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PubMed1981

Techniques for manipulating chromosomal rearrangements and their application to Drosophila melanogaster. I. Pericentric inversions.

Techniques have been developed for manipulating pericentric inversions in Drosophila that are based on the lethality of grossly aneuploid zygotes and the existence of recombinationally interconvertible genotypes for any heterozygous inversion complex: males of some of these genotypes will produce only aneuploid sperm, which can be used to rescue complementary aneuploid ova and selectively recover recombinational derivatives of inversions. Markers can be recombined into inversions through a sequence of selected single exchanges, and a novel type of duplication can be synthesized from overlapping inversions that has the characteristics of both insertional and tandem duplications; there are also applications to half-tetrad analyses.--Two cytogenetic screens are developed: (1) the dominant lethality of a large insertional-tandem duplication can be reverted by deletional events that give rise to net deficiencies or duplications, and (2) deficiencies and tandem duplications in proximal regions can be selectively recovered as the results of unequal exchanges within an inversion loop. Recombinants have been recovered between breakpoints separated by distances of as little as fifty bands, arguing against the existence of some small number of sites necessary for the initiation of recombinational pairing. In several instances, hyperploids for four to six numbered divisions were observed to be fertile in both sexes.

Aneuploidy↗
PubMed2007

Packing regularities in biological structures relate to their dynamics.

The high packing density inside proteins leads to certain geometric regularities and also is one of the most important contributors to the high extent of cooperativity manifested by proteins in their cohesive domain motions. The orientations between neighboring nonbonded residues in proteins substantially follow the similar geometric regularities, regardless of whether the residues are on the surface or buried, a direct result of hydrophobicity forces. These orientations are relatively fixed and correspond closely to small deformations from those of the face-centered cubic lattice, which is the way in which identical spheres pack at the highest density. Packing density also is related to the extent of conservation of residues, and we show this relationship for residue packing densities by averaging over a large sample or residue packings. There are three regimes: (1) over a broad range of packing densities the relationship between sequence entropy and inverse packing density is nearly linear, (2) over a limited range of low packing densities the sequence entropy is nearly constant, and (3) at extremely low packing densities the sequence entropy is highly variable. These packing results provide important justification for the simple elastic network models that have been shown for a large number of proteins to represent protein dynamics so successfully, even when the models are extremely coarse grained. Elastic network models for polymeric chains are simple and could be combined with these protein elastic networks to represent partially denatured parts of proteins. Finally, we show results of applications of the elastic network model to study the functional motions of the ribosome, based on its known structure. These results indicate expected correlations among its components for the step-wise processing steps in protein synthesis, and suggest ways to use these elastic network models to develop more detailed mechanisms, an important possibility because most experiments yield only static structures.

Amino Acid Sequence↗
PubMedDate not supplied

Phase-sensitive T1 inversion recovery imaging: a time-efficient interleaved technique for improved tissue contrast in neuroimaging.

BACKGROUND AND PURPOSE: High tissue contrast and short acquisition time are desirable when scanning patients. The purpose of this report is to describe the implementation of a new technique for generating high gray matter (GM) and white matter (WM) contrast in a short scan time, make a quantitative evaluation of the contrast efficiency, and explore its potential applications in neuroimaging. METHOD: A fully interleaved T1-weighted inversion recovery (T1IR) sequence with phase-sensitive reconstruction (PS-T1IR) is implemented. This sequence is compared with conventional T1-weighted spin-echo imaging (T1SE) and T1-weighted fluid-attenuated inversion recovery (T1FLAIR). The time efficiency and contrast enhancement have been quantitatively analyzed in normal volunteers. The performance of the sequence is evaluated in >30 patients with neurologic disorders. The sensitivity of PS-T1IR relative to T1SE in detecting gadolinium enhancements is also evaluated. RESULTS: PS-T1IR is more time-efficient than T1SE and generates better GM-WM contrast. It results in the best contrast-to-noise ratio (CNR) efficiency (1.16) compared with T1FLAIR (0.73) and T1SE (0.23). For a typical clinical protocol, PS-T1IR takes only 1:30 minutes versus 2:40 minutes for T1SE imaging for the whole brain coverage. Although gadolinium enhancements are detected with comparable sensitivity on both PS-T1IR and T1SE sequences, in certain instances, the latter sequence appears to be more sensitive in demonstrating gadolinium enhancements within WM. CONCLUSION: PS-T1IR has the highest CNR efficiency compared with T1FLAIR and T1SE. It is a very practical technique for neuroradiologic applications.

