Tae-Lim Kim

Methods and evaluations of MRI content-adaptive finite element mesh generation for bioelectromagnetic problems

In studying bioelectromagnetic problems, finite element analysis (FEA) offers several advantages over conventional methods such as the boundary element method. It allows truly volumetric analysis and incorporation of material properties such as anisotropic conductivity. For FEA, mesh generation is the first critical requirement and there exist many different approaches. However, conventional approaches offered by commercial packages and various algorithms do not generate content-adaptive meshes (cMeshes), resulting in numerous nodes and elements in modelling the conducting domain, and thereby increasing computational load and demand. In this work, we present efficient content-adaptive mesh generation schemes for complex biological volumes of MR images. The presented methodology is fully automatic and generates FE meshes that are adaptive to the geometrical contents of MR images, allowing optimal representation of conducting domain for FEA. We have also evaluated the effect of cMeshes on FEA in three dimensions by comparing the forward solutions from various cMesh head models to the solutions from the reference FE head model in which fine and equidistant FEs constitute the model. The results show that there is a significant gain in computation time with minor loss in numerical accuracy. We believe that cMeshes should be useful in the FEA of bioelectromagnetic problems.

A Small GTPase Activator Protein Interacts with Cytoplasmic Phytochromes in Regulating Root Development

Phytochromes enable plants to sense light information and regulate developmental responses. Phytochromes interact with partner proteins to transmit light signals to downstream components for plant development. PIRF1 (phytochrome-interacting ROP guanine-nucleotide exchange factor (RopGEF 1)) functions as a light-signaling switch regulating root development through the activation of ROPs (Rho-like GTPase of plant) in the cytoplasm. In vitro pulldown and yeast two-hybrid assays confirmed the interaction between PIRF1 and phytochromes. PIRF1 interacted with the N-terminal domain of phytochromes through its conserved PRONE (plant-specific ROP nucleotide exchanger) region. PIRF1 also interacted with ROPs and activated them in a phytochrome-dependent manner. The Pr form of phytochrome A enhanced the RopGEF activity of PIRF1, whereas the Pfr form inhibited it. A bimolecular fluorescence complementation analysis demonstrated that PIRF1 was localized in the cytoplasm and bound to the phytochromes in darkness but not in light. PIRF1 loss of function mutants (pirf1) of Arabidopsis thaliana showed a longer root phenotype in the dark. In addition, both PIRF1 overexpression mutants (PIRF1-OX) and phytochrome-null mutants (phyA-211 and phyB-9) showed retarded root elongation and irregular root hair formation, suggesting that PIRF1 is a negative regulator of phytochrome-mediated primary root development. We propose that phytochrome and ROP signaling are interconnected through PIRF1 in regulating the root growth and development in Arabidopsis.

3-D diffusion tensor MRI anisotropy content-adaptive finite element head model generation for bioelectromagnetic imaging

Realistic finite element (FE) head models have been successfully applied to bioelectromagnetic problems due to a realistic representation of arbitrary head geometry with inclusion of anisotropic material properties. In this paper, we propose a new automatic FE mesh generation scheme to generate a diffusion tensor MRI (DT-MRI) white matter anisotropy content-adaptive FE head model. We term this kind of mesh as wMesh. With this meshing technique, the anisotropic electrical conductivities derived from DT-MRIs can be best incorporated into the model. The influence of the white matter anisotropy on the EEG forward solutions has been studied via our wMesh head models. The scalp potentials computed from the anisotropic wMesh models against those of the isotropic models have been compared. The results describe that there are substantial changes in the scalp electrical potentials between the isotropic and anisotropic models, indicating that the inclusion of the white matter anisotropy is critical for accurate computation of E/MEG forward and inverse solutions. This fully automatic anisotropy-adaptive wMesh meshing scheme could be useful for modeling of individual-specific FE head models with better incorporation of the white matter anisotropic property towards bioelectromagnetic imaging.

Synthesis and biological evaluation of N-cyclopropylbenzamide-benzophenone hybrids as novel and selective p38 mitogen activated protein kinase (MAPK) inhibitors.

A series of hybrid molecules consisting of benzophenones and N-cyclopropyl-3-methylbenzamides were synthesized and biologically evaluated as novel p38 mitogen activated protein kinase (MAPK) inhibitors. In particular, we found that compound 10g displayed potent p38α MAPK inhibitory activity (IC50=0.027 μM), high kinase selectivity, and significant anti-inflammatory activity in THP-1 monocyte cells.

Characterization of Arabidopsis RopGEF family genes in response to abiotic stresses

Rho-related GTPase of plants (ROP) plays an important role in plant growth and development as a signaling protein. Plant RopGEFs are recently identified ROP activator proteins in Arabidopsis. In this study, we cloned 14 RopGEFs in Arabidopsis and characterized their expression patterns in response to abiotic stresses. Fourteen RopGEF genes were categorized into three groups based on their amino acid homologies and molecular sizes. Most RopGEFs were expressed predominantly in flower but some RopGEFs displayed a tissue-specific expression pattern. RopGEF1, 4, 5, and 11 were expressed in all tissues including root and leaves whereas RopGEF7, 8, 9, and 13 were expressed only in flowers. The transcript levels of 14 RopGEFs were changed significantly depending upon abiotic stresses such as cold, heat, drought and salts. RopGEF5 transcription was up-regulated by salt and drought treatment but down-regulated by heat. RopGEF14 transcript level was also increased by salt but decreased by heat stress. The transcript levels of RopGEF1, 7, 9, and 12 were enhanced in response to heat stress but showed no changes in response to cold stresses. Drought stress activated Group 3 RopGEFs such as RopGEF5 and 7. Taken together, 14 RopGEFs are responding to the abiotic stresses individually or as a group.

