Soyeon Kim

Structure of malonamidase E2 reveals a novel Ser-cisSer-Lys catalytic triad in a new serine hydrolase fold that is prevalent in nature

A large group of hydrolytic enzymes, which contain a conserved stretch of ∼130 amino acids designated the amidase signature (AS) sequence, constitutes a super family that is distinct from any other known hydrolase family. AS family enzymes are widespread in nature, ranging from bacteria to humans, and exhibit a variety of biological functions. Here we report the first structure of an AS family enzyme provided by the crystal structure of malonamidase E2 from Bradyrhizobium japonicum. The structure, representing a new protein fold, reveals a previously unidentified Ser‐cisSer‐Lys catalytic machinery that is absolutely conserved throughout the family. This family of enzymes appears to be evolutionarily distinct but has diverged to acquire a wide spectrum of individual substrate specificities, while maintaining a core structure that supports the catalytic function of the unique triad. Based of the structures of the enzyme in two different inhibited states, an unusual action mechanism of the triad is proposed that accounts for the role of the cis conformation in the triad.

Transparent and flexible organic semiconductor nanofilms with enhanced thermoelectric efficiency

Sequential doping and dedoping increased the conductivity and optimized the oxidation level of transparent and flexible poly(3,4-ethylenedioxythiophene):poly(4-styrene sulfonic acid) (PEDOT:PSS) films, resulting in an improvement in the thermoelectric figure of merit ZT. The electrical conductivity (σ) increased from 970 to 1260 S cm−1 and the power factor from 66.5 to 70.7 μW mK−2 at the optimum concentration of the chemical dopant p-toluenesulfonic acid monohydrate (TSA). Then, the doped PEDOT:PSS films were treated with hydrazine/DMSO solutions with different hydrazine concentrations to precisely control the oxidation level. During the hydrazine/DMSO treatment (dedoping), σ of the films continuously decreased from 1647 to 783 S cm−1 due to a decrease in the carrier concentration, whereas the Seebeck coefficient (S) steeply increased from 28 to 49.3 μV K−1 at the optimum oxidation level. A power factor of 318.4 μW mK−2 (σ = 1310 S cm−1, S = 49.3 μV K−1), the highest among all existing thermoelectric nanofilms, was achieved while maintaining polymer film flexibility and transparency (88.3% of optical transmittance). In addition, the thermal conductivity (κ) of the PEDOT:PSS films decreased from 0.38 to 0.30 W mK−1 upon removal of PSS. At the lowest κ value, a high ZT value of 0.31 was achieved at room temperature.

Tooth Discoloration after the Use of New Pozzolan Cement (Endocem) and Mineral Trioxide Aggregate and the Effects of Internal Bleaching

INTRODUCTION The aim of this study was to evaluate tooth discoloration after the use of mineral trioxide aggregate (MTA) and to examine the effect of internal bleaching on discoloration associated with MTA. METHODS Thirty-two teeth were endodontically treated. Three-millimeter plugs of MTA, ProRoot, Angelus, or Endocem were placed on the access cavities of 24 teeth. Eight teeth served as the control group. After 24 hours, the access cavities were restored, and the tooth color was recorded at baseline and at 1, 2, 4, 8, and 12 weeks. After 12 weeks, the MTA materials were removed under a microscope, and an internal bleaching treatment was performed. After removal of the MTA materials and after a 1-week bleaching treatment, the color changes were measured, and the MTA-dentin interfaces were observed under a microscope. RESULTS The ProRoot and Angelus groups displayed increasing discoloration during a period of 12 weeks. The discoloration associated with ProRoot and Angelus was observed at the MTA-dentin interface and on the interior surface of the dentin. However, the Endocem groups demonstrated no significant discoloration (P < .05). No marginal discoloration was observed around the material in the Endocem group. Removal of the discolored MTA was effective for resolving the discoloration in all of the experimental groups (P < .05). However, a subsequent internal bleaching treatment was not significantly effective compared with the removal of MTA. CONCLUSIONS ProRoot and Angelus caused tooth discoloration. However, Endocem did not affect the contacting dentin surface. Removing the discolored MTA materials contributed more to resolving the tooth discoloration than post-treatment internal bleaching.

Purification of PEDOT:PSS by Ultrafiltration for Highly Conductive Transparent Electrode of All-Printed Organic Devices.

A highly conductive, air stable and scalable poly(3,4-ethylenedioxythiophene) (PEDOT): poly(4-styrenesulfonate) (PEDOT:PSS) are prepared by using mass production ultrafiltration. By effectively removing excess PSS and various reaction impurities using repeated 100 nm pore membrane filtration, purified PEDOT:PSS exhibit conductivity as high as 2000 S cm-1 .

