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Advanced imaging concepts: a pictorial glossary of CT and MRI technology.

This article serves as an illustrative glossary of concepts related to computed tomography (CT) and magnetic resonance imaging (MRI) technology. The principles of tomography, digital processing, image resolution, CT windowing, CT gray levels, contrast enhancement, and MRI spin echo pulse sequences are reviewed. Techniques not commonly described for use in animal patients are also introduced, and include gradient echo, short time of inversion recovery, fluid attenuated inversion recovery and fat saturation pulse sequences, fast imaging, MRI angiography, perfusion and diffusion imaging, brain activation, CT angiography/functional CT, interventional procedures, and three-dimensional CT.

Animals↗

Hb Jambol: a new hyperunstable hemoglobin causing severe hemolytic anemia.

We describe a new hyperunstable beta-chain variant due to a complex genomic rearrangement. The abnormal hemoglobin (Hb) was found as a de novo mutation in a 2-year-old Bulgarian girl with severe hemolytic anemia. The mutation was detected through RNA/DNA analysis. It represents a complex genomic rearrangement involving an insertion of 23 nts after IVS-II-535 (derived by triplication of the 12-nts adjacent sequence and subsequent deletion of 1 nt), a deletion of 310 nts extending from IVS-II-550 to the first nt of Cd 108 and an insertion of 28 nts at the deletion junctions (derived from the inverted sequence between nts +3,707 and +3,734 3' to the beta-globin gene termination codon). At the protein level this mutation leads to a deletion of 4 amino acid residues (Leu-Leu-Glu-Asn) at positions 105-108 and an insertion of 9 residues (Val-Pro-Ser-Val-Thr-Leu-Phe-Phe-Asp) at the same location, creating an abnormal elongated beta-chain of 151 amino acid residues. This highly unstable variant was named 'Hb Jambol' after the geographic location in which the patient resides.

Amino Acid Sequence↗

Rare interstitial deletion (2)(p11.2p13) in a child with pericentric inversion (2)(p11.2q13) of paternal origin.

An unbalanced 46,XY,der(2)del(2)(p11.2p13) inv(2)(p11.2q13) karyotype was found in a phenotypically abnormal child with a de novo interstitial deletion of band 2p12 associated with an inv(2)(p11.2q13) inherited from the father. The inv(2) is generally considered a benign familial variant without significant reproductive consequences. However, our findings led us to consider a previously proposed mechanism of unequal meiotic crossing over at the base of a parental inversion loop, which could lead to either a deletion or duplication of a segment adjacent to the inverted region in the offspring. This phenomenon has been reported in other inversions of chromosomes 1, 7, 13, 15, and 17 and may explain the origin of the deletion in our patient. Although repetitive sequences might be present around such inversions, which could predispose to de novo deletions independently of the inversion, current evidence including this case favors a proposed causal relationship between the parental inversion and the deletion in the child. Our review and results suggest there could be a small risk for a related imbalance to couples with an inv(2)(p11.2q13). For del(2)(p11.2p13), which is rare, a more distinct phenotype has been proposed herein. Our patient shared several findings with the three previously published cases, namely the broad nasal bridge, abnormal ears, high-arched palate, psychomotor retardation, and micrognathia. However, our patient also had sensorineural hearing loss and significant hypotonia, which have not been previously reported, thereby expanding our understanding of this rare deletion. Am. J. Med. Genet. 87:139-142, 1999. Published 1999 Wiley-Liss, Inc.

Abnormalities, Multiple↗

Magnetic resonance imaging and magnetization transfer in experimental myonecrosis in the rat.

