STADIUM: Species-Specific tRNA Adaptive Index Compendium

Due to the increasing interest in synonymous codons, several codon bias-related terms were introduced. As one measure of them, the tRNA adaptation index (tAI) was invented about a decade ago. The tAI is a measure of translational efficiency for a gene and is calculated based on the abundance of intracellular tRNA and the binding strength between a codon and a tRNA. The index has been widely used in various fields of molecular evolution, genetics, and pharmacology. Afterwards, an improved version of the index, named specific tRNA adaptation index (stAI), was developed by adapting tRNA copy numbers in species. Although a subsequently developed webserver (stAIcalc) provided tools that calculated stAI values, it was not available to access pre-calculated values. In addition to about 100 species in stAIcalc, we calculated stAI values for whole coding sequences in 148 species. To enable easy access to this index, we constructed a novel web database, named STADIUM (Species-specific tRNA adaptive index compendium). STADIUM provides not only the stAI value of each gene but also statistics based on pathway-based classification. The database is expected to help researchers who have interests in codon optimality and the role of synonymous codons. STADIUM is freely available at http://stadium.pmrc.re.kr

Identification of New Potential APE1 Inhibitors by Pharmacophore Modeling and Molecular Docking

Apurinic/apyrimidinic endonuclease 1 (APE1) is an enzyme responsible for the initial step in the base excision repair pathway and is known to be a potential drug target for treating cancers, because its expression is associated with resistance to DNA-damaging anticancer agents. Although several inhibitors already have been identified, the identification of novel kinds of potential inhibitors of APE1 could provide a seed for the development of improved anticancer drugs. For this purpose, we first classified known inhibitors of APE1. According to the classification, we constructed two distinct pharmacophore models. We screened more than 3 million lead-like compounds using the pharmacophores. Hits that fulfilled the features of the pharmacophore models were identified. In addition to the pharmacophore screen, we carried out molecular docking to prioritize hits. Based on these processes, we ultimately identified 1,338 potential inhibitors of APE1 with predicted binding affinities to the enzyme

Magnetophoretic Decoupler for Disaggregation and Interparticle Distance Control

The manipulation of superparamagnetic beads has attracted various lab on a chip and magnetic tweezer platforms for separating, sorting, and labeling cells and bioentities, but the irreversible aggregation of beads owing to magnetic interactions has limited its actual functionality. Here, an efficient solution is developed for the disaggregation of magnetic beads and interparticle distance control with a magnetophoretic decoupler using an external rotating magnetic field. A unique magnetic potential energy distribution in the form of an asymmetric magnetic thin film around the gap is created and tuned in a controlled manner, regulated by the size ratio of the bead with a magnetic pattern. Hence, the aggregated beads are detached into single beads and transported in one direction in an array pattern. Furthermore, the simultaneous and accurate spacing control of multiple magnetic bead pairs is performed by adjusting the angle of the rotating magnetic field, which continuously changes the energy well associated with a specific shape of the magnetic patterns. This technique offers an advanced solution for the disaggregation and controlled manipulation of beads, can allow new possibilities for the enhanced functioning of lab on a chip and magnetic tweezers platforms for biological assays, intercellular interactions, and magnetic biochip systems. © 2021 The Authors. Advanced Science published by Wiley-VCH GmbH1

The Look-back Time Evolution of Far-Ultraviolet Flux from the Brightest Cluster Elliptical Galaxies at z < 0.2

We present the GALEX UV photometry of the elliptical galaxies in Abell clusters at moderate redshifts (z < 0.2) for the study of the look-back time evolution of the UV upturn phenomenon. The brightest elliptical galaxies (M_r < -22) in 12 remote clusters are compared with the nearby giant elliptical galaxies of comparable optical luminosity in the Fornax and Virgo clusters. The sample galaxies presented here appear to be quiescent without signs of massive star formation or strong nuclear activity, and show smooth, extended profiles in their UV images indicating that the far-UV (FUV) light is mostly produced by hot stars in the underlying old stellar population. Compared to their counterparts in nearby clusters, the FUV flux of cluster giant elliptical galaxies at moderate redshifts fades rapidly with ~ 2 Gyrs of look-back time, and the observed pace in FUV - V color evolution agrees reasonably well with the prediction from the population synthesis models where the dominant FUV source is hot horizontal-branch stars and their progeny. A similar amount of color spread (~ 1 mag) in FUV - V exists among the brightest cluster elliptical galaxies at z ~ 0.1, as observed among the nearby giant elliptical galaxies of comparable optical luminosity.Comment: Accepted for publication in the Special GALEX ApJ Supplement, December 200

SEALONE (Safety and Efficacy of Coronary Computed Tomography Angiography with Low Dose in Patients Visiting Emergency Room) trial: study protocol for a randomized controlled trial

Objective Chest pain is one of the most common complaints in the emergency department (ED). Cardiac computed tomography angiography (CCTA) is a frequently used tool for the early triage of patients with low- to intermediate-risk acute chest pain. We present a study protocol for a multicenter prospective randomized controlled clinical trial testing the hypothesis that a low-dose CCTA protocol using prospective electrocardiogram (ECG)-triggering and limited-scan range can provide sufficient diagnostic safety for early triage of patients with acute chest pain. Methods The trial will include 681 younger adult (aged 20 to 55) patients visiting EDs of three academic hospitals for acute chest pain or equivalent symptoms who require further evaluation to rule out acute coronary syndrome. Participants will be randomly allocated to either low-dose or conventional CCTA protocol at a 2:1 ratio. The low-dose group will undergo CCTA with prospective ECG-triggering and restricted scan range from sub-carina to heart base. The conventional protocol group will undergo CCTA with retrospective ECG-gating covering the entire chest. Patient disposition is determined based on computed tomography findings and clinical progression and all patients are followed for a month. The primary objective is to prove that the chance of experiencing any hard event within 30 days after a negative low-dose CCTA is less than 1%. The secondary objectives are comparisons of the amount of radiation exposure, ED length of stay and overall cost. Results and Conclusion Our low-dose protocol is readily applicable to current multi-detector computed tomography devices. If this study proves its safety and efficacy, dose-reduction without purchasing of expensive newer devices would be possible

