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Byung Il Lee

Publications and source records attributed to Byung Il Lee.

At least 19 recordsLinked to original sources
PubMed2006

Optimization of current injection pulse width in MREIT.

In magnetic resonance electrical impedance tomography (MREIT), we inject electrical current into a volume conductor to induce a distribution of magnetic flux density. By measuring the internal magnetic flux density using an MR scanner, we reconstruct images of cross-sectional conductivity and current density distributions. One of the most important technical problems in MREIT is to reduce the noise level in the measured magnetic flux density data since it limits the quality of reconstructed images. The noise level is inversely proportional to the current injection pulse width and signal-to-noise ratio (SNR) of MR magnitude images. Knowing that we cannot simultaneously increase both factors for a chosen echo time, we show that there is an optimal current injection pulse width minimizing the noise level. Experimental results demonstrate that the optimal current injection pulse width and appropriately chosen data acquisition time considerably reduce the noise level. We suggest future works to reduce undesirable side effects due to an increased data acquisition time.

Electric Conductivity↗
PubMed2006

Phase artefact reduction in magnetic resonance electrical impedance tomography (MREIT).

Cross-sectional conductivity imaging in magnetic resonance electrical impedance tomography (MREIT) requires the measurement of internal magnetic flux density using an MRI scanner. Current injection MRI techniques have been used to induce magnetic flux density distributions that appear in phase parts of the obtained MR signals. Since any phase error, as well as noise, deteriorates the quality of reconstructed conductivity images, we must minimize them during the data acquisition process. In this paper, we describe a new method to correct unavoidable phase errors to reduce artefacts in reconstructed conductivity images. From numerical simulations and phantom experiments, we found that the zeroth- and first-order phase errors can be effectively minimized to produce better conductivity images. The promising results suggest that this technique should be employed together with improved MREIT pulse sequences in future studies of high-resolution conductivity imaging.

Algorithms↗
PubMed2006

High field MREIT: setup and tissue phantom imaging at 11 T.

Magnetic resonance electrical impedance tomography (MREIT) has the potential to provide conductivity and current density images with high spatial resolution and accuracy. Recent experimental studies at a field strength of 3 T showed that the spatial resolution of conductivity and current density images may be similar to that of conventional MR images as long as enough current is injected, at least 20 mA when the object being imaged has a size similar to the human head. To apply the MREIT technique to image small conductivity changes using less injection current, we performed MREIT studies at 11 T field strength, where noise levels in measured magnetic flux density data are significantly lower. In this paper we present the experimental results of imaging biological tissues with different conductivity values using MREIT at 11 T. We describe technical difficulties encountered in using high-field MREIT systems and possible solutions. High-field MREIT is suggested as a research tool for obtaining accurate conductivity data from tissue samples and animal subjects.

Artifacts↗
PubMed2006

Basic setup for breast conductivity imaging using magnetic resonance electrical impedance tomography.

We present a new medical imaging technique for breast imaging, breast MREIT, in which magnetic resonance electrical impedance tomography (MREIT) is utilized to get high-resolution conductivity and current density images of the breast. In this work, we introduce the basic imaging setup of the breast MREIT technique with an investigation of four different imaging configurations of current-injection electrode positions and pathways through computer simulation studies. Utilizing the preliminary findings of a best breast MREIT configuration, additional numerical simulation studies have been carried out to validate breast MREIT at different levels of SNR. Finally, we have performed an experimental validation with a breast phantom on a 3.0 T MREIT system. The presented results strongly suggest that breast MREIT with careful imaging setups could be a potential imaging technique for human breast which may lead to early detection of breast cancer via improved differentiation of cancerous tissues in high-resolution conductivity images.

Algorithms↗
PubMed2006

Conductivity image reconstruction from defective data in MREIT: numerical simulation and animal experiment.

Magnetic resonance electrical impedance tomography (MREIT) is designed to produce high resolution conductivity images of an electrically conducting subject by injecting current and measuring the longitudinal component, Bz, of the induced magnetic flux density B = (Bx, By, Bz). In MREIT, accurate measurements of Bz are essential in producing correct conductivity images. However, the measured Bz data may contain fundamental defects in local regions where MR magnitude image data are small. These defective Bz data result in completely wrong conductivity values there and also affect the overall accuracy of reconstructed conductivity images. Hence, these defects should be appropriately recovered in order to carry out any MREIT image reconstruction algorithm. This paper proposes a new method of recovering Bz data in defective regions based on its physical properties and neighboring information of Bz. The technique will be indispensable for conductivity imaging in MREIT from animal or human subjects including defective regions such as lungs, bones, and any gas-filled internal organs.

