Development of Single Molecule Electronic SNP Assays using Polymer Tagged Nucleotides and Nanopore Detection

As knowledge of the human genome has accelerated, various diseases and individuals’ responses to drugs have been pinpointed to specific DNA variations in one’s genome. Among many different types of variants, the most common and simplest is the single nucleotide polymorphism (SNP) in which a single base substitution occurs. Although there have been considerable improvements in technologies that can reveal a single base difference in a DNA strand, simple and affordable methods that have high detection sensitivity and require small sample volume are expected to facilitate widespread adoption of routine SNP analysis in clinical settings. One such method that meets these requirements is to use nanopore as a single molecule detector, an emerging analytic system that detects changes in current related to molecules occupying a nanometer aperture. This dissertation thus chronicles our endeavors in developing a nanopore-based SNP assay using polymer tagged dideoxynucleotides (ddNTPs). The fundamental principles of this method rely on single base extension (SBE) of a primer by DNA polymerase using polymer tagged ddNTP analogs for allele discrimination and simple electronic readout of an alpha hemolysin (αHL) nanopore current for allele detection at the single molecule level. Using four uniquely tagged ddNTPs, a characteristic current level that is specific to each base is produced, thus identifying the SNP alleles present and the genotype at the site. To demonstrate the feasibility of this approach, four polymer attached ddNTPs, each with a different tag that generates a characteristic current blockade level in the αHL nanopore, were designed and synthesized. To search for a DNA polymerase that can accept these tagged ddNTP analogs as substrates, several candidate DNA polymerases were surveyed and their relative efficiencies for incorporation of the analogs were compared (Chapter 2). To generate a steady and stable blockade event for accurate SNP analysis, two different means of positioning a tag molecule in the αHL nanopore after the SBE reaction have been explored: covalent conjugation of DNA primer to the pore and immobilization of biotinylated primer within the pore by streptavidin. To find a suitable position for primer attachment on the pore, three αHL mutants, each with a different single conjugation point, were constructed. Using these mutants, different DNA-pore conjugates were produced and purified via various chromatography systems (Chapter 3). In the nanopore system, charged molecules such as DNA are electrophoretically driven through the pore under an applied voltage, thereby modulating the ionic current through the nanopore. This current reveals useful information about the structure and dynamic motion of the molecule at the single molecule level. Before performing SNP analysis, we first studied single molecule behaviors of oligonucleotides of different lengths and structures in the αHL pore and their ensuing current signatures in the system (Chapter 4). Finally, harnessed with tools and insights from the nanopore single molecule studies, actual SNP assays were performed in our nanopore system using the polymer tagged ddNTPs and SBE. Chapter 5 discusses the integrated approach where SBE is achieved on a primer-conjugated αHL nanopore and Chapter 6 presents the results using a biotin-streptavidin complex for immobilization of tag molecules in the pore. Overall, this thesis validates adaptation of the nanopore detection system for SNP analysis using the polymer tagged ddNTPs

Podosomes and Invadopodia: Related structures with Common Protein Components that May Promote Breast Cancer Cellular Invasion

A rate-limiting step in breast cancer progression is acquisition of the invasive phenotype, which can precede metastasis. Expression of cell-surface proteases at the leading edge of a migrating cell provides cells with a mechanism to cross tissue barriers. A newly appreciated mechanism that may be relevant for breast cancer cell invasion is the formation of invadopodia, well-defined structures that project from the ventral membrane and promote degradation of the extracellular matrix, allowing the cell to cross a tissue barrier. Recently, there has been some controversy and discussion as to whether invadopodia, which are associated with carcinoma cells, are related to a similar structure called podosomes, which are associated with normal cells. Invadopodia and podosomes share many common characteristics, including a similar size, shape, subcellular localization and an ability to promote invasion. These two structures also share many common protein components, which we outline herein. It has been speculated that podosomes may be precursors to invadopodia and by extension both structures may be relevant to cancer cell invasion. Here, we compare and contrast the protein components of invadopodia and podosomes and discuss a potential role for these proteins and the evidence that supports a role for invadopodia and podosomes in breast cancer invasion

Facile Synthesis of Porous Silicon Nanofibers by Magnesium Reduction for Application in Lithium Ion Batteries