자기영동 어플리케이션을 위한 스핀트로닉스 디바이스의 개발

Spintronics device, Spintrophoresis, Magnetic domain, Mechanical-Barkhausen, Lab-on-a-chip, Single-cell manipulation, Single-cell analysisNⅠ. Introduction 1 1.1 Cell manipulation for single cell analysis 3 1.2 Spintronic micro-devices for magnetic material manipulation 11 1.3 Spintrophoretic circuit 15 1.4 Mechanical-Barkhausen analysis by discontinuity of bead movement 20 Ⅱ. Experimental methods 24 1. Fabrication of On-chip micromagnet 25 1.1 Lithography 25 1.1.1 Photolithography 27 1.1.2 Thermal scanning probe lithography (t-SPL) 29 1.1.3 Electron beam lithography 31 1.2 Magnetron sputtering 33 2. Domain structures of micromagnets 35 3. Single cell conjugation with magnetic particles 37 4. Experimental set-up 41 5. Data and image analysis methods 41 Ⅲ. Theoretical background 42 1. Magnetic energy in the micromagnet 43 2.Magnetic domain 46 3. Numerical calculations 48 3.1 Magnetization 48 3.2. Driving forces on magnetic particles 49 3.3. Simulation of magnetic particles trajectories 52 4. Mechanical-Barkhausen analysis 54 Ⅳ. Result and discussion 57 1. Analysis of Momentary Mechanical-Barkhausen 57 1.1 Discontinuous movement of magnetic domain on Disk shaped micromagnet 57 1.2 Discontinuous movement of magnetic domain on Ellipse shaped micromagnet 61 2. Control of Periodic Mechanical-Barkhausen 64 2.1 Controlling discontinuous motion of magnetic particles using cracks 64 2.2 Controlling physical properties of magnetically labeled micro-object using Ellipse curvature 76 3. Magnetophoretic application based on Mechanical-Barkhausen analysis 91 3.1 Flower shaped Junction in Spintrophoresis POCT application 91 3.2 Spintrophoretic micro-distributor for controlled clustering of cells 95 Ⅴ. Summary and Future Perspectives 105 1 Summary 106 2. Future Perspectives 108 Reference 110 요약문 115 List of Publications 117DoctordCollectio

Structural Analysis of Recombinant Human Preproinsulins by Structure Prediction, Molecular Dynamics, and Protein-Protein Docking

More effective production of human insulin is important, because insulin is the main medication that is used to treat multiple types of diabetes and because many people are suffering from diabetes. The current system of insulin production is based on recombinant DNA technology, and the expression vector is composed of a preproinsulin sequence that is a fused form of an artificial leader peptide and the native proinsulin. It has been reported that the sequence of the leader peptide affects the production of insulin. To analyze how the leader peptide affects the maturation of insulin structurally, we adapted several in silico simulations using 13 artificial proinsulin sequences. Three-dimensional structures of models were predicted and compared. Although their sequences had few differences, the predicted structures were somewhat different. The structures were refined by molecular dynamics simulation, and the energy of each model was estimated. Then, protein-protein docking between the models and trypsin was carried out to compare how efficiently the protease could access the cleavage sites of the proinsulin models. The results showed some concordance with experimental results that have been reported; so, we expect our analysis will be used to predict the optimized sequence of artificial proinsulin for more effective production

All natural cork composites with suberin-based polyester and lignocellulosic residue

Suberin is an aromatic-aliphatic cross-linked polyester structure which constitutes cell wall structures of cork. It is particularly interesting for its use of monomeric compounds towards renewable bio-based polymers. In this study, the extraction of suberin monomers was successfully done by green method using alkaline hydrolysis combined with mechanical grinding. As the mechanical grinding was applied along with hydrolysis process, the maximum yield of depolymerized suberin monomer (DSM) with relatively low energy and less time was acheived. The polarity and functionality of DSM extracted in this study also showed higher values compared to conventional reflux hydrolysis process. Polyesterification and curing behavior of DSM were examined with molecular weights and mechanical properties of the ensuing polyesters. Tensile properties of suberin-based polyesters are reported for the first time that the maximum strength was found to be 7.3 MPa while Young's modulus was found to be 105 MPa. Furthermore, all natural cork composites were fabricated which comprise suberin-based polyester as matrix and lignocellulosic residue as reinforcement, and also reported their significantly enhanced tensile properties showing the great potential as an alternative green polymer composites for various engineering applications

Magnetophoretic Micro-Distributor for Controlled Clustering of Cells

Cell clustering techniques are important to produce artificial cell clusters for in vitro models of intercellular mechanisms at the single-cell level. The analyses considering physical variables such as the shape and size of cells have been very limited. In addition, the precise manipulation of cells and control of the physical variables are still challenging. In this paper, a magnetophoretic device consisting of a trampoline micromagnet and active elements that enable the control of individual selective jumping motion and positioning of a micro-object is proposed. Based on a numerical simulation under various conditions, automatic separation or selective clustering of micro-objects according to their sizes is performed by parallel control and programmable manipulation. This method provides efficient control of the physical variables of cells and grouping of cells with the desired size and number, which can be a milestone for a better understanding of the intercellular dynamics between clustered cells at the single-cell level for future cell-on-chip applications.1