Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8

Krieger, Elmar,Joo, Keehyoung,Lee, Jinwoo,Lee, Jooyoung,Raman, Srivatsan,Thompson, James,Tyka, Mike,Baker, David,Karplus, Kevin Wiley Subscription Services, Inc., A Wiley Company 2009 Proteins Vol.77 No.suppl9

<P>A correct alignment is an essential requirement in homology modeling. Yet in order to bridge the structural gap between template and target, which may not only involve loop rearrangements, but also shifts of secondary structure elements and repacking of core residues, high-resolution refinement methods with full atomic details are needed. Here, we describe four approaches that address this 'last mile of the protein folding problem' and have performed well during CASP8, yielding physically realistic models: YASARA, which runs molecular dynamics simulations of models in explicit solvent, using a new partly knowledge-based all atom force field derived from Amber, whose parameters have been optimized to minimize the damage done to protein crystal structures. The LEE-SERVER, which makes extensive use of conformational space annealing to create alignments, to help Modeller build physically realistic models while satisfying input restraints from templates and CHARMM stereochemistry, and to remodel the side-chains. ROSETTA, whose high resolution refinement protocol combines a physically realistic all atom force field with Monte Carlo minimization to allow the large conformational space to be sampled quickly. And finally UNDERTAKER, which creates a pool of candidate models from various templates and then optimizes them with an adaptive genetic algorithm, using a primarily empirical cost function that does not include bond angle, bond length, or other physics-like terms.</P>

Influence of Drying Temperature and Duration on the Quantification of Particulate Organic Matter

Lee, Jin-Ho,Doolittle, James J.,Lee, Do-Kyoung,Malo, Douglas D. The Korean Society of Environmental Agriculture 2006 한국환경농학회지 Vol.25 No.4

Various drying conditions, temperatures (40 to $80^{\circ}C$) and durations (overnight to 72 hrs), for the particulate organic matter (POM) fraction after wet-sieving size fractionation have been applied for determination of POM contents in the weight loss-on-ignition method. In this study, we investigated the optimum drying condition for POM fraction in quantification of POM and/or mineral-associated organic matter (MOM; usually indirectly estimated). The influence of the drying conditions on quantifying POM was dependent upon soil properties, especially the amount of soil organic components. In relatively high organic soils (total carbon > 40 g/kg in this study), the POM values were significantly higher (overestimated) with drying at $55^{\circ}C$ than those values at $105^{\circ}C$, which were, for example, 173.2 and 137.3 mg/kg, respectively, in a soil studied. However, drying at $55^{\circ}C$ for longer than 48 hrs of periods produced consistent POM values even though the values were much higher than those at $105^{\circ}C$. Thus, indirect estimates of MOM (MOM = SOM-POM) also tended to be significantly impacted by the dry conditions. Therefore, we suggest POM fractions should be dried at $105^{\circ}C$ for 24 hrs as determining POM and MOM contents. If the POM traction is needed to be dried at a lower temperature (e.g. $55^{\circ}C$) with a specific reason, at least 48 hrs of drying period is necessary to obtain consistent POM values, and a moisture correction factor should be determined to adjust the values back to a $105^{\circ}C$ weight basis.

A subset of human rapidly self-renewing marrow stromal cells preferentially engraft in mice

Lee, Ryang Hwa,Hsu, Shu Ching,Munoz, James,Jung, Jin Sup,Lee, Na Rea,Pochampally, Radhika,Prockop, Darwin J. American Society of Hematology 2006 Blood Vol.107 No.5

<P>Controversies have arisen as to whether adult stem cells or progenitor cells from bone marrow can engraft into nonhematopoietic tissues in vivo. To resolve some of the controversies, we developed a highly sensitive polymerase chain reaction-based single nucleotide polymorphism (PCR-SNP) assay for competitive engraftment of mixtures of stem/progenitor cells. We used the assay to follow engraftment in immunodeficient mice of subpopulations of the stem/progenitor cells from human bone marrow referred to as either mesenchymal stem cells or marrow stromal cells (MSCs). The engraftment into adult mice without induced tissue injury was low and variable, but there was preferential engraftment of a subpopulation of rapidly self-renewing MSCs (RS-MSCs) compared with a subpopulation of slowly renewing MSCs (SR-MSCs). After intravenous infusion, there was a tendency for the cells to engraft into the hippocampal region that was previously designated a “vascular niche.” Migration assays suggested that preferential engraftment of RS-MSCs was in part explained by their expression of CXCR4 and CX3R1, the receptors for SDF-1 and fractalkine.</P>

Surface-fluorinated proton-exchange membrane with high electrochemical durability for direct methanol fuel cells.

