ISSR markers on linkage groups LG I, II and III. The intraspecific linkage map spanned 534.5 cM with an average interval of 8.1 cM between markers. Sixteen markers (19.5%) were unlinked, while l1 chickpea-STMS markers (20.4%) deviated significantly ( P < 0.05) from the expected Mendelian segregation ratio and segregated in favor of the maternal alleles. However, ten of the distorted chickpea-STMS markers were mapped and clustered mostly on LG VII, suggesting the association of these loci in the preferential transmission of the maternal germ line. Preliminary comparative mapping revealed that chickpea may have evolved from Cicer reticulatum, possibly via inversion of DNA sequences and minor chromosomal translocation. At least three linkage groups that spanned a total of approximately 79.2 cM were conserved in the speciation process.

Cicer↗
PubMed1999

MRI image plane nonuniformity in evaluation of ferrous sulphate dosimeter gel (FeGel) by means of T1-relaxation time.

MR image nonuniformity can vary significantly with the spin-echo pulse sequence repetition time. When MR images with different nonuniformity shapes are used in a T1-calculation the resulting T1-image becomes nonuniform. As shown in this work the uniformity TR-dependence of the spin-echo pulse sequence is a critical property for T1 measurements in general and for ferrous sulfate dosimeter gel (FeGel) applications in particular. The purpose was to study the characteristics of the MR image plane nonuniformity in FeGel evaluation. This included studies of the possibility of decreasing nonuniformities by selecting uniformity optimized repetition times, studies of the transmitted and received RF-fields and studies of the effectiveness of the correction methods background subtraction and quotient correction. A pronounced MR image nonuniformity variation with repetition and T1 relaxation time was observed, and was found to originate from nonuniform RF-transmission in combination with the inherent differences in T1 relaxation for different repetition times. The T1 calculation itself, the uniformity optimized repetition times, nor none of the correction methods studied could sufficiently correct the nonuniformities observed in the T1 images. The nonuniformities were found to vary considerably less with inversion time for the inversion-recovery pulse sequence, than with repetition time for the spin-echo pulse sequence, resulting in considerably lower T1 image nonuniformity levels.

Background Radiation↗
PubMed1998

Cloning and characterization of the gene encoding beta subunit of mitochondrial processing peptidase from the basidiomycete Lentinula edodes.

We have isolated the gene encoding the beta subunit of mitochondrial processing peptidase (beta-MPP) from the shiitake mushroom Lentinula edodes. It is a nuclear gene with two small introns. Comparison with known beta-MPP genes revealed that the L. edodes gene is most closely related with that from Neurospora crassa, with 60.8% identities and 87% similarity in the amino-acid sequences. The deduced L. edodes beta-MPP peptide sequence contains the inverse zinc-binding motif (H-X-E-H) that has been found in a large family of zinc-binding metalloproteinases including bacterial proteinases, insulin degrading enzymes and beta-MPPs. The two histidines are thought to contribute two of the three residues for zinc binding. The expression of L. edodes beta-MPP is higher during the development of the fruiting bodies, suggesting that higher mitochondrial activities may be required to meet the energy demand in the rapid growth of the fruiting bodies.

Amino Acid Sequence↗
PubMed1989

Characterization of alpha and beta tubulin genes in the dimorphic fungus Histoplasma capsulatum.

Evidence from our laboratory indicates that microtubules are involved in the differentiation of the dimorphic, pathogenic fungus Histoplasma capsulatum; therefore, we cloned the tubulin genes from a virulent strain of the organism. We report that the H. capsulatum genome contains a single alpha (TUB1) and a single beta (TUB2) tubulin gene rather than the more typical multigene family which is common in even the simplest eukaryotes. Sequence data from these genes reveal a high degree of nucleotide and protein sequence conservation relative to tubulins from other species. The coding regions of TUB1 and TUB2 contain five and eight intervening sequences, respectively. Field inversion gel electrophoresis of H. capsulatum chromosome-sized DNA fragments indicates that the TUB1 and TUB2 genes are unlinked. Potential regulatory elements common to both genes have been identified in the 5' promoter regions. These elements may direct the coordinate expression of TUB1 and TUB2 during differentiation. The cloning and characterization of alpha and beta tubulin genes from H. capsulatum provides the first description of gene structure in this widely distributed pathogenic fungus. Isolation of the tubulin genes will facilitate future studies of tubulin gene expression during the dimorphic phase transitions and clarify the role of microtubules in the differentiation process.