Clinical relevance of lymph node ratio in breast cancer patients with one to three positive lymph nodes

Background:To test the hypotheses that breast cancer patients with one to three positive lymph nodes (pN1) consist of heterogeneous prognostic subsets and that the ratio of positive nodes to total nodes dissected (lymph node ratio, LNR) might discriminate patients with a higher risk as candidates for post-mastectomy radiation therapy (PMRT).Methods:Using information from 7741 node-positive patients, we first identified cutoff values of the LNR using the nonparametric bootstrap method. Focusing on 3477 patients with pN1 disease, we then evaluated the clinical relevance of the LNR categorised by the estimated cutoff values (categorised LNR, cLNR).Results:Among 3477 patients with pN1 disease, 3059 and 418 patients were assigned into the low and intermediate cLNR groups, respectively, based on a cutoff value of 0.18. The prognostic factors associated with poor overall survival (OS) included younger age, T2 stage, negative oestrogen/progesterone receptors, high histologic grade, and intermediate cLNR. Post-mastectomy radiation therapy significantly increased OS in patients assigned to the intermediate cLNR (hazard ratio, 0.39; 95% confidence interval, 0.17–0.89; P=0.0248), whereas patients in the low cLNR group derived no additional survival benefit from PMRT.Conclusion:This study suggests that PMRT should be recommended for patients with pN1 disease and an intermediate cLNR.

Aqueous chemical synthesis of tellurium nanowires using a polymeric template for thermoelectric materials

We report the simple synthesis of tellurium nanowires (TeNWs) by a one-pot scale-up hydrothermal process. A clean wet-chemical method, employing telluric acid (Te(OH)6) as a source of tellurium, ascorbic acid as a weak reducing agent, and a linear polymer as a template, has been developed for the synthesis of TeNWs with a diameter of 30–140 nm and a length of several micrometers at 105 °C. A possible explanation for the one-dimensional growth of TeNWs is the linear polymer template. The effects of the concentration of the polymeric template on the nanowire morphology were investigated. Evaluation of the thermoelectric properties indicated a high Seebeck coefficient and a power factor of about 568 μV K−1 and 8.44 μW mK−2, respectively, of the optimized TeNW films, and these values were about 80 times larger than those of the TeNW films formed without a polymeric template. We expect this simple process to be widely applicable for large-scale production of one-dimensional inorganic nanomaterials for energy harvesting and electronic devices.

False negative results in axillary lymph nodes by ultrasonography and ultrasonography-guided fine-needle aspiration in patients with invasive ductal carcinoma

PURPOSE For preoperative evaluation of ALN status using various methods, axillary US and subsequent US-FNA targeting the LNs suspicious for metastasis are the most widely used methods. The purpose of our study was to assess the rate of false-negative results at preoperative ultrasonography (US) and ultrasonography guided fine needle aspiration (US-FNA) of axillary lymph nodes (ALNs) in breast cancer patients and the number of false-negative lymph nodes, and to evaluate factors related to ALN false negative results in US and/or US-FNA in patients diagnosed with invasive ductal carcinoma. MATERIALS AND METHODS Among 317 patients who underwent surgery for invasive ductal carcinoma during 2009 in Severance hospital, 237 patients had no reported ALN metastasis on preoperative US-FNA and US. We retrospectively reviewed the subsequent surgical pathology and clinicopathologic findings and assessed the rate of false-negative results from US and US-FNA of ALN and the number of false-negative lymph node. We performed univariate analysis and multivariate logistic regression analysis to evaluate the relationships between variable clinicopathologic factors (T-stage, position of ALN, hormone receptors, histologic grade, lymphovascular invasion (LVI) and performance of FNA) and cytologic results (false-negative result; FNALN and true negative result; TNALN) from US and/or US-FNA of ALN. RESULTS The rate of false-negative results was 42.4 % (59/139) in both US and US-FNA of ALN but among them, 57.6 % (34/59) showed only one metastatic ALN. Breast cancer with FNALN on US and US-FNA was significantly related to positive estrogen receptor (p = 0.003), positive progesterone receptor (p = 0.001), and the presence of LVI (p = 0.004) in univariate analysis. In multivariate analysis, high T stages (≥ T2, odds ratio (OR) 4.007, p = 0.004) and LVI (OR 7.951, p = 0.001) showed significant correlation with FNALN on US and US-FNA. CONCLUSION More than half of patients with FNALN showed only one metastatic ALN. LVI and high T-stages were the most important factors attributed to FNALN on US and US-FNA in patients with invasive ductal carcinoma.