Algorithms↗
PubMed2005

Noise analysis in magnetic resonance electrical impedance tomography at 3 and 11 T field strengths.

In magnetic resonance electrical impedance tomography (MREIT), we measure the induced magnetic flux density inside an object subject to an externally injected current. This magnetic flux density is contaminated with noise, which ultimately limits the quality of reconstructed conductivity and current density images. By analysing and experimentally verifying the amount of noise in images gathered from two MREIT systems, we found that a carefully designed MREIT study will be able to reduce noise levels below 0.25 and 0.05 nT at main magnetic field strengths of 3 and 11 T, respectively, at a voxel size of 3 x 3 x 3 mm(3). Further noise level reductions can be achieved by optimizing MREIT pulse sequences and using signal averaging. We suggest two different methods to estimate magnetic flux noise levels, and the results are compared to validate the experimental setup of an MREIT system.

Electric Impedance↗
PubMed2005

Crystallization and preliminary X-ray crystallographic analysis of UDP-N-acetylglucosamine enolpyruvyl transferase from Haemophilus influenzae in complex with UDP-N-acetylglucosamine and fosfomycin.

The bacterial enzyme UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes the first committed step of peptidoglycan biosynthesis, i.e., transfer of enolpyruvate from phosphoenolpyruvate to UDP-N-acetyl-glucosamine. We have overexpressed the enzyme from Haemophilus influenzae in Escherichia coli and crystallized it in the apo-form, as well as in a complex with UDP-N-acetylglucosamine and fosfomycin using ammonium sulfate as the precipitant. X-ray diffraction data from a crystal of the apo-form were collected to 2.8 A resolution at 293 K. The crystal quality was improved by co-crystallization with UDP-N-acetylglucosamine and fosfomycin. X-ray data to 2.2 A have been collected at 100 K from a flash-frozen crystal of the complex. The complex crystals belong to the orthorhombic space group I222 (or I212121) with unit-cell parameters of a = 63.7, b = 124.5, and c = 126.3 A. Assuming a monomer of the recombinant enzyme in the crystallographic asymmetric unit, the calculated Matthews parameter (VM) is 2.71 A3 Da-1 and solvent content is 54.6%.

Alkyl and Aryl Transferases↗
PubMed2005

Electrical conductivity images of biological tissue phantoms in MREIT.

We present cross-sectional conductivity images of two biological tissue phantoms. Each of the cylindrical phantoms with both diameter and height of 140 mm contained chunks of biological tissues such as bovine tongue and liver, porcine muscle and chicken breast within a conductive agar gelatin as the background medium. We attached four recessed electrodes on the sides of the phantom with equal spacing among them. Injecting current pulses of 480 or 120 mA ms into the phantom along two different directions, we measured the z-component Bz of the induced magnetic flux density B=(Bx, By, Bz) with a magnetic resonance electrical impedance tomography (MREIT) system based on a 3.0 T MRI scanner. Using the harmonic Bz algorithm, we reconstructed cross-sectional conductivity images from the measured Bz data. Reconstructed images clearly distinguish different tissues in terms of both their shapes and conductivity values. In this paper, we experimentally demonstrate the feasibility of the MREIT technique in producing conductivity images of different biological soft tissues with a high spatial resolution and accuracy when we use a sufficient amount of the injection current.

Algorithms↗
PubMed2005

Harmonic decomposition in PDE-based denoising technique for magnetic resonance electrical impedance tomography.

Recent progress in magnetic resonance electrical impedance tomography (MREIT) research via simulation and biological tissue phantom studies have shown that conductivity images with higher spatial resolution and accuracy are achievable. In order to apply MREIT to human subjects, one of the important remaining problems to be solved is to reduce the amount of the injection current such that it meets the electrical safety regulations. However, by limiting the amount of the injection current according to the safety regulations, the measured MR data such as the z-component of magnetic flux density Bz in MREIT tend to have low SNR and get usually degraded in their accuracy due to the nonideal data acquisition system of an MR scanner. Furthermore, numerical differentiations of the measured Bz required by the conductivity image reconstruction algorithms tend to further deteriorate the quality and accuracy of the reconstructed conductivity images. In this paper, we propose a denoising technique that incorporates a harmonic decomposition. The harmonic decomposition is especially suitable for MREIT due to the physical characteristics of Bz. It effectively removes systematic and random noises, while preserving important key features in the MR measurements, so that improved conductivity images can be obtained. The simulation and experimental results demonstrate that the proposed denoising technique is effective for MREIT, producing significantly improved quality of conductivity images. The denoising technique will be a valuable tool in MREIT to reduce the amount of the injection current when it is combined with an improved MREIT pulse sequence.