Amino Acid Sequence↗
PubMed2000

impA, a gene coding for an inner membrane protein, influences colonial morphology of Actinobacillus actinomycetemcomitans.

Directed mutagenesis of a gene coding for a membrane protein of the periodontopathogen Actinobacillus actinomycetemcomitans was achieved by conjugation. The gene was disrupted by insertion of an antibiotic cassette into a unique endonuclease restriction sequence engineered by inverse PCR. The disrupted gene was cloned into a conjugative plasmid and transferred from Escherichia coli to A. actinomycetemcomitans. The allelic replacement mutation resulted in the loss of a 22-kDa inner membrane protein. The loss of this protein (ImpA) resulted in changes in the outer membrane protein composition of the bacterium. Concurrent with the mutation in impA was a change in the pattern of growth of the mutant bacteria in broth cultures. The progenitor bacteria grew as a homogeneous suspension of cells compared to a granular, autoaggregating adherent cell population described for the mutant bacteria. These data suggest that ImpA may play a regulatory role or be directly involved in protein(s) that are exported and associated with colony variations in A. actinomycetemcomitans.

Aggregatibacter actinomycetemcomitans↗
PubMed2002

[Cloning and sequencing of junction fragment with exon 51 deletion of Dystrophin gene].

To study the mechanism of Dystrophin gene deletion, we obtained the deletion junction fragment of exon 51 by inverse PCR and analyzed the sequence characteristic of breakpoints and deletion junction fragment. After the full sequence of intron 51 was finished, the rough site of breakpoint in intron 51 of a DMD patient with exon 51 deletion was detected by PCR with 9 pairs of primers spaced every 3-5 kb in intron 51. Then the junction fragment was amplified by nested inverse PCR. After sequencing the junction fragment, the 3' breakpoint and partial sequences of intron 50 were determined by comparing with the normal sequences in intron 51. The primer was designated to sequence intron 50 according to the sequence of junction fragment, and then the 5' breakpoint was determined. A total of 1,614 bp in intron 50 was sequenced. The 5' and 3' breakpoints were located in the THE-1 internal sequence (Transposon-like Human Element, THE) and L2 sequence respectively. There are 3 bp junctional homology and no errors near the junction point. This is the second report that the deletion breakpoint located directly in THE-1 sequence studied at the DNA level. We here firstly reported that there is a THE-1 sequence in intron 50. THE-1 and non-homologue end joining repair mechanism may be associated with the Dystrophin gene deletion.

Child↗
PubMed2004

NMR and EPR structural delineation of copper(II) complexes formed by kanamycin A in water.

The complexes formed by kanamycin A at three different pH values (5.5, 7.4 and 12.0) were investigated by NMR and EPR spectroscopy. Paramagnetic relaxation contributions to proton relaxation rates were measured using a combination of the TOCSY sequence with the inversion recovery experiment in order to gain signal resolution in the bulk region. Measured contributions were converted into distances and used for structural determination by restrained simulated annealing where all possible chair and boat conformations of the rings were taken into account. The interaction of the Cu(II) ion with the nitrogen of the C ring is apparent at all pH values. At higher pH also the amino group of ring A starts to be involved in the metal coordination sphere. This is accompanied by a switch in conformation of ring C. Structures are consistent with the involvement in the coordination sphere either of the 2' or 4' hydroxyl oxygens at pH 5.5 and the 5 and the 6' hydroxyl oxygens (or the ring oxygen) at pH 12.0.

Carbohydrate Sequence↗
PubMed2000

Intragenic inversion of mtDNA: a new type of pathogenic mutation in a patient with mitochondrial myopathy.

We report an unusual molecular defect in the mitochondrially encoded ND1 subunit of NADH ubiquinone oxidoreductase (complex I) in a patient with mitochondrial myopathy and isolated complex I deficiency. The mutation is an inversion of seven nucleotides within the ND1 gene, which maintains the reading frame. The inversion, which alters three highly conserved amino acids in the polypeptide, was heteroplasmic in the patient's muscle but was not detectable in blood. This is the first report of a pathogenic inversion mutation in human mtDNA.