Brain Diseases↗
PubMed1990

Enzyme kinetics and relaxation measurements with surface coils.

A pulse sequence which produces the inversion of magnetization at a selected chemical shift for in vivo surface coil spectroscopy is proposed. The sequence uses a shaped, complex sech inversion pulse and "depth pulse" phase alternation. The sequence can be used for both in vivo inversion transfer and inversion recovery experiments.

Adenosine Triphosphate↗
PubMedDate not supplied

Chromosomal and behavioral studies of Mexican Drosophila. III. Inversion polymorphism of D. pseudoobscura.

Four new gene arrangements of chromosome 3 of Drosophila pseudoobscura are reported, as well as an updated phylogenetic sequence of the inversion polymorphism in this species. Evidence that the Tree Line gene arrangement of chromosome 3 was the original form in D. pseudoobscura, and that Central Mexico is the center of distribution of this species is discussed.

Animals↗
PubMed1999

An alternative inverse PCR (IPCR) method to amplify DNA sequences flanking Tn5 transposon insertions.

We have developed an alternative method to amplify DNA sequences flanking Tn5 transposon insertions. This method relies on the identical sequences of inverted terminal repeats, located at the 5' and 3' ends of Tn5, to determine the location and orientation of a transposon insertion within a restriction endonuclease fragment. From this information, PCR primers can be designed to selectively amplify by inverse PCR the DNA flanking one side of the transposon. This method avoids the problem of amplifying or cloning long sequences flanking Tn5. To demonstrate the applicability of this method, we generated Tn5 transposon mutants of Pseudomonas abietaniphila BKME-9 which no longer grew on dehydroabietic acid (DhA). The flanking sequence of one of the mutant (strain BKME-941) which accumulated 7-oxoDhA, was amplified.

Abietanes↗
PubMed2006

Detection of coronary stenoses with contrast enhanced, three-dimensional free breathing coronary MR angiography using the gadolinium-based intravascular contrast agent gadocoletic acid (B-22956).

PURPOSE: To determine the diagnostic value of the intravascular contrast agent gadocoletic acid (B-22956) in three-dimensional, free breathing coronary magnetic resonance angiography (MRA) for stenosis detection in patients with suspected or known coronary artery disease. METHODS: Eighteen patients underwent three-dimensional, free breathing coronary MRA of the left and right coronary system before and after intravenous application of a single dose of gadocoletic acid (B-22956) using three different dose regimens (group A 0.050 mmol/kg; group B 0.075 mmol/kg; group C 0.100 mmol/kg). Precontrast scanning followed a coronary MRA standard non-contrast T2 preparation/turbo-gradient echo sequence (T2Prep); for postcontrast scanning an inversion-recovery gradient echo sequence was used (real-time navigator correction for both scans). In pre- and postcontrast scans quantitative analysis of coronary MRA data was performed to determine the number of visible side branches, vessel length and vessel sharpness of each of the three coronary arteries (LAD, LCX, RCA). The number of assessable coronary artery segments was determined to calculate sensitivity and specificity for detection of stenosis > or = 50% on a segment-to-segment basis (16-segment-model) in pre- and postcontrast scans with x-ray coronary angiography as the standard of reference. RESULTS: Dose group B (0.075 mmol/kg) was preferable with regard to improvement of MR angiographic parameters: in postcontrast scans all MR angiographic parameters increased significantly except for the number of visible side branches of the left circumflex artery. In addition, assessability of coronary artery segments significantly improved postcontrast in this dose group (67 versus 88%, p < 0.01). Diagnostic performance (sensitivity, specificity, accuracy) was 83, 77 and 78% for precontrast and 86, 95 and 94% for postcontrast scans. CONCLUSIONS: The use of gadocoletic acid (B-22956) results in an improvement of MR angiographic parameters, asssessability of coronary segments and detection of coronary stenoses > or = 50%.