DT-MRI regularization using 3D nonlinear gradient vector flow anisotropic diffusion

In DT-MRI, diffusion-weighted multislice echoplanar images (EPIs) are processed to represent water diffusion characteristics as a diffusion tensor, reflecting the amount of diffusion in 3D. However imaging quality is generally compromised by several factors including the number of imaging slices, averages, diffusion sensitization steps (b-values), voxel size, and gradient directions, resulting in suboptimal SNR. In this study, we focus on improving imaging quality and SNR by denoising and reducing systematic and random errors through nonlinear anisotropic regularization. The raw EPIs are directly regularized through a newly proposed nonlinear anisotropic diffusion regularization method in 3D utilizing the gradient vector flow fields and its performance is compared to conventional 2D and vector-valued 2D anisotropic regularization methods. The effects of these variants of anisotropic regularization are examined through the maps of color-coded fractional anisotropy and tracked neural fibers. The results show that DT-MRI regularization using the proposed 3D anisotropic diffusion significantly improves the quality of fiber tracking and diffusion indices such as fractional anisotropy.

NJK14013, a novel synthetic estrogen receptor-α agonist, exhibits estrogen receptor-independent, tumor cell-specific cytotoxicity.

Estrogens act through interactions with estrogen receptors (ERs) to play diverse roles in various pathophysiological conditions. A number of synthetic selective estrogen receptor modulators (SERMs), such as tamoxifen and raloxifene, have been developed and used to treat ER-related diseases, including breast cancer and osteoporosis. Here, we identified a novel compound, bis(4-hydroxyphenyl)methanone-O-isopentyl oxime, designated NJK14013, as an ER agonist. NJK14013 activated ER-dependent transcription in a concentration-dependent manner, while suppressing androgen receptor-dependent transcriptional activity. It induced the activation-related phosphorylation of ER and enhanced the transcription of growth regulation by estrogen in breast cancer 1 (GREB1), further supporting its ER-stimulating activity. NJK14013 exerted anti-proliferative effects on various cancer cell lines, including an ER-negative breast cancer cell line, suggesting that it is capable of suppressing the growth of cancer cells independent of its ER-modulating activity. In addition, NJK14013 treatment resulted in significant apoptotic death of MCF7 and Ishikawa cancer cells, but did not induce apoptosis in non-cancer human umbilical vein endothelial cells. Collectively, our findings demonstrate that NJK14013 is a novel SERM that can activate ER-mediated transcription in MCF7 cells and suppress the proliferation of various cancer cells, including breast cancer cells and endometrial cancer cells. These results suggest that NJK14013 has potential as a novel SERM for anticancer or hormone-replacement therapy with reduced risk of carcinogenesis.

Epitope mapping of monoclonal antibodies for the Deinococcus radiodurans bacteriophytochome

Bacteriophytochromes (BphP) are phytochrome‐like light sensing proteins in bacteria, which use biliverdin as a chromophore. In order to study the biochemical properties of the DrBphP protein, five (2B8, 2C11, 3B2, 3D2, and 3H7) anti‐DrBphP monoclonal antibodies were produced through the immunization of mice with purified full‐length DrBphP and DrBphN (1–321 amino acid) proteins, and epitope mapping was then carried out. Among the five antibodies, 2B8 and 2C11 preferentially recognized the N‐terminal region of BphP whereas 3B2, 3D2, and 3H7 showed preference for the C‐terminal region. We performed further epitope mapping using recombinant truncated BphP proteins to narrow down their target sequences. The results demonstrated that each of the five monoclonal antibodies recognized different regions on the DrBphP protein. Additionally, epitopes of 2B8 and 3H7 antibodies were discovered to be shorter than 10 amino acids (2B8: RDPLPFFPP, 3H7: PGEIEEA). These two antibodies with such specific recognition epitopes could be especially valuable for developing new peptide tags for protein detection and purification.

Fine Mutational Analysis of 2B8 and 3H7 Tag Epitopes with Corresponding Specific Monoclonal Antibodies

Bacteriophytochromes are phytochrome-like light-sensing photoreceptors that use biliverdin as a chromophore. To study the biochemical properties of the Deinococcus radiodurans bacteriophytochrome (DrBphP) protein, two anti-DrBphP mouse monoclonal antibodies (2B8 and 3H7) were generated. Their specific epitopes were identified in our previous report. We present here fine epitope mapping of these two antibodies by using truncation and substitution of original epitope sequences in order to identify minimized epitope peptides. The previously reported original epitope sequences for 2B8 and 3H7 were truncated from both sides. Our analysis showed that the minimal peptide sequence lengths for 2B8 and 3H7 antibodies were nine amino acids (RDPLPFFPP) and six amino acids (PGEIEE), respectively. We further characterized these peptides in order to investigate their reactivity after single deletion and single substitution of the original peptides. We found that single-substituted 2B8 epitope (RDPLPAFPP) and dual-substituted 3H7 epitope (PGEIAD) showed significantly increased reactivity. These two antibodies with high reactivity for the short modified peptide sequences are valueble for developing new peptide tags for protein research.

Identification of novel estrogen receptor (ER) agonists that have additional and complementary anti-cancer activities via ER-independent mechanism

In this study, a series of bis(4-hydroxy)benzophenone oxime ether derivatives such as 12c, 12e and 12h were identified as novel estrogen receptor (ER) agonists that have additional and complementary anti-proliferative activities via ER-independent mechanism in cancer cells. These compounds are expected to overcome the therapeutic limitation of existing ER agonists such as estradiol and tamoxifen, which have been known to induce the proliferation of cancer cells.