Experimental myonecrosis--induced by injection of notexin into rat tibialis anterior muscle--and subsequent regeneration were studied from 1 h to 20 days postinjury with magnetic resonance imaging using conventional and magnetization transfer sequences, and these findings were correlated with histopathology. MR images revealed necrosis within 1 h postinjection. Histopathologically, necrotized fibers enlarged and intercellular spaces widened, indicating intracellular and extracellular edema, which began to decrease after 48 h, whereafter the formation of new myofibers predominated. T2 increased progressively until 7.5 h, while T1 increased until 24 h. Magnetization transfer contrast (MTC) and magnetization transfer rate (Rwm) decreased rapidly postinjection; the decrease in Rwm lasted longer than in MTC (96 h versus 48 h, respectively). Spin echo, inversion recovery and magnetization transfer sequences revealed the lesions equally effectively. MR images and relaxation parameters reflect well the extent of histopathological injury and edema in the acute phase, whereas specific tissue changes in the regenerative phase were not detectable by MRI. MT imaging and especially magnetization transfer rate are as sensitive as conventional T2 contrast to alterations in water imbalance.

Animals↗

Lineage sorting accounting for the disassociation between chloroplast and mitochondrial lineages in oaks of southern France.

Dumolin-Lapégue et al. (Mol. Biol. Evol. 15: 1321-1331. 1998) suggested that recurrent inversions of a 4-bp sequence of the mtDNA nad4-1/2 locus due to intramolecular recombination were responsible for the disassociation of chloroplast and mitochondrial genomes of French oaks. Based on their PCR-RFLP (PCR-restriction fragment length polymorphism) data obtained from three noncoding spacers, a minimum spanning network representing the phylogeny of the cpDNA was reconstructed. The mapping of alleles b and c of the mtDNA nad4-1/2 locus on the cpDNA network revealed a nonrandom distribution, which contradicted the expected patterns when repeated, and ongoing inversions had been occurring. The fact that polymorphisms (a mixed c + d type) were mostly restricted to the interior nodes of the network, which represented ancient haplotypes and geographically coincided with probable glacial refugia in southern Europe, agreed with a migrant-pool model. Evidence of a widespread pattern of polymorphism distribution indicated that mtDNA haplotypes were likely to be more ancient than the cpDNA haplotypes. Lineage sorting, due to relative age of cpDNA vs. mtDNA, plus the specific migratory mode, which recruited colonists from a random sample of resource populations during glacial expansion (thereby extending the lineage sorting period, LSP), may have resulted in the disassociation of chloroplast and mitochondrial genomes in oaks.

Chloroplasts↗

Analysis of direct and inverted DJH rearrangements in a human Ig heavy chain transgenic minilocus.

D to JH rearrangement can occur either by a deletional or an inversional mechanism. In this study, we have analyzed deletional and inversional D to JH recombination in a human Ig heavy chain transgenic minilocus. The analysis of these events in a transgenic minilocus rather than in vivo in the human is simplified by the presence of a limited number of well defined VH, D, and JH gene segments in the minilocus. We show that in the transgenic minilocus, all D gene segments can be rearranged by deletion and virtually all can be rearranged by inversion. We also show that depending upon the D gene segment, rearrangement by deletion occurs approximately 1 to 1000 times more frequently than rearrangement by inversion. Our data suggest that in vivo, signal and coding end sequences are the major influences on the rearrangement frequency of a particular gene segment in a given orientation rather than its position within the transgenic locus. Additionally, our data indicate that intronic and recombination signal sequences are involved in the bias for deletion over inversion rather than the recombinase machinery itself.

Animals↗

Polytene chromosomes as indicators of phylogeny in several species groups of Drosophila.

BACKGROUND: Polytene chromosome banding patterns have long been used by Drosophila evolutionists to infer degree of relatedness among taxa. Recently, nucleotide sequences have preempted this traditional method. We place the classical Drosophila evolutionary biology tools of polytene chromosome inversion analysis in a phylogenetic context and assess their utility in comparison to nucleotide sequences. RESULTS: A simultaneous analysis framework was used to examine the congruence of the chromosomal inversion data with more recent DNA sequence data in four Drosophila species groups - the melanogaster, virilis, repleta, and picture wing. Inversions and nucleotides were highly congruent with one another based on incongruence length difference and partitioned Bremer support values. Inversion phylogenies were less resolved because of fewer numbers of characters. Partitioned Bremer supports, corrected for the number of characters in each matrix, were higher for inversion matrices. CONCLUSIONS: Polytene chromosome data are highly congruent with DNA sequence data and, when placed in a simultaneous analysis framework, are shown to be more information rich than nucleotide data.