Aged↗
PubMed1997

alphavbeta3 integrin mediates the cell-adhesive capacity and biological activity of basic fibroblast growth factor (FGF-2) in cultured endothelial cells.

Fibroblast growth factor-2 (FGF-2) immobilized on non-tissue culture plastic promotes adhesion and spreading of bovine and human endothelial cells that are inhibited by anti-FGF-2 antibody. Heat-inactivated FGF-2 retains its cell-adhesive activity despite its incapacity to bind to tyrosine-kinase FGF receptors or to cell-surface heparan sulfate proteoglycans. Recombinant glutathione-S-transferase-FGF-2 chimeras and synthetic FGF-2 fragments identify two cell-adhesive domains in FGF-2 corresponding to amino acid sequences 38-61 and 82-101. Both regions are distinct from the FGF-receptor-binding domain of FGF-2 and contain a DGR sequence that is the inverse of the RGD cell-recognition sequence. Calcium deprivation, RGD-containing eptapeptides, soluble vitronectin (VN), but not fibronectin (FN), inhibit cell adhesion to FGF-2. Conversely, soluble FGF-2 prevents cell adhesion to VN but not FN, thus implicating VN receptor in the cell-adhesive activity of FGF-2. Accordingly, monoclonal and polyclonal anti-alphavbeta3 antibodies prevent cell adhesion to FGF-2. Also, purified human alphavbeta3 binds to immobilized FGF-2 in a cation-dependent manner, and this interaction is competed by soluble VN but not by soluble FN. Finally, anti-alphavbeta3 monoclonal and polyclonal antibodies specifically inhibit mitogenesis and urokinase-type plasminogen activator (uPA) up-regulation induced by free FGF-2 in endothelial cells adherent to tissue culture plastic. These data demonstrate that FGF-2 interacts with alphavbeta3 integrin and that this interaction mediates the capacity of the angiogenic growth factor to induce cell adhesion, mitogenesis, and uPA up-regulation in endothelial cells.

Amino Acid Motifs↗
PubMed2002

Molecular analysis of a haemagglutinin of Haemophilus paragallinarum.

The gene encoding a haemagglutinin of H. paragallinarum, hagA, has been identified and the full-length nucleotide sequence determined. A approximately 39 kDa protein, recognized by an anti-haemagglutinin monoclonal antibody, mAb4D, was purified from H. paragallinarum strain 0083 and the N-terminal sequence obtained. The full-length nucleotide sequence was obtained by inverse PCR and the deduced amino acid sequence of the protein encoded was shown to be similar to other outer-membrane proteins of closely related organisms in the HAP group (Haemophilus, Actinobacillus, Pasteurella), especially the P5 protein of Haemophilus influenzae. The hagA gene was cloned into a His-tag expression vector and overexpressed in Escherichia coli strain M15(pREP4). The identity of the purified recombinant protein as a H. paragallinarum haemagglutinin was confirmed by haemagglutination of chicken red blood cells and reactivity, in a Western blot, with the monoclonal antibody specific for the serovar A haemagglutinin.

Amino Acid Sequence↗
PubMed2006

Assaying chromosomal inversions by single-molecule haplotyping.

Inversions are an important form of structural variation, but they are difficult to characterize, as their breakpoints often fall within inverted repeats. We have developed a method called 'haplotype fusion' in which an inversion breakpoint is genotyped by performing fusion PCR on single molecules of human genomic DNA. Fusing single-copy sequences bracketing an inversion breakpoint generates orientation-specific PCR products, exemplified by a genotyping assay for the int22 hemophilia A inversion on Xq28. Furthermore, we demonstrated that inversion events with breakpoints embedded within long (>100 kb) inverted repeats can be genotyped by haplotype-fusion PCR followed by bead-based single-molecule haplotyping on repeat-specific markers bracketing the inversion breakpoint. We illustrate this method by genotyping a Yp paracentric inversion sponsored by >300-kb-long inverted repeats. The generality of our methods to survey for, and genotype chromosomal inversions should help our understanding of the contribution of inversions to genomic variation, inherited diseases and cancer.

Chromosome Inversion↗
PubMed2004

Mirror inversion of quantum states in linear registers.