Lee, Chang Hyun,Lee, So Young,Lee, Young Moo,Lee, Sang Yun,Rhim, Ji Won,Lane, Ozma,McGrath, James E American Chemical Society 2009 ACS APPLIED MATERIALS & INTERFACES Vol.1 No.5

<P>Random disulfonated poly(arylene ether sulfone)-silica nanocomposite (FSPAES-SiO(2)) membranes were physicochemically tuned via surface fluorination. Surface fluorination for 30 min converted about 20% of the C-H bonds on the membrane surface into C-F bonds showing hydrophobicity and electronegativity at the same time. The membranes with hydrophobic surface properties showed high dimensional stability and low methanol permeability when hydrated for direct methanol fuel cell applications. In particular, the surface enrichment of fluorine atoms led to anisotropic swelling behavior, associated with a stable electrode interface formation. Interestingly, in spite of the use of a random copolymer as a polymer matrix, the low surface free energy of the C-F bonds induced a well-defined continuous ionic channel structure, similar to those of multiblock copolymers. In addition to the morphological transition, fluorine atoms with high electron-withdrawing capability promoted the dissociation of sulfonic acid (-SO(3)H) groups. Consequently, FSPAES-SiO(2) membranes exhibited improved proton conductivity. Thus, FSPAES-SiO(2) membranes exhibited significantly improved single-cell performances (about 200%) at a constant voltage of 0.4 V in comparison with those of Nafion 117 and nonfluorinated membranes. Surprisingly, their good electrochemical performances were maintained with very low nonrecovery loss over the time period of 1400 h and interfacial resistances 380% times lower than those of conventional membrane-electrode assemblies comprising the control hydrocarbon membrane and a Nafion binder for the electrodes.</P>

Berberine, a Natural Plant Product, Activates AMP-Activated Protein Kinase With Beneficial Metabolic Effects in Diabetic and Insulin-Resistant States

Lee, Y. S.,Kim, W. S.,Kim, K. H.,Yoon, M. J.,Cho, H. J.,Shen, Y.,Ye, J.-M.,Lee, C. H.,Oh, W. K.,Kim, C. T.,Hohnen-Behrens, C.,Gosby, A.,Kraegen, E. W.,James, D. E.,Kim, J. B. American Diabetes Association 2006 Diabetes Vol.55 No.8

<P>Berberine has been shown to have antidiabetic properties, although its mode of action is not known. Here, we have investigated the metabolic effects of berberine in two animal models of insulin resistance and in insulin-responsive cell lines. Berberine reduced body weight and caused a significant improvement in glucose tolerance without altering food intake in db/db mice. Similarly, berberine reduced body weight and plasma triglycerides and improved insulin action in high-fat-fed Wistar rats. Berberine downregulated the expression of genes involved in lipogenesis and upregulated those involved in energy expenditure in adipose tissue and muscle. Berberine treatment resulted in increased AMP-activated protein kinase (AMPK) activity in 3T3-L1 adipocytes and L6 myotubes, increased GLUT4 translocation in L6 cells in a phosphatidylinositol 3' kinase-independent manner, and reduced lipid accumulation in 3T3-L1 adipocytes. These findings suggest that berberine displays beneficial effects in the treatment of diabetes and obesity at least in part via stimulation of AMPK activity.</P>

A Near-Infrared Fluorescence-Based Optical Thermosensor

Lee, Seung-Young,Lee, Seulki,Youn, In-Chan,Yi, Dong Kee,Lim, Yong Taik,Chung, Bong Hyun,Leary, James F.,Kwon, Ick Chan,Kim, Kwangmeyung,Choi, Kuiwon WILEY-VCH Verlag 2009 Chemistry Vol.15 No.25

<P>A polymeric thermosensor composed of the thermo-responsive block copolymer Pluronic F127 (PF127) and the near-infrared (NIR) dye Cy5.5 can simply monitor, image, and analyze temperature changes. The thermoprobe exhibited linear NIR fluorescent emission changes (see figure) over a broad temperature range (0–80 °C). <img src='wiley_img/09476539-2009-15-25-CHEM200900683-content.gif' alt='wiley_img/09476539-2009-15-25-CHEM200900683-content'> </P> <B>Graphic Abstract</B> <P>A polymeric thermosensor composed of the thermo-responsive block copolymer Pluronic F127 (PF127) and the near-infrared (NIR) dye Cy5.5 can simply monitor, image, and analyze temperature changes. The thermoprobe exhibited linear NIR fluorescent emission changes (see figure) over a broad temperature range (0–80 °C). <img src='wiley_img/09476539-2009-15-25-CHEM200900683-content.gif' alt='wiley_img/09476539-2009-15-25-CHEM200900683-content'> </P>

Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in <i>Arabidopsis</i>

Lee, Hanna,Yoo, Seong Jeon,Lee, Jeong Hwan,Kim, Wanhui,Yoo, Seung Kwan,Fitzgerald, Heather,Carrington, James C.,Ahn, Ji Hoon Oxford University Press 2010 Nucleic acids research Vol.38 No.9

<P>Flowering is the primary trait affected by ambient temperature changes. Plant microRNAs (miRNAs) are small non-coding RNAs playing an important regulatory role in plant development. In this study, to elucidate the mechanism of flowering-time regulation by small RNAs, we identified six ambient temperature-responsive miRNAs (miR156, miR163, miR169, miR172, miR398 and miR399) in <I>Arabidopsis</I> via miRNA microarray and northern hybridization analyses. We also determined the expression profile of 120 unique miRNA loci in response to ambient temperature changes by miRNA northern hybridization analysis. The expression of the ambient temperature-responsive miRNAs and their target genes was largely anticorrelated at two different temperatures (16 and 23°C). Interestingly, a lesion in <I>short vegetative phase</I> (<I>SVP</I>), a key regulator within the thermosensory pathway, caused alteration in the expression of miR172 and a subset of its target genes, providing a link between a thermosensory pathway gene and miR172. The miR172-overexpressing plants showed a temperature-independent early flowering phenotype, suggesting that modulation of miR172 expression leads to temperature insensitivity. Taken together, our results suggest a genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs under non-stress temperature conditions.</P>

Strain Hardening of Red Blood Cells by Accumulated Cyclic Supraphysiological Stress

Lee, Sung S.,Antaki, James F.,Kameneva, Marina V.,Dobbe, Johannes G.,Hardeman, Max R.,Ahn, Kyung H.,Lee, Seung J. Blackwell Publishing Inc 2007 Artificial Organs Vol.31 No.1

<P>Abstract: </P><P>The effect of elevated shear stress upon cellular trauma has been studied for many years, but the effect of long-term cyclic stress trauma on hemorheology has never been explored systematically. This study investigated sublytic trauma of red blood cells (RBCs) caused by repeated exposure to shear stress. A suspension of bovine blood was throttled through a capillary tube (inner diameter 1 mm and length 70 mm) connected to a recirculating flow loop. Samples were withdrawn every 30 min to measure deformability and characteristic time. The deformability of the cell was measured microscopically by observing the shape of the cell during the shear flow. It was found that cyclic shear irreversibly stiffened the cell membrane while the effect was not so much as that of continuous shear. The cell deformability was dramatically reduced by 73% when the stress of 300 Pa was applied for 288 s, while it was 7% under 90 Pa. These results elucidate the need for improved models to predict cellular trauma within the unsteady flow environment of mechanical circulatory assist devices.</P>

What the Taiwan Relations Act Really Means for US Policy

James Lee 동아시아재단 2022 Global Asia Vol.17 No.3

Microfluidics within a well: an injection-molded plastic array 3D culture platform

Lee, Younggyun,Choi, Jin Woo,Yu, James,Park, Dohyun,Ha, Jungmin,Son, Kyungmin,Lee, Somin,Chung, Minhwan,Kim, Ho-Young,Jeon, Noo Li The Royal Society of Chemistry 2018 Lab on a chip Vol.18 No.16

<P>Polydimethylsiloxane (PDMS) has been widely used in fabricating microfluidic devices for prototyping and proof-of-concept experiments. Due to several material limitations, PDMS has not been widely adopted for commercial applications that require large-scale production. This paper describes a novel injection-molded plastic array 3D culture (IMPACT) platform that incorporates a microfluidic design to integrate patterned 3D cell cultures within a single 96-well (diameter = 9 mm) plate. Cell containing gels can be sequentially patterned by capillary-guided flow along the corner and narrow gaps designed within the 96-well form factor. Compared to PDMS-based hydrophobic burst valve designs, this work utilizes hydrophilic liquid guides to obtain rapid and reproducible patterned gels for co-cultures. When a liquid droplet (<I>i.e.</I> cell containing fibrin or collagen gel) is placed on a corner, spontaneous patterning is achieved within 1 second. Optimal dimensionless parameters required for successful capillary loading have been determined. To demonstrate the utility of the platform for 3D co-culture, angiogenesis experiments were performed by patterning HUVEC (human umbilical endothelial cells) and LF (lung fibroblasts) embedded in 3D fibrin gels. The angiogenic sprouts (with open lumen tip cells expressing junctional proteins) are comparable to those observed in PDMS based devices. The IMPACT device has the potential to provide a robust high-throughput experimental platform for vascularized microphysiological systems.</P>