Animals↗

Variations in T1 and T2 relaxation times of normal appearing white matter and lesions in multiple sclerosis.

OBJECTIVE: To investigate the variation in T1 and T2 relaxation times of normal appearing white matter (NAWM) and lesions in multiple sclerosis (MS) throughout the brain. BACKGROUND: The magnetic resonance imaging (MRI) sequence fast FLAIR (fluid attenuated inversion recovery) has demonstrated overall increased lesion detection when compared to conventional or fast spin echo (FSE) but fewer lesions in the posterior fossa and spinal cord. The reasons for this are unknown, but may be due to variations in the T1 and T2 relaxation times within NAWM and MS lesions. METHOD: Ten patients and 10 controls underwent MRI of the brain which involved FSE, fast FLAIR and the measurement of T1 and T2 relaxation times. RESULTS: Of 151 lesions analysed (22 infra-tentorial, 129 supra-tentorial), eight were missed by the fast FLAIR sequence. T1 and T2 relaxation times in normal controls were longer in the infra-tentorial, than supra-tentorial, region. Patient NAWM relaxation times were prolonged compared with control values in both regions. Lesions demonstrated longer relaxation times than either control white matter or patient NAWM in both regions, however this difference was less marked infra-tentorially. The eight posterior fossa lesions not visible on the fast FLAIR sequence were characterised by short T1 and T2 relaxation times which overlapped with the patient NAWM for both T1 and T2 and with control values for T2 relaxation times. CONCLUSION: Both lesion and NAWM relaxation time characteristics vary throughout the brain. The T1 and T2 relaxation times of infra-tentorial lesions are closer to the relaxation times of local NAWM than supra-tentorial lesions, resulting in reduced contrast between posterior fossa lesions and the background NAWM. Consequently the characteristics of some lesions overlap with those of NAWM resulting in reduced conspicuity. By utilising this information, it may be possible to optimise fast FLAIR sequences to improve infra-tentorial lesion detection.

Brain↗

A general method of polymerase-chain-reaction-enabled protein domain mutagenesis: construction of a human protein S-osteonectin gene.

Polymerase chain reaction (PCR) amplification was employed to construct a mosaic gene consisting of the propeptide region of protein S and the glutamic acid-rich domain of osteonectin. The strategy is straightforward, results in large amounts of material, and is universally applicable for the generation of protein domain chimeras. In some cases 10% dimethyl sulfoxide aided the amplification. Four base CCGC "clamp" sequences adjacent to BamHI restriction sites at the ends of the PCR products were used to enhance the ligation of products. A hybrid inverse complement oligonucleotide primer composed of sequences containing 20 nucleotides of protein S and 16 nucleotides of osteonectin was used in the first round of PCR. An additional osteonectin sequence was added to the initial amplified product by performing PCR using a second "boot-strap" primer containing 18 nucleotides of osteonectin. Primers used to amplify osteonectin encompassed the 146-aminoacid NH2-terminal half of osteonectin. The double-stranded first-round fragments of protein S-osteonectin and osteonectin were subsequently mixed together and one elongation cycle of PCR was performed. Annealing occurred as the result of the 34-base-pair overlap region composed of osteonectin sequence. Taq polymerase was used for elongation with subsequent recombinant DNA synthesis. After elongation, external primers were added to amplify the protein S-osteonectin gene construct. The protocol we have developed allows noncoding and coding segments of DNA to be linked, GC-rich areas of DNA to be amplified, hybridization temperatures to be increased, annealing times to be reduced, and PCR of products to be subcloned.

Base Sequence↗

Enhanced viability imaging: improved contrast in myocardial delayed enhancement using dual inversion time subtraction.

