Suhyung Cho

DNA-Assisted Exfoliation of Tungsten Dichalcogenides and Their Antibacterial Effect

This study reports a method for the facile and high-yield exfoliation of WX2 (X = S, Se) by sonication under aqueous conditions using single-stranded DNA (abbreviated as ssDNA) of high molecular weight. The ssDNA provided a high degree of stabilization and prevented reaggregation, and it enhanced the exfoliation efficiency of WX2 nanosheets due to adsorption on the WX2 surface and the electrostatic repulsion of sugars in the ssDNA backbone. The exfoliation yield was higher with ssDNA (80%-90%) than without (2%-4%); the yield with ssDNA was also higher than the value previously reported for aqueous exfoliation (∼10%). Given that two-dimensional nanomaterials have potential health and environmental applications, we investigated antibacterial activity of exfoliated WX2-ssDNA nanosheets, relative to graphene oxide (GO), and found that WSe2-ssDNA nanosheets had higher antibacterial activity against Escherichia coli K-12 MG1655 cells than GO. Our method enables large-scale exfoliation in an aqueous environment in a single step with a short reaction time and under ambient conditions, and it can be used to produce surface-active or catalytic materials that have broad applications in biomedicine and other areas.

Rational design of modular allosteric aptamer sensor for label-free protein detection.

An aptamer can be redesigned to new functional molecules by conjugating with other oligonucleotides. However, it requires experimental trials to optimize the conjugating module with the sensitivity and selectivity toward a target. To reduce these efforts, we report rationally-designed modular allosteric aptamer sensor (MAAS), which is composed of coupled two aptamers and the regulator. For label-free protein detection, the protein-aptamer was conjugated with the malachite green (MG) aptamer for signaling. The MAAS additionally has the regulator domain which is designed to hybridize to a protein binding domain. The regulator makes MAAS to be inactive by destructing the original structure of the two aptamers. However, its conformation becomes active by dissociating the hybridization from the protein recognition signal, thereby inducing the binding of MG emitting the enhanced fluorescence. The design of regulator is based on the thermodynamic energy difference by the RNA conformational change and protein-aptamer affinity. Here we first demonstrated the MAAS for hepatitis C helicase and replicase. The target proteins were detected up to 250nM with minimized blank signals and displayed high specificities 10-fold greater than in non-specific proteins. The MAAS provides valuable tools that can be adapted to a wide range of configurations in bioanalytical applications.

Multilayer fluorescence optically encoded beads for protein detection

An easy preparation method of multilayer fluorescence optically encoded beads for protein detection is presented. The beads, which consist of multicolored layers, are made from amino polyethylene glycol grafted polystyrene (PS-g-PEG) beads by using several fluorescent dyes such as fluorescein isothiocyanate (FITC) and rhodamine via controlling diffusion of an Fmoc-protecting group after HCl solution swelling. A biotin, glutathione S-transferase (GST) antibody, and an RNA aptamer that specifically recognize streptavidin, GST antigen, and hepatitis C virus (HCV) helicase are introduced to the optically encoded beads and monitored for their binding activity to the target molecules. After binding, the ligands are identified easily by their color codes.

Emerging tools for synthetic genome design

Synthetic biology is an emerging discipline for designing and synthesizing predictable, measurable, controllable, and transformable biological systems. These newly designed biological systems have great potential for the development of cheaper drugs, green fuels, biodegradable plastics, and targeted cancer therapies over the coming years. Fortunately, our ability to quickly and accurately engineer biological systems that behave predictably has been dramatically expanded by significant advances in DNA-sequencing, DNA-synthesis, and DNA-editing technologies. Here, we review emerging technologies and methodologies in the field of building designed biological systems, and we discuss their future perspectives.

In vitro selection of sialic acid specific RNA aptamer and its application to the rapid sensing of sialic acid modified sugars

Sialic acids (SAs) are located on the terminal positions of glycan on a cell surface, which play important role in the spread and metastasis of cancer cells and infection of pathogen. For their detection and diagnosis, the finding of SA specific ligand is an essential prerequisite. Here, RNA aptamer for N‐acetylneuraminic acid (Neu5Ac), a representative of SAs, with the high affinity of 1.35 nM and the selectivity was screened by in vitro selection method. The strong binding of the screened aptamer was enough to protect the hydrolysis of Neu5Ac by neuraminidase with the stoichiometry of 1:1 molar ratio. For the rapid detection of SAs, the RNA aptamer was further engineered to the aptazyme sensor by conjugating with a ribozyme following the characterization of selected aptamer by RNase footprinting assay. Without additional desialylation, modification, or/and purification processes, the aptazyme indicated high catalytic activities in the presence of Neu5Ac over 20 µM in several minutes. Also, we observed that the aptazyme sensor shows high sensitivities to Neu5Ac‐conjugated sugars as well as Neu5Ac monomer, but not in non‐Neu5Ac modified sugars. The aptamer for Neu5Ac can support valuable tools in a wide range of bioanalytical applications as well as biosensors. Biotechnol. Bioeng. 2013; 110: 905–913.