Transfer of data in linear quantum registers can be significantly simplified with preengineered but not dynamically controlled interqubit couplings. We show how to implement a mirror inversion of the state of the register in each excitation subspace with respect to the center of the register. Our construction is especially appealing as it requires no dynamical control over individual interqubit interactions. If, however, individual control of the interactions is available then the mirror inversion operation can be performed on any substring of qubits in the register. In this case, a sequence of mirror inversions can generate any permutation of a quantum state of the involved qubits.

Journal Article↗
PubMed2005

Functional analysis of a reproductive organ predominant expressing promoter in cotton plants.

Transgenic Bt insect-resistant cotton plants have high insect resistance in the early stage of development, but relatively low resistance in the late stage. Substituting a reproductive organ-specific promoter for the CaMV35S promoter presently being used could be an ideal solution. For the first time, the promoter sequence of ADP-ribosylation factor 1 (arf1) gene was isolated from Gossypium hirsutumY18 by means of inverse PCR. The sequencing result discovered the unique structure of the arf1 promoter, including four promoter-specific elements, the initiator, TATA box, CAAT box and GC box, and also an intron in 5'-untranslation region. Four plant expression vectors were constructed for functional analysis of the promoter. Based on the pBl121 plant expression vector, four truncated arf1 promoters took the place of the CaMV35S promoter. These vectors were different only in their promoter regions. They were introduced into cotton plants via pollen tube pathway. Histochemical GUS staining and fluorescence quantitative analyses were performed to examine the expression patterns of the GUS gene driven by the 4 arf1 truncated promoters in transgenic cotton plants respectively. The results showed that the arf1 promoter was a typical reproductive organ-specific promoter. Hopefully, the arf1 promoter can be a regulatory element for designing cotton reproductive organs with desired characteristics.

ADP-Ribosylation Factor 1↗
PubMed2001

Characteristics of spongiform leukoencephalopathy induced by heroin: MRI detection.

OBJECTIVE: To elucidate the imaging characteristics of spongiform leukoencephalopathy induced by heroin and the diagnostic value of MRI examination. METHODS: Eleven cases of heroin addiction were examined by MRI. The sequences included T1-weighted imaging (T1WI), T2-weighted imaging (T2WI) and fast fluid-attenuated inversion recovery pulse sequence (Flair). RESULTS: Bilateral symmetrical lesions were located in the white matter of the cerebrum and cerebellum, the internal capsule in all cases, and the callosum in 6 cases. Elliptical lesions in the mesencephalon were found in two cases. These lesions were shown as hypointense signals on T1WI and hyperintense signals on T2WI and Flair's imaging. Cerebellar white matter suffered more severely, but the dentate nuclei were not invaded. CONCLUSION: Heroin-induced spongiform leukoencephalopathy has characteristic patterns in MRI, which are very specific to this form of the disease.

Adult↗
PubMedDate not supplied

Magnetic resonance imaging of meningiomas.

Twenty-eight patients with 32 meningiomas were studied on a 0.5-T superconductive magnetic resonance (MR) imager. This common, benign treatable tumor was more clearly seen on computed tomography (CT) than MRI in 53% of cases. This is a result of poor contrast between the tumor and the adjacent brain on all spin-echo and inversion-recovery pulse sequences. Those sequences that provide the greatest anatomic detail were best for identifying this low-contrast lesion. Inversion-recovery scans in particular demonstrated the tumor as a discrete hypointense mass (relative to nearby white matter) with excellent visualization of the dural base and white matter buckling indicative of extracerebral mass effect. Other characteristic features include: a hypointense rim because of the venous capsule (66%); mottling due to hypervascularity; a well defined edema collar that demarcates the tumor from adjacent brain; and hyperostosis with thickening of the calvaria and obliteration of its normal landmarks. MRI did not demonstrate tumor calcification but did demonstrate vascular encasement, displacement, and occlusion better than CT and as well as digital venous angiography.

Adult↗
PubMed1996

[Magnetic resonance tomography diagnosis of neuronal migration disorders].