In delayed contrast-enhanced MRI for the assessment of myocardial viability, the TI time in a gated inversion-recovery segmented gradient echo sequence is usually selected to null signal from normal myocardium. Although this TI time generates good contrast between the enhancing infarcted tissue and normal myocardium, there is usually less contrast between the infarct and the blood pool. A subtractive technique utilizing two acquisitions at a long and short TI time is proposed to improve the delineation between infarct-blood and infarct-myocardium. The concept was demonstrated in six mongrel dogs with reperfused myocardial infarction. Infarct-normal myocardium contrast (signal difference) using the proposed enhanced viability imaging (ENVI) technique was 142 +/- 50% (P < 0.001) that of standard magnitude inversion recovery (IR), while at the same TI time for the primary image, infarct-blood contrast, was 247 +/- 136% (P < 0.002) that of magnitude IR. Accounting for increased noise due to the subtraction, signal difference-to-noise ratios (SDNR) did not show a significant change for infarct-myocardium but infarct-blood SDNR for ENVI was 174 +/- 105% that of magnitude-IR (P < 0.03). Thus, marked improvement in the delineation of the infarcted zone was noted over a range of TI times.

Animals↗

R46 encodes a site-specific recombination system interchangeable with the resolution function of TnA.

Transposition of Tn4 onto the IncN plasmic R46 generates unstable DNA molecules. The R46::TnA recombinant plasmids undergo further DNA rearrangements which depend on the orientation in which the TnA element is inserted into the plasmid, and deletions and inversions of R46 and TnA sequences have been observed. Both types of rearrangement have the same specific endpoints, one within TnA and one located between the R46 coordinates, 36.0 and 37.0. The results are consistent with the operation of a recA-independent, site-specific recombination system utilizing, at least in part, the transposon cointegrate resolution system of TnA, together with R46-encoded functions. Data are presented that indicate that R46 encodes analogs of both the res site of TnA and its tnpR gene, although little homology between this element and the plasmid is apparent. Models for the TnA-induced generation of site-specific deletions and inversions upon transposition of TnA to R46 are presented.

Chromosome Deletion↗

The use of an improved transposon mutagenesis system for DNA sequencing leads to the characterization of a new insertion sequence of Streptomyces lividans 66.

A DNA sequencing strategy was developed based on the tetracycline resistance transposon Tn1721. A universal M13 primer binding site (UP) for DNA sequencing and restriction sites for mapping were inserted near one end of Tn1721 and the new derivative, Tn5491, introduced onto a conjugative F' plasmid. The target sequence is inserted between two inverted resolution sites (res) of Tn1721 present on the high-copy plasmid pJOE2114. Due to the inviability of long palindromic sequences in Escherichia coli insertions between the inversely orientated res sites of pJOE2114 are positively selected. Transposition of Tn5491 into the target sequence is selected by cointegrate formation of Tn5491 during transposition, mating and transfer of the nonconjugative sequencing vector. After cointegrate resolution, the additional res sites in the vector result in a second site-specific recombination removing most of the transposon (except of 136 bp) and part of the target sequence. The reduced plasmid sizes and the use of the universal primer improved the quality of the sequencing results obtained on an automated fluorescent sequencer. A 3.35-kb EcoRI fragment from the 30-kb terminal inverted repeats (TIR) of the Streptomyces lividans chromosome was sequenced by this method. A 1304-bp sequence was found on this fragment with the features of insertion elements. The element called IS1372 had 27-bp IR and two potential open reading frames. The predicted gene products had similar sizes and high similarity to gene products encoded by insertion sequences of the IS3 family. Furthermore, a potential signal stimulating ribosomal shifts and typical for members of the IS3 family was identified. Five to seven copies of IS1372 were found in different strains of S. lividans but none in other Streptomyces species tested.

Amino Acid Sequence↗

Riemann zeros, prime numbers, and fractal potentials.

Using two distinct inversion techniques, the local one-dimensional potentials for the Riemann zeros and prime number sequence are reconstructed. We establish that both inversion techniques, when applied to the same set of levels, lead to the same fractal potential. This provides numerical evidence that the potential obtained by inversion of a set of energy levels is unique in one dimension. We also investigate the fractal properties of the reconstructed potentials and estimate the fractal dimensions to be D=1.5 for the Riemann zeros and D=1.8 for the prime numbers. This result is somewhat surprising since the nearest-neighbor spacings of the Riemann zeros are known to be chaotically distributed, whereas the primes obey almost Poissonlike statistics. Our findings show that the fractal dimension is dependent on both level statistics and spectral rigidity, Delta(3), of the energy levels.

