Computational modeling approaches for developing a synergistic effect prediction model of estrogen agonistic activity.

The concerns regarding the potential health threats caused by estrogenic endocrine-disrupting chemicals (EDCs) and their mixtures manufactured by the chemical industry are increasing worldwide. Conventional experimental tests for understanding the estrogenic activity of mixtures are expensive and time-consuming. Although non-testing methods using computational modeling approaches have been developed to reduce the number of traditional tests, they are unsuitable for predicting synergistic effects because current prediction models consider only a single chemical. Thus, the development of predictive models is essential for predicting the mixture toxicity, including chemical interactions. However, selecting suitable computational modeling approaches to develop a high-performance prediction model requires considerable time and effort. In this study, we provide a suitable computational approach to develop a predictive model for the synergistic effects of estrogenic activity. We collected datasets on mixture toxicity based on the synergistic effect of estrogen agonistic activity in binary mixtures. Using the model deviation ratio approach, we classified the labels of the binary mixtures as synergistic or non-synergistic effects. We assessed five molecular descriptors, four machine learning-based algorithms, and a deep learning-based algorithm to provide a suitable computational modeling approach. Compared with other modeling approaches, the prediction model using the deep learning-based algorithm and chemical-protein network descriptors exhibited the best performance in predicting the synergistic effects. In conclusion, we developed a new high-performance binary classification model using a deep neural network and chemical-protein network-based descriptors. The developed model will be helpful for the preliminary screening of the synergistic effects of binary mixtures during the development process of chemical products.

Yeast lunapark regulates the formation of trans-Sey1p complexes for homotypic ER membrane fusion.

The endoplasmic reticulum (ER) consists of the nuclear envelope and a connected peripheral network of tubules and interspersed sheets. The structure of ER tubules is generated and maintained by various proteins, including reticulons, DP1/Yop1p, atlastins, and lunapark. Reticulons and DP1/Yop1p stabilize the high membrane curvature of ER tubules, and atlastins mediate homotypic membrane fusion between ER tubules; however, the exact role of lunapark remains poorly characterized. Here, using isolated yeast ER microsomes and reconstituted proteoliposomes, we directly examined the function of the yeast lunapark Lnp1p for yeast atlastin Sey1p-mediated ER fusion and found that Lnp1p inhibits Sey1p-driven membrane fusion. Furthermore, by using a newly developed assay for monitoring trans-Sey1p complex assembly, a prerequisite for ER fusion, we found that assembly of trans-Sey1p complexes was increased by the deletion of LNP1 and decreased by the overexpression of Lnp1p, indicating that Lnp1p inhibits Sey1p-mediated fusion by interfering with assembly of trans-Sey1p complexes.

Structural and functional insights into the flexible ß-hairpin of glycerol dehydrogenase.

During glycerol metabolism, the initial step of glycerol oxidation is catalysed by glycerol dehydrogenase (GDH), which converts glycerol to dihydroxyacetone in a NAD+ -dependent manner via an ordered Bi-Bi kinetic mechanism. Structural studies conducted with GDH from various species have mainly elucidated structural details of the active site and ligand binding. However, the structure of the full GDH complex with both cofactor and substrate bound is not determined, and thus, the structural basis of the kinetic mechanism of GDH remains unclear. Here, we report the crystal structures of Escherichia coli GDH with a substrate analogue bound in the absence or presence of NAD+ . Structural analyses including molecular dynamics simulations revealed that GDH possesses a flexible ß-hairpin, and that during the ordered progression of the kinetic mechanism, the flexibility of the ß-hairpin is reduced after NAD+ binding. It was also observed that this alterable flexibility of the ß-hairpin contributes to the cofactor binding and possibly to the catalytic efficiency of GDH. These findings suggest the importance of the flexible ß-hairpin to GDH enzymatic activity and shed new light on the kinetic mechanism of GDH.

Structural and biochemical insights into Zn2+-bound EF-hand proteins, EFhd1 and EFhd2.