We report a facile fabrication of porous silicon nanofibers by a simple three-stage procedure. Polymer/silicon precursor composite nanofibers are first fabricated by electrospinning, a water-based spinning dope, which undergoes subsequent heat treatment and then reduction using magnesium to be converted into porous silicon nanofibers. The porous silicon nanofibers are coated with a graphene by using a plasma-enhanced chemical vapor deposition for use as an anode material of lithium ion batteries. The porous silicon nanofibers can be mass-produced by a simple and solvent-free method, which uses an environmental-friendly polymer solution. The graphene-coated silicon nanofibers show an improved cycling performance of a capacity retention than the pure silicon nanofibers due to the suppression of the volume change and the increase of electric conductivity by the graphene.Korea Institute of Energy Technology Evaluation and Planning (Human Resources Development Program Grant 20144030200600

META-BTS: Bootstrapping Precision Beyond the Limit

Bootstrapping, which enables the full homomorphic encryption scheme that can perform an infinite number of operations by restoring the modulus of the ciphertext with a small modulus, is an essential step in homomorphic encryption. However, bootstrapping is the most time and memory consuming of all homomorphic operations. As we increase the precision of bootstrapping, a large amount of computational resources is required. Specifically, for any of the previous bootstrap designs, the precision of bootstrapping is limited by rescaling precision. In this paper, we propose a new bootstrapping algorithm of the Cheon-Kim-Kim-Song (CKKS) scheme to use a known bootstrapping algorithm repeatedly, so called { Meta-BTS}. By repeating the original bootstrapping operation twice, one can obtain another bootstrapping with its precision essentially doubled; it can be generalized to be $k$-fold bootstrapping operations for some $k>1$ while the ciphertext size is large enough. Our algorithm overcomes the precision limitation given by the rescale operation

Benserazide, the first allosteric inhibitor of Coxsackievirus B3 3C protease

AbstractCoxsackievirus B3 is the main cause of human viral myocarditis and cardiomyopathy. Virally encoded Coxsackievirus 3C protease (3Cpro) plays an essential role in viral proliferation. Here, benserazide was discovered as a novel inhibitor from a drug library screen targeting Coxsackievirus 3Cpro using a FRET-based enzyme assay. Benserazide, whose chemical structure has no electrophilic functional groups, was characterized as a non-competitive inhibitor by enzyme kinetic studies. A molecular docking study with benserazide and its analogs indicated that a novel putative allosteric binding site was involved. Specifically, a 2,3,4-trihydroxybenzyl moiety was determined to be a key pharmacophore for the enzyme’s inhibitory activity. We suggest that the putative allosteric binding site may be a novel target for future therapeutic strategies

Updates on the genetic variations of Norovirus in sporadic gastroenteritis in Chungnam Korea, 2009-2010

Previously, we explored the epidemic pattern and molecular characterization of noroviruses (NoVs) isolated in Chungnam, Korea in 2008, and the present study extended these observations to 2009 and 2010. In Korea, NoVs showed the seasonal prevalence from late fall to spring, and widely detected in preschool children and peoples over 60 years of age. Epidemiological pattern of NoV was similar in 2008 and in 2010, but pattern in 2009 was affected by pandemic influenza A/H1N1 2009 virus. NoV-positive samples were subjected to sequence determination of the capsid gene region, which resolved the isolated NoVs into five GI (2, 6, 7, 9 and 10) and eleven GII genotypes (1, 2, 3, 4, 6, 7, 8, 12, 13, 16 and 17). The most prevalent genotype was GII.4 and occupied 130 out of 211 NoV isolates (61.6%). Comparison of NoV GII.4 of prevalent genotype in these periods with reference strains of the same genotype was conducted to genetic analysis by a phylogenetic tree. The NoV GII.4 strains were segregated into seven distinct genetic groups, which are supported by high bootstrap values and previously reported clusters. All Korean NoV GII.4 strains belonged to either VI cluster or VII cluster. The divergence of nucleotide sequences within VI and VII intra-clusters was > 3.9% and > 3.5%, respectively. The "Chungnam(06-117)/2010" strain which was isolated in June 2010 was a variant that did not belong to cluster VI or VII and showed 5.8-8.2%, 6.2-8.1% nucleotide divergence with cluster VI and VII, respectively