Journal Article↗

AAPM/RSNA physics tutorial for residents: fundamental physics of MR imaging.

Learning the basic concepts required to understand magnetic resonance (MR) imaging is a straightforward process. Although the individual concepts are simple, there are many concepts to learn and retain simultaneously; this situation may give the illusion that learning the physics of MR imaging is complicated. It is important for the radiologist who interprets MR images to understand the methods used to create the images because image contrast specifically depends on how the image data were acquired. Initial concepts include formation of magnetic fields from electric currents in loops of wire, the resonance phenomenon, the hydrogen proton and its frequency of precession, and absorption of radiofrequency energy. These concepts can then be applied to learn about T1 and T2 relaxation and contrast and how the acquisition parameters of echo time and repetition time can be used to achieve these image contrasts. Basic pulse sequences include the spin-echo, multiecho spin-echo, turbo spin-echo, inversion-recovery, and gradient-recalled-echo sequences.

Internship and Residency↗

Magnetic resonance imaging: comparative study of radiofrequency pulse techniques in the evaluation of focal cerebral ischemia.

The recently developed technique of magnetic resonance (MR) imaging utilizes radiofrequency (RF) radiation in the presence of a strong magnetic field to provide cross sectional displays of body anatomy similar to computed tomography. When utilizing MR, the operator alters tissue contrast electronically by changing RF pulse sequences. The three most frequently used RF pulse sequences are partial-saturation (PS), inversion-recovery (IR), and spin-echo (SE). We evaluated the sensitivity of these RF sequences to detect ischemic changes in our primate model. Serial MR scans were carried out using all three pulse formats 5 to 60 hours after middle cerebral artery occlusion (MCAO) in four animals. SE- and IR-sequenced proton MR images readily identified areas of evolving infarct 5 to 60 hours after MCAO, whereas PS scans that were performed during this acute period appeared normal. From 24 to 60 hours after MCAO, PS-sequenced scans showed focal areas of progressively decreasing signal intensity. However, SE and IR scans performed at the same intervals always demonstrated more extensive tissue changes. The basis of MR imaging, the effects of altering RF pulse sequences, and the resulting interpretation of changes observed in MR sections are presented.

Animals↗

Towards a single-sequence neurologic magnetic resonance imaging examination: multiple-contrast images from an IR TrueFISP experiment.

OBJECTIVE: The objective of this study was to reconstruct images bearing multiple contrasts from a single sequence magnetic resonance imaging (MRI) experiment. MATERIALS AND METHODS: Using a segmented IR-TrueFISP imaging sequence, the signal recovery after inversion and alpha/2 preparation was sampled in 6 volunteers. These images were used to generate T1, T2, and spin-density maps, allowing construction of images with multiple contrasts, including T1-, T2-, spin-density-weighted, and also FLAIR contrast. Traditionally acquired images bearing the corresponding contrast were obtained for comparison. Regression analysis was performed to compare the synthetic and traditionally acquired images for the whole brain and a region of interest in the occipital region. RESULTS: The synthetic images closely reproduced the contrast from the "standard" examination. Using regression analysis, the obtained image signal intensities for the calculated images compare favorably (P <0.0001-<<0.000001) with images acquired using multiple sequences. CONCLUSIONS: Perfectly registered images with any desired contrast based on T1, T2, and spin density, along with underlying quantitative maps, can be obtained using a single IR-TrueFISP sequence.

Brain↗

MR pulse sequences for selective relaxation time measurements: a phantom study.

The accuracy of relaxation time measurements of spectroscopic inversion recovery and CPMG multi-echo pulse sequences together with ISIS and stimulated echo-pulse methods have been tested on a reference phantom (test object no. 5, of the EEC Concerted Research Project). For the measurements a Siemens Magnetom wholebody magnetic resonance scanner operating at 1.5 Tesla was used. For comparison six imaging pulse sequences for relaxation time measurements were tested on the same phantom. The spectroscopic pulse sequences all had an accuracy better than 10% of the reference values.

Humans↗