EF-hand proteins, which contain a Ca2+-binding EF-hand motif, are involved in regulating diverse cellular functions. Ca2+ binding induces conformational changes that modulate the activities of EF-hand proteins. Moreover, these proteins occasionally modify their activities by coordinating metals other than Ca2+, including Mg2+, Pb2+ and Zn2+, within their EF-hands. EFhd1 and EFhd2 are homologous EF-hand proteins with similar structures. Although separately localized within cells, both are actin-binding proteins that modulate F-actin rearrangement through Ca2+-independent actin-binding and Ca2+-dependent actin-bundling activity. Although Ca2+ is known to affect the activities of EFhd1 and EFhd2, it is not known whether their actin-related activities are affected by other metals. Here, the crystal structures of the EFhd1 and EFhd2 core domains coordinating Zn2+ ions within their EF-hands are reported. The presence of Zn2+ within EFhd1 and EFhd2 was confirmed by analyzing anomalous signals and the difference between anomalous signals using data collected at the peak positions as well as low-energy remote positions at the Zn K-edge. EFhd1 and EFhd2 were also found to exhibit Zn2+-independent actin-binding and Zn2+-dependent actin-bundling activity. This suggests the actin-related activities of EFhd1 and EFhd2 could be regulated by Zn2+ as well as Ca2+.

Human atlastins are sufficient to drive the fusion of liposomes with a physiological lipid composition.

The dynamin-like GTPase atlastin is believed to be the minimal machinery required for homotypic endoplasmic reticulum (ER) membrane fusion, mainly because Drosophila atlastin is sufficient to drive liposome fusion. However, it remains unclear whether mammalian atlastins, including the three human atlastins, are sufficient to induce liposome fusion, raising doubts about their major roles in mammalian cells. Here, we show that all human atlastins are sufficient to induce fusion when reconstituted into liposomes with a lipid composition mimicking that of the ER. Although the fusogenic activity of ATL1, which is predominantly expressed in neuronal cells, was weaker than that of ATL2 or ATL3, the addition of M1-spastin, a neuron-specific factor, markedly increased ATL1-mediated liposome fusion. Although we observed efficient fusion between ER microsomes isolated from cultured, non-neuronal cells that predominantly express ATL2-1, an autoinhibited isoform of ATL2, ATL2-1 failed to support liposome fusion by itself as reported previously, indicating that cellular factors enable ATL2-1 to mediate ER fusion in vivo.

H2 Plasma and PMA Effects on PEALD-Al2O3 Films with Different O2 Plasma Exposure Times for CIS Passivation Layers.

In this study, the electrical properties of Al2O3 film were analyzed and optimized to improve the properties of the passivation layer of CMOS image sensors (CISs). During Al2O3 deposition processing, the O2 plasma exposure time was adjusted, and H2 plasma treatment as well as post-metallization annealing (PMA) were performed as posttreatments. The flat-band voltage (Vfb) was significantly shifted (ΔVfb = 2.54 V) in the case of the Al2O3 film with a shorter O2 plasma exposure time; however, with a longer O2 plasma exposure time, Vfb was slightly shifted (ΔVfb = 0.61 V) owing to the reduction in the carbon impurity content. Additionally, the as-deposited Al2O3 sample with a shorter O2 plasma exposure time had a larger number of interface traps (interface trap density, Dit = 8.98 × 1013 eV-1·cm-2). However, Dit was reduced to 1.12 × 1012 eV-1·cm-2 by increasing the O2 plasma exposure time and further reduced after PMA. Consequently, we fabricated an Al2O3 film suitable for application as a CIS passivation layer with a reduced number of interface traps. However, the Al2O3 film with increased O2 plasma exposure time deteriorated owing to plasma damage after H2 plasma treatment, which is a method of reducing carbon impurity content. This deterioration was validated using the C-V hump and breakdown characteristics.

Engineering vacancy and hydrophobicity of two-dimensional TaTe2 for efficient and stable electrocatalytic N2 reduction.