Algorithms↗
PubMed2004

Crystal structure of the schiff base intermediate prior to decarboxylation in the catalytic cycle of aspartate alpha-decarboxylase.

l-Aspartate alpha-decarboxylase (ADC), encoded by the panD gene, catalyzes the conversion of l-aspartate into beta-alanine. In the microorganisms, beta-alanine is required for the synthesis of pantothenate (vitamin B(5)), which is the precursor of 4'-phosphopantetheine and coenzyme A. We have determined the crystal structure of Helicobacter pylori ADC, a tetrameric enzyme, in two forms: the apo structure at 2.0 A resolution and the isoasparagine complex structure at 1.55 A resolution. All subunits of the tetramer are self-processed at the Gly24-Ser25 linkage, producing the smaller beta chain (residues 1-24) and the larger alpha chain (residues 25-117). Each subunit contains nine beta-strands and three alpha-helices; it is folded into the double-psi beta-barrel structure. In the apo structure, the new amino terminus of the alpha chain, Ser25, is converted into a pyruvoyl group. In the isoasparagine complex structure, the substrate analog is covalently attached to the pyruvoyl group. This structure represents the enzyme-substrate Schiff base intermediate that was proposed to form prior to the decarboxylation step in the catalytic cycle of ADC. Thus our study provides direct structural evidence for the reaction mechanism of ADC.

Amino Acid Sequence↗
PubMed2004

Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair.

RecR, together with RecF and RecO, facilitates RecA loading in the RecF pathway of homologous recombinational DNA repair in procaryotes. The human Rad52 protein is a functional counterpart of RecFOR. We present here the crystal structure of RecR from Deinococcus radiodurans (DR RecR). A monomer of DR RecR has a two-domain structure: the N-terminal domain with a helix-hairpin-helix (HhH) motif and the C-terminal domain with a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif. Four such monomers form a ring-shaped tetramer of 222 symmetry with a central hole of 30-35 angstroms diameter. In the crystal, two tetramers are concatenated, implying that the RecR tetramer is capable of opening and closing. We also show that DR RecR binds to both dsDNA and ssDNA, and that its HhH motif is essential for DNA binding.

Amino Acid Sequence↗
PubMed2004

Crystallization and preliminary X-ray crystallographic analysis of nicotinic acid mononucleotide adenylyltransferase from Pseudomonas aeruginosa.

The enzyme nicotinic acid mononucleotide adenylyltransferase (NaMN AT; EC 2.7.7.18) is essential for the synthesis of nicotinamide adenine dinucleotide and is a potential target for antibiotics. It catalyzes the transfer of an adenyl group from ATP to nicotinic acid mononucleotide to form nicotinic acid adenine dinucleotide. NaMN AT from Pseudomonas aeruginosa was overexpressed in Escherichia coli and crystallized at 291 K using 100 mM bis-Tris propane pH 7.0, 700 mM trisodium citrate and 15%(v/v) glycerol. X-ray diffraction data have been collected to 1.70 A. The crystals are tetragonal, belonging to space group P4(1)22 (or P4(3)22), with unit-cell parameters a = b = 65.02, c = 109.80 A. The presence of one monomer in the asymmetric unit gives a reasonable V(M) of 2.15 A(3) Da(-1), with a solvent content of 42.7%.

Amino Acid Sequence↗
PubMed2004

Crystallization and preliminary X-ray crystallographic analysis of the RecR protein from Deinococcus radiodurans, a member of the RecFOR DNA-repair pathway.

The RecR protein plays a key role in the RecFOR pathway of recombination, which is necessary for the repair of ssDNA gaps. RecR from Deinococcus radiodurans has been overexpressed in Escherichia coli and crystallized at 297 K using polyethylene glycol 1000 as a precipitant. X-ray diffraction data to 2.90 A resolution have been collected at 100 K using Cu Kalpha X-rays from a mercury-soaked crystal. The crystal belongs to space group C222(1), with unit-cell parameters a = 106.96, b = 122.25, c = 156.01 A. The asymmetric unit contains four monomers of RecR, with a crystal volume per protein weight (V(M)) of 2.57 A(3) Da(-1) and a solvent content of 51.0%.

Bacterial Proteins↗
PubMed2004

Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase.