Twenty-one MRI examinations of the brain were performed in 19 children with neuronal migration disorders. Multiplanar oriented spin-echo sequences were on a scanner with 1.5 T. In 8 children we performed an additional turbo-inversion recovery (TIR) sequence. Results of sonography or CT from five children were compared with MRI scans. Using the actual nomenclature, we found the following migration disorders: lissencephaly (n = 6), cobblestone lissencephaly with Walker-Warburg syndrome (WWS) (n = 2), polymicrogyria and schizencephaly (n = 2), focal heterotopia (n = 5), diffuse heterotopia (n = 2) and hemimegalencephaly (n = 2). MRI was superior to CT and sonography in all children. Except for the two boys with WWS, the TIR sequence was the best to demonstrate the changes in migration disorder because of the high contrast between gray and white matter. We demonstrate the characteristic features of the different migration disorders and compare them with the existing literature.

Brain↗
PubMed2001

Suppression of cerebrospinal fluid and blood flow artifacts in FLAIR MR imaging with a single-slab three-dimensional pulse sequence: initial experience.

The authors compared high-signal-intensity flow-related artifacts present with a conventional two-dimensional (2D) fluid-attenuated inversion recovery (FLAIR) sequence with those seen with a single-slab, three-dimensional (3D) FLAIR sequence. Four readers graded the subarachnoid space and intraventricular artifacts, the pulsation artifacts, and the conspicuity of cranial nerves in the posterior fossa. For all comparisons, differences between 2D and 3D images were highly statistically significant, with 3D imaging being superior in all cases.

Adult↗
PubMed1995

[Turbo-spin-echo (TSE) sequences with selective fat suppression (SPIR) compared with chemical shift sequences in MRI for differentiation of adrenal tumors. Spectral Presaturation by Inversion Recovery].

AIM: The value of chemical-shift-gradient-echo sequences and turbo-spin-echo sequences with selective fat suppression (SPIR = Spectral Presaturation by Inversion Recovery) in the differentiation of benign and malignant adrenal tumours was investigated. METHODS: Both techniques were performed at 1.5 T in 22 patients with 24 tumours. The loss of signal intensity of the tumour or of the signal intensity ratio between tumour and liver or muscle on the opposed phase Fast-Field-Echo (FFE) sequence in comparison to the in phase FFE sequence or on the TSE-SPIR sequence compared to the TSE sequence was the criterion for intratumoral lipid, suggesting a benign mass. RESULTS: The sensitivity and specificity of the chemical shift technique was 62-77 and 100%, respectively. In adrenal tumours larger than 1.5 cm sensitivity of the chemical-shift technique was 89%. On the contrary sensitivity of the TSE-SPIR sequence was only 11-78%. Both techniques had a specificity of 100%. CONCLUSION: The chemical shift technique is more accurate in the differentiation of adrenal masses than the TSE-SPIR sequence.

Adenoma↗
PubMed1989

[Magnetic resonance imaging of the metastatic vertebral tumor].

Fourty two patients underwent MR studies for a variety of lesions in the vertebral body. A 0.15-T MR system was employed. Twenty five patients were found to have malignant metastatic lesions (group 1); 16 had non-neoplastic lesions (group 2). The ability to discriminate between group 1 and group 2 with MR imaging was evaluated. All malignant metastatic lesions appeared as low intensity areas on both T1-weighted spin echo image and inversion recovery image, but 44 to 53% of the non-neoplastic lesions appeared as low intensity areas, respectively. The diagnostic ability with signal intensity of the vertebral column was evaluated on various pulse sequences; sensitivity of inversion recovery and T1-weighted spin echo image was 100%, in contrast specificity of these pulse sequences was 47 to 56%, overall accuracy was the highest on T1-weighted spin echo image (86%). The signal intensity of intervertebral disk was also evaluated in both groups. The intervertebral disks adjacent to the all malignant metastatic lesions showed normal intensity on both T1-weighted spin echo image and inversion recovery image, but non-neoplastic lesions showed variable intensities on images with all pulse sequences. The diagnostic ability with the signal intensities of the vertebral column and intervertebral disk was higher than that of the vertebral columns alone. Consequently accuracy was the highest in that case of both intervertebral disk and bone marrow which were imaged on T1-weighted spin echo (93%). We concluded that this diagnostic method was useful in distinguishing malignant metastatic from non-neoplastic lesions.

Adenocarcinoma↗