Demand for ammonia continues to increase to sustain the growing global population. The direct electrochemical N2 reduction reaction (NRR) powered by renewable electricity offers a promising carbon-neutral and sustainable strategy for manufacturing NH3, yet achieving this remains a grand challenge. Here, we report a synergistic strategy to promote ambient NRR for ammonia production by tuning the Te vacancies (VTe) and surface hydrophobicity of two-dimensional TaTe2 nanosheets. Remarkable NH3 faradic efficiency of up to 32.2% is attained at a mild overpotential, which is largely maintained even after 100 h of consecutive electrolysis. Isotopic labeling validates that the N atoms of formed NH4 + originate from N2. In situ X-ray diffraction indicates preservation of the crystalline structure of TaTe2 during NRR. Further density functional theory calculations reveal that the potential-determining step (PDS) is ∗NH2 + (H+ + e-) → NH3 on VTe-TaTe2 compared with that of ∗ + N2 + (H+ + e-) → ∗N-NH on TaTe2. We identify that the edge plane of TaTe2 and VTe serve as the main active sites for NRR. The free energy change at PDS on VTe-TaTe2 is comparable with the values at the top of the NRR volcano plots on various transition metal surfaces.

Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69.

DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed.

S92 phosphorylation induces structural changes in the N-terminus domain of human mitochondrial calcium uniporter.

The mitochondrial calcium uniporter (MCU) plays essential roles in mitochondrial calcium homeostasis and regulates cellular functions, such as energy synthesis, cell growth, and development. Thus, MCU activity is tightly controlled by its regulators as well as post-translational modification, including phosphorylation by protein kinases such as proline-rich tyrosine kinase 2 (Pyk2) and AMP-activated protein kinase (AMPK). In our in vitro kinase assay, the MCU N-terminal domain (NTD) was phosphorylated by protein kinase C isoforms (PKCßII, PKCδ, and PKCε) localized in the mitochondrial matrix. In addition, we found the conserved S92 was phosphorylated by the PKC isoforms. To reveal the structural effect of MCU S92 phosphorylation (S92p), we determined crystal structures of the MCU NTD of S92E and D119A mutants and analysed the molecular dynamics simulation of WT and S92p. We observed conformational changes of the conserved loop2-loop4 (L2-L4 loops) in MCU NTDS92E, NTDD119A, and NTDS92p due to the breakage of the S92-D119 hydrogen bond. The results suggest that the phosphorylation of S92 induces conformational changes as well as enhancements of the negative charges at the L2-L4 loops, which may affect the dimerization of two MCU-EMRE tetramers.

Structure of the MICU1-MICU2 heterodimer provides insights into the gatekeeping threshold shift.

Mitochondrial calcium uptake proteins 1 and 2 (MICU1 and MICU2) mediate mitochondrial Ca2+ influx via the mitochondrial calcium uniporter (MCU). Its molecular action for Ca2+ uptake is tightly controlled by the MICU1-MICU2 heterodimer, which comprises Ca2+ sensing proteins which act as gatekeepers at low [Ca2+] or facilitators at high [Ca2+]. However, the mechanism underlying the regulation of the Ca2+ gatekeeping threshold for mitochondrial Ca2+ uptake through the MCU by the MICU1-MICU2 heterodimer remains unclear. In this study, we determined the crystal structure of the apo form of the human MICU1-MICU2 heterodimer that functions as the MCU gatekeeper. MICU1 and MICU2 assemble in the face-to-face heterodimer with salt bridges and me-thio-nine knobs stabilizing the heterodimer in an apo state. Structural analysis suggests how the heterodimer sets a higher Ca2+ threshold than the MICU1 homodimer. The structure of the heterodimer in the apo state provides a framework for understanding the gatekeeping role of the MICU1-MICU2 heterodimer.

Surface Energy Change of Atomic-Scale Metal Oxide Thin Films by Phase Transformation.