1,4-beta-D-Xylan is the major component of plant cell-wall hemicelluloses. beta-D-Xylosidases are involved in the breakdown of xylans into xylose and belong to families 3, 39, 43, 52, and 54 of glycoside hydrolases. Here, we report the first crystal structure of a member of family 39 glycoside hydrolase, i.e. beta-D-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI. This study also represents the first structure of any beta-xylosidase of the above five glycoside hydrolase families. Each monomer of T. saccharolyticum beta-xylosidase comprises three distinct domains; a catalytic domain of the canonical (beta/alpha)(8)-barrel fold, a beta-sandwich domain, and a small alpha-helical domain. We have determined the structure in two forms: D-xylose-bound enzyme and a covalent 2-deoxy-2-fluoro-alpha-D-xylosyl-enzyme intermediate complex, thus providing two snapshots in the reaction pathway. This study provides structural evidence for the proposed double displacement mechanism that involves a covalent intermediate. Furthermore, it reveals possible functional roles for His228 as the auxiliary acid/base and Glu323 as a key residue in substrate recognition.

Catalysis↗
PubMed2003

Conductivity and current density image reconstruction using harmonic Bz algorithm in magnetic resonance electrical impedance tomography.

Magnetic resonance electrical impedance tomography (MREIT) is to provide cross-sectional images of the conductivity distribution sigma of a subject. While injecting current into the subject, we measure one component Bz of the induced magnetic flux density B = (Bx, By, Bz) using an MRI scanner. Based on the relation between (inverted delta)2 Bz and inverted delta sigma, the harmonic Bz algorithm reconstructs an image of sigma using the measured Bz data from multiple imaging slices. After we obtain sigma, we can reconstruct images of current density distributions for any given current injection method. Following the description of the harmonic Bz algorithm, this paper presents reconstructed conductivity and current density images from computer simulations and phantom experiments using four recessed electrodes injecting six different currents of 26 mA. For experimental results, we used a three-dimensional saline phantom with two polyacrylamide objects inside. We used our 0.3 T (tesla) experimental MRI scanner to measure the induced Bz. Using the harmonic Bz algorithm, we could reconstruct conductivity and current density images with 82 x 82 pixels. The pixel size was 0.6 x 0.6 mm2. The relative L2 errors of the reconstructed images were between 13.8 and 21.5% when the signal-to-noise ratio (SNR) of the corresponding MR magnitude images was about 30. The results suggest that in vitro and in vivo experimental studies with animal subjects are feasible. Further studies are requested to reduce the amount of injection current down to less than 1 mA for human subjects.

Algorithms↗
PubMed2003

Three-dimensional forward solver and its performance analysis for magnetic resonance electrical impedance tomography (MREIT) using recessed electrodes.

In magnetic resonance electrical impedance tomography (MREIT), we try to reconstruct a cross-sectional resistivity (or conductivity) image of a subject. When we inject a current through surface electrodes, it generates a magnetic field. Using a magnetic resonance imaging (MRI) scanner, we can obtain the induced magnetic flux density from MR phase images of the subject. We use recessed electrodes to avoid undesirable artefacts near electrodes in measuring magnetic flux densities. An MREIT image reconstruction algorithm produces cross-sectional resistivity images utilizing the measured internal magnetic flux density in addition to boundary voltage data. In order to develop such an image reconstruction algorithm, we need a three-dimensional forward solver. Given injection currents as boundary conditions, the forward solver described in this paper computes voltage and current density distributions using the finite element method (FEM). Then, it calculates the magnetic flux density within the subject using the Biot-Savart law and FEM. The performance of the forward solver is analysed and found to be enough for use in MREIT for resistivity image reconstructions and also experimental designs and validations. The forward solver may find other applications where one needs to compute voltage, current density and magnetic flux density distributions all within a volume conductor.

Algorithms↗
PubMed2003

Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition.

tRNA(m(1)G37)methyltransferase (TrmD) catalyzes the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to G(37) within a subset of bacterial tRNA species, which have a G residue at the 36th position. The modified guanosine is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation. Here we report four crystal structures of TrmD from Haemophilus influenzae, as binary complexes with either AdoMet or S-adenosyl-L-homocysteine (AdoHcy), as a ternary complex with AdoHcy and phosphate, and as an apo form. This first structure of TrmD indicates that it functions as a dimer. It also suggests the binding mode of G(36)G(37) in the active site of TrmD and the catalytic mechanism. The N-terminal domain has a trefoil knot, in which AdoMet or AdoHcy is bound in a novel, bent conformation. The C-terminal domain shows structural similarity to trp repressor. We propose a plausible model for the TrmD(2)-tRNA(2) complex, which provides insights into recognition of the general tRNA structure by TrmD.

Amino Acid Sequence↗