Automatic consultation system for patients with cardiac implantable electronic devices undergoing magnetic resonance imaging

Background Safety evaluation for patients with cardiac implantable electronic devices (CIEDs) undergoing magnetic resonance imaging (MRI) scanning is often overlooked. We developed an automatic consultation system (ACS) to improve the screening rate in these patients. Methods ACS was developed by the Hospital Information System Development Department of Seoul National University Bundang Hospital. It was designed to automatically request pre-MRI cardiac evaluation in patients with CIED when MRI orders are issued. The proportion of the patients without pre-MRI cardiologic evaluation was evaluated before and after the ACS application. Results From January 2016 to June 2018, a total of 157 patients with CIEDs [pacemaker 136 (86.6%), ICD or CRT-D 21 (13.4%), MR-conditional 117 (74.5%)] visited the MRI facility. Before the ACS application, 23 out of 84 patients (27.4%) did not have adequate pre-MRI cardiologic evaluation. Despite urgent request for pre-MRI cardiac evaluation, MRI examination was postponed or cancelled in 14 (60.8%) cases. After the ACS application, all 73 patients underwent proper cardiologic evaluation before their MRI examinations (P < 0.001). The proportion of immediate request for pre-MRI evaluation at the moment of MRI order also improved with the ACS application (before ACS 57.1%, after ACS 100%, P < 0.001). Conclusions The newly developed ACS helped the patients with CIED receive MRI scan safely on the schedule, improving the quality of care in this population

Impact of successful restoration of sinus rhythm in patients with atrial fibrillation and acute heart failure: Results from the Korean Acute Heart Failure registry

Background: Restoring and maintaining sinus rhythm (SR) in patients with atrial fibrillation (AF) failed to show superior outcomes over rate control strategies in prior randomized trials. However, there is sparse data on their outcomes in patients with acute heart failure (AHF).Methods: From December 2010 to February 2014, 5,625 patients with AHF from 10 tertiary hospitals were enrolled in the Korean Acute Heart Failure registry, including 1,961 patients whose initial electrocardiogram showed AF. Clinical outcomes of patients who restored SR by pharmacological or electrical cardioversion (SR conversion group, n = 212) were compared to those of patients who showed a persistent AF rhythm (AF persistent group, n = 1,662).Results: All-cause mortality both in-hospital and during the follow-up (median 2.5 years) were significantly lower in the SR conversion group than in the AF persistent group after adjustment for risk factors (adjusted hazard ratio [HR]; 95% confidence interval [CI] = 0.26 [0.08–0.88], p = 0.031 and 0.59 [0.43–0.82], p = 0.002, for mortality in-hospital and during follow-up, respectively). After 1:3 propensity score matching (SR conversion group = 167, AF persistent group = 501), successful restoration of SR was associated with lower all-cause mortality (HR [95% CI] = 0.68 [0.49–0.93], p = 0.015), heart failure rehospitalization (HR [95% CI] = 0.66 [0.45–0.97], p = 0.032), and composite of death and heart failure rehospitalization (HR [95% CI] = 0.66 [0.51–0.86], p = 0.002).Conclusions: Patients with AHF and AF had significantly lower mortality in-hospital and during follow-up if rhythm treatment for AF was successful, underscoring the importance of restoring SR in patients with AHF

Seawater Battery-Based Wireless Marine Buoy System with Battery Degradation Prediction and Multiple Power Optimization Capabilities

This paper presents a wireless marine buoy system based on the seawater battery (SWB), providing self-powered operation, power-efficient management, and degradation prediction and fault detection. Since conventional open circuit voltage (OCV) methods cannot be applied due to inherent cell characteristics of SWB, the coulomb counting (CC) method is adopted for the state of charge (SOC) monitoring. For the state of health (SOH), a variance-based detection scheme is proposed to provide degradation prediction and fault detection of the SWB. The self-powered operation is augmented by two proposed power optimization schemes such as multiple power management and three-step LED light control. A wireless buoy system prototype is manufactured, and its functional feasibility is experimentally verified, where its location and SOC are periodically monitored in a smartphone-based wireless platform