Synthesis of conductive and transparent PEDOT:P(SS-co-PEGMA) with excellent water-, weather-, and chemical-stabilities for organic solar cells

The water-, weather- and chemical-resistant conductive poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate)-co-poly(ethylene glycol methacrylate) (PEDOT:P(SS-co-PEGMA)) copolymer was successfully synthesized with thermally curable P(SS-co-PEGMA) copolymers. The PSS and P(SS-co-PEGMA) copolymers were synthesized by solution polymerization and PEDOT:PSS and PEDOT:P(SS-co-PEGMA) were synthesized by Fe+-catalyzed oxidative polymerization. PSS and P(SS-co-PEGMA) were characterized by Fourier-transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance spectroscopy (NMR). The electrical properties of the conductive PEDOT:P(SS-co-PEGMA) thin films were characterized in two parts; first, the mechanism and characterization of the conductivity change, and second, the characterization of the water-, chemical-, and weather-stability of the films. The conductivity and transmittance, respectively, of PEDOT:P(SS-co-PEGMA) at 550 nm under optimized conditions were maintained at the levels found in PEDOT:PSS, 160.3 S cm−1 and 86.7%. The introduction of PEGMA to the PSS copolymer improved the mechanical properties and weather stability. The PEDOT:P(SS-co-PEGMA) was highly stable to chemical solvents and independent of the type of solvents used for stability analysis. The conductivity in the weather stability test of PEDOT:PSS decreased by 44.9%, on the other hand, the conductivity of PEDOT:P(SS-co-PEGMA) was decreased by only 22.2%. The PEDOT:PSS and PEDOT:P(SS-co-PEGMA) copolymers were used as buffer layers in organic solar cells (OSC) and showed as high efficiency as conventional PEDOT:PSS materials. The decrease of OSC efficiency with PEDOT:P(SS-co-PEGMA) was 30% less than the OSCs with the commercial and reference PEDOT:PSS buffer layers.

Multi-purpose overcoating layers based on PVA/silane hybrid composites for highly transparent, flexible, and durable AgNW/PEDOT:PSS films

Flexible hybrid overcoating layers with antireflective properties are fabricated by a catalyzed two-step sol–gel process using poly(vinyl alcohol) (PVA) and silane precursors, followed by simple bar coating. Hydrolysis of alkoxysilanes followed by the condensation reaction forms chemical bonds between Si–OH and C–OH groups. A glass substrate with the hybrid overcoating layer shows higher transmittance than a bare glass substrate because the overcoating provides an antireflective layer with an intermediate refractive index. Haziness and surface roughness of the hybrid overcoating decrease with increasing PVA content. Further, complexation of PVA and silanes yields greater mechanical flexibility. Various silanes functionalized with methyl, epoxy, amino, and phenyl groups are also incorporated into the hybrid overcoating to adjust the hydrophobicity, transparency, and protective properties. A methyltrimethoxysilane (MTMS)-based hybrid overcoating shows the best optical transparency and water repellency. Application of a PVA/MTMS hybrid overcoating over silver nanowire (AgNW)/poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) conducting films dramatically improves the long-term stability of the sheet resistance through enhanced resistance to moisture penetration. Consequently, highly stable and durable AgNW/PEDOT:PSS conducting films (sheet resistance, 20 Ω sq−1; transmittance, 95.4%) are fabricated by passivating them on both sides with the hybrid overcoating.

Crystallization and preliminary X-ray crystallographic analysis of malonamidase E2, an amidase signature family member.

Malonamidase E2 from Bradyrhizobium japonicum catalyzes the hydrolysis of malonamate. The enzyme belongs to an amidase signature family which has a highly conserved serine- and glycine-rich sequence over a stretch of approximately 45 amino acids. More than 100 known or predicted members belonging to this family, whose biological functions vary widely, can be identified in sequence databases. Although urgently needed, no three-dimensional structure of any protein of this family is yet available. The crystallization of malonamidase E2 was undertaken as a first step toward the goal of providing information on the canonical structure of the amidase signature family. The enzyme was crystallized using the hanging-drop vapour-diffusion method at 277 K under two different conditions. One crystal form, which is easier to work with than the other form, belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 104.29, b = 95.58, c = 74.90 A. The unit cell is likely to contain two molecules of MAE2, with a crystal volume per protein mass (V(M)) of 2.045 A(3)Da(-1) and solvent content of about 39.9% by volume. A native data set to 1.8 A resolution was obtained from a flash-cooled crystal using synchrotron radiation.