Fine-tuning of the surface free energy (SFE) of a solid material facilitates its use in a wide range of applications requiring precise control of the ubiquitous presence of liquid on the surface. In this study, we found that the SFE of rare-earth oxide (REO) thin films deposited by atomic layer deposition (ALD) gradually decreased with increasing film thickness; however, these changes could not be understood by classical interaction models. Herein, the mechanism underlying the aforesaid decrease was systematically studied by measuring contact angles, surface potential, adhesion force, crystalline structures, chemical compositions, and morphologies of the REO films. A growth mode of the REO films was observed: layer-by-layer growth at the initial stage with an amorphous phase and subsequent crystalline island growth, accompanied by a change in the crystalline structure and orientation that affects the SFE. The portion of the surface crystalline facets terminated with (222) and (440) planes evolved with an increase in ALD cycles and film thickness, as an amorphous phase was transformed. Based on this information, we demonstrated an SFE-tuned liquid tweezer with selectivity to target liquid droplets. We believe that the results of this fundamental and practical study, with excellent selectivity to liquids, will have significant impacts on coating technology.

Structural and Biochemical Characterization of EFhd1/Swiprosin-2, an Actin-Binding Protein in Mitochondria.

Ca2+ regulates several cellular functions, including signaling events, energy production, and cell survival. These cellular processes are mediated by Ca2+-binding proteins, such as EF-hand superfamily proteins. Among the EF-hand superfamily proteins, allograft inflammatory factor-1 (AIF-1) and swiprosin-1/EF-hand domain-containing protein 2 (EFhd2) are cytosolic actin-binding proteins. AIF-1 modulates the cytoskeleton and increases the migration of immune cells. EFhd2 is also a cytoskeletal protein implicated in immune cell activation and brain cell functions. EFhd1, a mitochondrial fraternal twin of EFhd2, mediates neuronal and pro-/pre-B cell differentiation and mitoflash activation. Although EFhd1 is important for maintaining mitochondrial morphology and energy synthesis, its mechanism of action remains unclear. Here, we report the crystal structure of the EFhd1 core domain comprising a C-terminus of a proline-rich region, two EF-hand domains, and a ligand mimic helix. Structural comparisons of EFhd1, EFhd2, and AIF-1 revealed similarities in their overall structures. In the structure of the EFhd1 core domain, two Zn2+ ions were observed at the interface of the crystal contact, suggesting the possibility of Zn2+-mediated multimerization. In addition, we found that EFhd1 has Ca2+-independent ß-actin-binding and Ca2+-dependent ß-actin-bundling activities. These findings suggest that EFhd1, an actin-binding and -bundling protein in the mitochondria, may contribute to the Ca2+-dependent regulation of mitochondrial morphology and energy synthesis.

New Korean isolates of Pepper mild mottle virus (PMMoV) differ in symptom severity and subcellular localization of the 126 kDa protein.

Two isolates of Pepper mild mottle virus (PMMoV) were selected from a nationwide survey of pepper fields in South Korea in 2014 and 2015, in which Cucumber mosaic virus was also detected; the two PMMoV isolates, Sangcheong 47 (S-47, KX399390) and Jeongsong 76 (J-76, KX399389), share ~99% nucleotide and amino acid identity and are closely related to Japanese and Chinese isolates at the nucleotide level. Amino acid sequence comparisons revealed 99.73, 99.81, 98.44, and 100% identity in the ORF1, ORF2, MP, and CP, respectively, between S-47 and J-76. In addition, we generated infectious clones of S-47 and J-76, and T7 promoter driven transcripts of each inoculated to Nicotiana benthamiana produced very severe symptoms, whereas only mild symptoms developed in Capsicum annuum. Gene silencing suppressor function of 126 kDa and cytoskeleton-connected plasmodesmata localization of movement protein of S-47 and J-76 showed no difference between isolates, whereas 126 kDa of J-76 clearly formed intracellular aggregates not observed with S-47 126 kDa protein. Differences between these isolates in 126/183 kDa-related functions including subcellular localization suggest that differential interactions with host proteins may affect symptom development in C. annuum.

Complete nucleotide sequences and construction of full-length infectious cDNA clones of cucumber green mottle mosaic virus (CGMMV) in a versatile newly developed binary vector including both 35S and T7 promoters.