Adult↗
PubMed2000

[MRI of drug-resistant epilepsies: contribution of FLAIR sequence in a series of 150 patients].

We studied the usefulness of the Fluid-Attenuated Inversion-Recovery (FLAIR) pulse sequence for patients with intractable seizures by reviewing the MR images of 150 consecutive patients including a standard imaging protocol and a FLAIR sequence. FLAIR images revealed a cortical lesion in 8 of the 81 patients with no lesion detected on the standard MR imaging protocol. In addition, FLAIR images provided additional informations for 13 patients of the 69 patients for whom a lesion was already detected on the standard MR imaging protocol. Therefore, our results indicated that FLAIR sequences were a useful imaging tool for patients with intractable seizures since it improved the MR diagnosis in 21 of 150 patients (14%).

Adolescent↗
PubMed2003

The gyr genes of Salmonella enterica serovar Typhimurium are repressed by the factor for inversion stimulation, Fis.

The DNA sequence of the gyr genes from Salmonella enterica serovar Typhimurium revealed strong similarity between gyrB and its counterpart in Escherichia coli. However, the gyrA gene showed similarity to the E. coli homologue only downstream from the Pribnow box of the promoter, with the sequence upstream diverging markedly. Since this region encompasses the binding sites for the Fis DNA binding protein in E. coli, we investigated the possibility that the gyrA genes in the two species might differ in their responses to this regulatory protein. Fis was found to act as a transcriptional repressor of both gyr genes in S. enterica. In electrophoretic mobility shift assays, Fis was found to bind to both the gyrA and gyrB promoters of S. enterica, despite the strong divergence from the E. coli sequence on the part of the former. The binding sites were mapped by DNase I protection assays, and the results are consistent with conservation of the mechanism of Fis-mediated repression between the two bacterial species.

Base Sequence↗
PubMed1999

Isolation and characterization of MELt gene from Torulaspora delbrueckii IFO 1255.

Torulaspora delbrueckii IFO 1255 is a melibiose-fermenting strain in Torulaspora species. From the genome of strain IFO 1255, we obtained a 770 bp fragment by PCR with oligonucleotides synthesized based on the MEL genes of Saccharomyces cerevisiae and its related species. The region encompassing the 770 bp fragment was cloned by inverse PCR and sequenced. The nucleotide sequence revealed an open reading frame of 1422 bp encoding a 474 amino acid protein with a molecular weight of 52 360. The similarity of the presumed mature protein to Saccharomyces species and Zygosaccharomyces cidri alpha-galactosidases was 69.7-73.2% and 58.4%, respectively. The phylogenetic relationship between these species is discussed. The sequence is deposited in the DDBJ/EMBL/GenBank database under Accession No. AB027130.

Amino Acid Sequence↗
PubMed1997

Musculoskeletal complications of neutron therapy for prostate cancer.