Pax-7 Immunoreactivity in the Post-natal Chicken Central Nervous System

In this immunocytochemical study on the constitutive expression of Pax‐7 protein in the postnatal chicken brain, Pax‐7 showed region and cell type specific expression. In the optic tectum, only cells in grey matter showed positive immunoreactivities (IRs), whereas those in the white matters did not show any IRs. In thalamic nuclei and several pontine nuclei, we also localized Pax‐7 positive IRs. On the contrary, in the cerebellum, Pax‐7 was mainly localized within the Bergmann glia, whereas Purkinje cells did not show any IRs. In double immunolabelling studies, most of the Pax‐7 IRs did not originate from neuroglial cells such as oligodendrocytes, microglia or astrocytes, but from neurons, with the exception of Bergmann glia in the cerebellum. The presence of Pax‐7 IRs in the adult chicken brain could suggest that Pax‐7 might play a role in maintaining normal physiological function in some postnatal chicken brain cells.

Cerebral glucose metabolism in oculopalatal tremor

No study adopted the statistical parametric mapping (SPM) analyses of 18F‐fluorodeoxy glucose (FDG) PET in a large number of patients with oculopalatal tremor (OPT). To determine regional cerebral glucose metabolism in patients with OPT, nine patients with OPT underwent FDG‐PET of the brain. Their glucose metabolism was compared with that of 50 normal controls (NC) by using SPM analyses. Three patients had bilateral and six showed unilateral pseudohypertrophic degeneration of the inferior olivary nucleus (ION) on MRI. Compared with NC, OPT patients did not show any metabolic derangement in the anterolateral medulla where the pseudohypertrophic ION locates. Instead, six patients with unilateral ION changes had hypometabolism in ipsilesional pontine tegmentum and hypermetabolism in contralesional thalamus. Their metabolic changes did not depend on the lateralization of ION changes. Our study failed to present any metabolic evidence for the role of ION in the generation of OPT. In part, the failure might originate from the different pathomechanism between OPT and pure palatal tremor or sensitivity/specificity issues of PET and SPM analyses. But, our results suggest that impaired cell groups of the paramedian tract and thalamic tremor cells may contribute to the generation of OPT.

Genome-wide primary transcriptome analysis of H 2 -producing archaeon Thermococcus onnurineus NA1

In spite of their pivotal roles in transcriptional and post-transcriptional processes, the regulatory elements of archaeal genomes are not yet fully understood. Here, we determine the primary transcriptome of the H2-producing archaeon Thermococcus onnurineus NA1. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA box, A-rich B recognition element (BRE), and promoter proximal element (PPE) motif in promoter regions, a high pyrimidine nucleotide content (T/C) at the −1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5′ untranslated regions (5′ UTRs). Along with differential transcript levels, 117 leaderless genes and 86 non-coding RNAs (ncRNAs) were identified, representing diverse cellular functions and potential regulatory functions under the different growth conditions. Interestingly, we observed low GC content in ncRNAs for RNA-based regulation via unstructured forms or interaction with other cellular components. Further comparative analysis of T. onnurineus upstream regulatory sequences with those of closely related archaeal genomes demonstrated that transcription of orthologous genes are initiated by highly conserved promoter sequences, however their upstream sequences for transcriptional and translational regulation are largely diverse. These results provide the genetic information of T. onnurineus for its future application in metabolic engineering.

Effect of stroke volume variation-directed fluid management on blood loss during living-donor right hepatectomy: a randomised controlled study.

Reducing blood loss is beneficial in living liver donor hepatectomy. Although it has been suggested that maintaining a low central venous pressure is important, it is known that low stroke volume variation may be associated with increased blood loss. Therefore, we compared the effect on blood loss of 40 patients randomly assigned to a high stroke volume variation group (maintaining 10–20% of stroke volume variation) vs 38 patients in a control group (maintaining < 10% stroke volume variation) during living‐donor right hepatectomy. Mean (SD) blood loss during donor hepatectomy was significantly lower in the high stroke volume variation group than in the control group: 476 (131) ml vs 836 (341) ml, respectively (p < 0.001). Blood pressure and peri‐operative laboratory values did not differ between the two groups. However, in the high stroke volume variation group, central venous pressure values were also significantly lower. We were unable to disentangle the effects of stroke volume variation and central venous pressure, but our results confirm that the two together appear beneficial.

Intraoperative factors associated with delayed recovery of liver function after hepatectomy: analysis of 1969 living donors

The safety of healthy living donors who are undergoing hepatic resection is a primary concern. We aimed to identify intraoperative anaesthetic and surgical factors associated with delayed recovery of liver function after hepatectomy in living donors.