Seed-transmitted viruses have caused significant damage to watermelon crops in Korea in recent years, with cucumber green mottle mosaic virus (CGMMV) infection widespread as a result of infected seed lots. To determine the likely origin of CGMMV infection, we collected CGMMV isolates from watermelon and melon fields and generated full-length infectious cDNA clones. The full-length cDNAs were cloned into newly constructed binary vector pJY, which includes both the 35S and T7 promoters for versatile usage (agroinfiltration and in vitro RNA transcription) and a modified hepatitis delta virus ribozyme sequence to precisely cleave RNA transcripts at the 3' end of the tobamovirus genome. Three CGMMV isolates (OMpj, Wpj, and Mpj) were separately evaluated for infectivity in Nicotiana benthamiana, demonstrated by either Agroinfiltration or inoculation with in vitro RNA transcripts. CGMMV nucleotide identities to other tobamoviruses were calculated from pairwise alignments using DNAMAN. CGMMV identities were 49.89% to tobacco mosaic virus; 49.85% to pepper mild mottle virus; 50.47% to tomato mosaic virus; 60.9% to zucchini green mottle mosaic virus; and 60.96% to kyuri green mottle mosaic virus, confirming that CGMMV is a distinct species most similar to other cucurbit-infecting tobamoviruses. We further performed phylogenetic analysis to determine relationships of our new Korean CGMMV isolates to previously characterized isolates from Canada, China, India, Israel, Japan, Korea, Russia, Spain, and Taiwan available from NCBI. Analysis of CGMMV amino acid sequences showed three major clades, broadly typified as 'Russian,' 'Israeli,' and 'Asian' groups. All of our new Korean isolates fell within the 'Asian' clade. Neither the 128 nor 186 kDa RdRps of the three new isolates showed any detectable gene silencing suppressor function.

IR and py/GC/MS examination of amber relics excavated from 6th century royal tomb in Korean Peninsula.

Relics of amber were excavated from King Muryeong's tomb constructed in the 6th century on the Korean peninsula. To estimate the provenance, FTIR (Fourier transform infrared spectroscopy) and py/GC/MS (pyrolysis/gas chromatography/mass spectrometry) analysis were utilized. The reference Baltic amber sample was also analyzed with the same method for comparison. The relics were confirmed to be amber from the FTIR analysis where an absorption band near 1150cm(-1), characteristic one in Baltic amber, was also observed. In py/GC/MS analysis, pyrolyzed products like butanedioic acid and dehydroabietic acid, known constituents of amber, were observed. In addition, d-fenchyl alcohol, camphor, borneol and butanedioic acid, typical constituents of Baltic amber, were observed in some samples. From this, it appears that some of relics were made from Baltic amber and that Baltic amber was transported to the Korean peninsula in the time of tomb construction.

Role of inferior orbital wall morphologic properties in isolated orbital blow-out fracture.

PURPOSE: To compare inferior orbital wall morphology between isolated inferior and medial orbital wall fracture patients. METHODS: The morphologic properties of patients with isolated blow-out fractures involving the medial wall or inferior wall treated from August 2004 to August 2009 were reviewed. The cross-sectional area, thickness, gradient, and curvature of the inferior wall were measured via orbital CT in the opposite non-traumatized eye. RESULTS: Patients with isolated inferior wall fractures (n = 77) and isolated medial wall fractures (n = 78) evidenced no differences in sex, age, etiology of trauma, laterality of trauma, and associated concomitant intraocular injuries. The cross-sectional area, thickness, and gradient of the inferior wall did not differ significantly between the 2 groups. However, the coefficient of curvature was significantly greater in patients with inferior wall fracture than in patients with medial wall fracture (0.016 ± 0.006 vs. 0.006 ± 0.002, respectively; p = 0.000). CONCLUSION: Patients with more convex and steep inferior walls are more likely to incur isolated inferior wall fractures than isolated medial wall fractures.

The application of isotope ratio mass spectrometry for discrimination and comparison of adhesive tapes.