The purpose of this study was to investigate the cause of hip complaints following conformal neutron therapy delivered by opposed lateral and oblique anterior ports to treat prostate cancer. Twenty-seven patients with hip complaints following neutron or mixed neutron and photon therapy for prostate cancer had 34 magnetic resonance imaging (MRI) studies 3-39 (mean 15.3) months following treatment; for comparison, 13 similarly treated patients without hip complaints were imaged 1-32 (mean 13.8) months post-treatment; 25/40 imaged patients received concurrent nonsteroidal hormone therapy. Coronal and axial images of the hips/pelvis were obtained utilizing T1 weighted spin echo and fat suppressed inversion recovery (STIR) sequences. Signal amplitude (SA) of involved muscles was measured on the STIR images and normalized to that of the psoas outside the treatment field. Hip complaints ranged from mild soreness or motion limitation to severe pain and limitation of ambulation; presence and severity of symptoms (sx) were significantly related to neutron dose (P = 0.020 and 0.0001) but not to hormone therapy (each P > 0.17). Normalized SA of the obturator muscles differed significantly with neutron dose (P = 0.013), the presence, and the severity, of sx (P = 0.0002 and 0.0007); estimated extent of abnormal muscle also differed significantly with neutron dose (P = 0.039), presence, and severity, of sx (P = 0.00004 and 0.0007); [hormone treatment had a profound effect on SA (P = 0.0001) and extent (P = 0.005) which was independent of sx (P = 0.10 and 0.14, respectively) and neutron dose (P = 0.33 and 0.32, respectively)]. Subcutaneous changes localized lateral to the greater trochanter were seen in all, and edema of the subjacent gluteus muscles in many, symptomatic hips; only 4/13 asymptomatic hips showed subcutaneous changes, 6 had mild gluteus edema. Avascular necrosis of the femoral head was seen in 5 symptomatic hips, with marked acetabular necrosis in 3 of these; small joint effusions were seen in 8 symptomatic hips; asymptomatic hips had no significant bone or joint abnormalities. Neutron therapy for prostate cancer designed to spare the rectum results in significant dose-dependent, musculoskeletal complications which are well demonstrated by MRI. SA abnormalities of irradiated muscle correlate significantly with neutron dose and both presence and severity of hip sx. Protocol modifications have been implemented to reduce these complications. MRI provides an objective means to assess both complications and the success of new protocols in ameliorating them. Concurrent hormone therapy has a profound effect on muscle changes on MRI which is independent of neutron dose and sx.

Adipose Tissue↗
PubMed1999

Echo-train STIR MRI of the liver: comparison of breath-hold and non-breath-hold imaging strategies.

The purpose of this study was to evaluate echo-train short inversion-time inversion recovery (STIR) sequences and compare the results obtained with breath-hold and non-breath-hold imaging strategies. Forty-one patients referred for hepatic magnetic resonance were imaged with both a breath-hold STIR (BH-STIR; acquisition time [TA] 16-20 seconds x 2) and a non-breath-hold STIR (NBH-STIR; TA 210-256 seconds). Quantitative analysis of the liver, spleen, and up to five hepatic lesions per patient was performed. Three blinded readers recorded the number of focal lesions depicted by each study and qualitatively evaluated overall image quality, lesion conspicuity, and image artifacts. The BH-STIR had greater sensitivity (98.8% vs. 91.6%) for detection of hepatic lesions than the NBH-STIR. The BH-STIR was statistically superior in four measures of image quality and had fewer image artifacts. The NBH-STIR images had statistically higher signal-to-noise (S/N, P < 0.001) and liver-lesion contrast-to-noise (C/N, P = 0.005) ratios. For the evaluation of focal hepatic lesions, a breath-hold echo-train STIR sequence provided superior overall image quality and allowed for detection of more lesions in a shorter amount of time than a non-breath-hold echo-train STIR sequence.

Artifacts↗
PubMed1999

Study of focused ultrasound tissue damage using MRI and histology.

This paper reports on an experimental study of in vivo tissue damage in the rabbit brain with focused ultrasound (FUS) using magnetic resonance imaging (MRI) and histopathological analysis. Ten ultrasonic lesions (tissue damage) were created in five rabbits using a focused ultrasound beam of 1.5 MHz, electrical power input to the transducer of 70-85 W, and an exposure duration of 15-20 seconds. T1- and T2-weighted fast spin-echo (FSE) and Fluid attenuated inversion recovery (FLAIR) sequences were used to detect the ultrasonic lesions after treatment. Imaging was performed for 4-8 hours after treatment, after which the animals were immediately sacrificed. Ultrasonic lesion diameter was measured on MRI and histological sections after correction for tissue shrinkage during the histological processing. The T1-weighted images showed lesions poorly, whereas both T2-weighted and FLAIR images showed lesions clearly. The lesion diameters on both T2 and FLAIR imaging correlated well with measurements from histology. The time delay before lesions appeared on T2-weighted imaging was 15 minutes to 1 hour, depending on the exposure location in the brain. J. Magn. Reson. Imaging 1999;10:146-153.

Animals↗
PubMed2000

A method for fast multislice T1 measurement: feasibility studies on phantoms, young children, and children with Canavan's disease.

We have developed a multislice protocol for quantitative T1 measurements in which the processing time and the acquisition time are under 2 minutes each for a complete brain study of 15 slices. An echoplanar, inversion-recovery image sequence is designed to collect data suitable for analysis using a linear regression algorithm. The precision is approximately twice the noise to signal ratio of the images. The accuracy of the protocol is better than 1% for T1 in the range 0-2 seconds and deviates slightly for longer T1 values. The protocol is insensitive to B1 field values. If needed, the data can be postprocessed using a slow, nonlinear algorithm to give an accuracy of less than 1% and a precision of approximately the noise to signal ratio throughout a range of T1 values from 0 to 4 seconds.

Algorithms↗
PubMed1988

Chronic unilateral optic neuropathy: a magnetic resonance study.

We studied the clinical, electrophysiological, and magnetic resonance imaging (MRI) features of 20 patients with chronic unilateral optic neuropathy (CUON): progressive unilateral visual failure lasting a minimum of 6 months. The patients, 10 male and 10 female, ranged in age from 12 to 77 years (mean 44) and had a mean duration of symptoms of 22 months. All had signs of optic nerve dysfunction. Each patient was studied with MRI using a short TI inversion recovery (STIR) sequence to delineate the optic nerve from surrounding orbital tissue. Three distinct groups of patients with CUON were identified using MRI. In the first group (8/20) the optic nerve was compressed by an extrinsic mass, whereas in the second group (5/20) CUON resulted from an intrinsic tumor of the optic nerve or sheath. In both groups STIR sequences compared favorably with computed tomography in identifying mass lesions. MRI was superior in delineating distortion of the optic nerve by mass or tumor extension beyond the orbit. In the third group (7/20) no mass was evident on MRI. However, STIR sequences revealed altered signal (long T1) in clinically symptomatic nerves. In 4 of the patients T2-weighted cerebral MRI disclosed periventricular lesions suggestive of disseminated white matter disease. We conclude that MRI complements clinical and electrophysiological testing in the assessment of CUON.

Adolescent↗
PubMed2003

Molecular cloning of a constitutional t(7;22) translocation associated with risk of hematological malignancy.

We report the molecular characterization of a reciprocal constitutional translocation t(7;22)(p13;q11.2) carried by three family members who have each developed a hematological malignancy. The chromosome 7 breakpoint was localized to a single BAC clone, RP11-571N3, by sequential fluorescence in situ hybridization analysis of clones selected from the NCBI chromosome 7 map. This was further refined to a 739-bp region by Southern blot analysis of DNA from the two cell lines 1193 and 1194 digested with EcoRI, HindIII, PstI, and PvuII. A 2.8-kb fragment spanning the der(22) breakpoint was amplified by long-range inverse PCR. The sequence of this fragment was used to predict the composition of the der(7) breakpoint, and a 1.3-kb fragment was amplified by use of primers from both chromosomes 7 and 22 based on this prediction. The breakpoint on chromosome 22 is located between the 3rd and 4th V regions of the immunoglobulin lambda (IGL) locus, and the breakpoint on chromosome 7 is located 122 kb proximal to the insulin-like growth factor binding protein (IGFBP) 3 gene. Examination of both reciprocal junctions showed that four bases were lost from chromosome 22, whereas 75 bases were lost from chromosome 7. Small insertions of 46 bases and 13 bases were found at the der(22) and the der(7) junctions, respectively. As a consequence of this event, the entire IGL locus, less the first three Vlambda elements, is translocated to chromosome 7, whereas the three remaining Vlambda elements on the der(22) are juxtaposed with IGFBP3 and IGFBP1.

Aged↗
PubMed2002

Resection of soft tissue sarcomas with intra-operative magnetic resonance guidance.

PURPOSE: To report on a preliminary series of magnetic resonance (MR)-guided sarcoma resections. MATERIALS AND METHODS: Three patients with the skin sarcoma dermatofibrosarcoma protuberans underwent MR-guided resection. RESULTS: The extent of the tumor at MR imaging was greater in each case than suggested by clinical examination. Adequate resection margins were planned using short Tau inversion recovery (STIR) sequences and intra-operative imaging was used to confirm complete tumor excision. Histological examination confirmed clear surgical margins of at least 1 cm in each case. CONCLUSION: We believe this technique may reduce the incidence of specimen margins positive for tumor following resection, and consequently reduce the need for further excisional surgery.

Adult↗