Forensic scientists are frequently requested to differentiate between, or compare, adhesive tapes from a suspect or a crime scene. The most common polymers used to back packaging tape are polypropylene and polyvinyl chloride. Much of the oriented polypropylene (OPP) needed to produce packaging tapes, regardless of the tape brand, is supplied by just a few polymer manufacturers. Consequently, the composition of the backing material varies little. Therefore, the discriminating power of classical methods (physical fit, tape dimensions, colour, morphology, FTIR, PyGC/MS, etc.) is limited. Analysis of stable isotopes using isotope ratio mass spectrometry (IRMS) has been applied in the broad area of forensics and it has been reported that isotope analysis is a valuable tool for the identification of adhesive tapes. We have tested the usefulness of this method by distinguishing different South Korean adhesive tapes produced by just a few manufacturers in the small South Korean market. Korean adhesive tapes were collected and analysed for their isotope signatures. The glue of the tapes was separated from the backing material and these sub-samples were analysed for their H- and C-isotope composition. The result shows the possibility for discriminating most tape samples, even from the same brand. Variations within single rolls have also been investigated, where no variations in H- and C-isotope composition significantly exceeding the standard deviation were found.

Immunochromatographic analysis of hippuric acid in urine.

Toluene, a clear, colorless liquid with a distinctive smell, is the most commonly used industrial organic solvent. The adverse effects of chronic toluene exposure have been reported. The abuse of volatile substances is practiced mainly by adolescents and young adults. Chronic toluene abuse causes permanent changes in brain structure correlated with brain dysfunction; therefore, it is important to monitor the level of toluene exposure to prevent neurological damages. In this study, immunochromatographic analysis was performed to measure a level of the exposed toluene easily and accurately in urine. Inhaled toluene is metabolized to hippuric acid (HA) in the liver and secreted in urine. Therefore, the monoclonal antibodies against HA were generated and characterized by indirect competitive ELISA. The sensitivity was then monitored in order to adjust the cutoff concentration to 2 mg of HA/mL of urine. Using these monoclonal antibodies as raw materials, the immunochromatographic device was manufactured with the lateral flow system. The clinical studies were performed with suspected users' urine samples, and the results were confirmed by high-performance liquid chromatography.

[Effects of the personal stereo system on hearing in adolescents].

OBJECTIVES: This study was conducted to evaluate the effects of the personal stereo system on the hearing in adolescents. METHODS: A total of 68 adolescents (age: 13-18 years) who visited the ENT Department at a University Hospital in Daegu were personally interviewed. The questionnaires were about general characteristics of the subjects, the time of personal stereo system use (year, hour) and place. Cumulative exposure to the personal stereo system was calculated by the product of the total years and the daily hours of their use. Pure tone audiometry was performed and the hearing threshold was measured at 500, 1000, 2000, 4000 and 8000 Hz. RESULTS: The average time of using a personal stereo system a day was about 3 hours and 75% of the subjects used a personal stereo system for 2-5 years. The elevation of threshold was more prominent in the subjects who used personal stereo systems for 4 years and more compared with those subjects who used them for 3 years and under. The elevation of hearing threshold was also more prominent in the subjects who used personal stereo systems for 4 hours and more a day compared with those subjects who used personal stereo systems for 3 hours and under a day. The elevation of hearing threshold was more prominent in the subjects who used personal stereo systems for 13 hour x years and more compared to the subjects who used them 12 hour x years and under. CONCLUSIONS: These results suggest that the elevation of hearing threshold can happen to adolescents who used personal stereo systems for a long time. In order to prevent hearing loss, we need to teach adolescents appropriate usage of the personal stereo system and hearing tests should be included in the periodic school-based physical examination for the adolescents.

Quantification of propane in biological materials by head-space GC.

Propane was measured in specimens taken from two persons who died from a LPG explosion in an apartment using head-space-GC/FID. Because of the variation of instrument performance and sample injection, the internal standard pentane was used. Calibration standards were prepared by injecting each calculated volume of pure propane gas into capped vials containing 2 ml of blood and 5 microl of internal standard. The calibration curve revealed good linearity from 0.09 microg/ml to at least 90 microg/ml. The method validation data also included repeatability and recovery. The propane quantities in blood, fat and brain tissue were between 0.27 and 71 microg/ml (microg/g) with the highest concentration observed in fat. The confirmation of propane was conducted by the means of solid phase micro-extraction and mass spectrometry.