Biomedical subjects

Sunhee Kim

Publications and source records attributed to Sunhee Kim.

10 recordsLinked to original sources

PubMed2026

A portable recalibration workflow for reference-based variant calling in non-human genomes.

A key computational step in reference-based variant calling is distinguishing true genetic variants from sequencing errors. Advanced tools and workflows have been developed to handle this by computational modelling of technical errors from the sequencing machines. However, these recalibration workflows have largely been evaluated for human data only and its exact applicability for non-human data remains unknown. Here, we conducted a systematic evaluation of variant calling on human, rice, sheep, and chickpea data, and found that existing workflows introduce unexpected statistical bias, thus leading to suboptimal variant calls for non-human data. To address this problem, we present simple guidelines for constructing a "pseudo-"database (pseudoDB) of genetic variants as a scalable and portable solution for recalibration and variant calling. With human data, our pseudoDB-based workflow performs comparably to existing dbSNP-based GATK3 workflows and those using DeepVariant, Strelka2, and FreeBayes. We extend this to other non-human genomes, namely cattle, brown bear, swan goose, African oil palm, Komodo dragon, and stevia, altogether resulting in the identification of up to 242.0% unique genetic variants. The majority of newly identified variants are within the non-coding regions, hinting at the rich diversity of genome regulation in the non-human population. Our pseudoDB-based workflow is agnostic to reference genomes and modular for easy integration with other computational workflows for human and non-human resequencing data.

Humans↗

PubMed2006

Spectroscopic measurement of diffusion kinetics through subnanometer and larger Al2O3 particles by a new method: the interaction of 2-chloroethylethyl sulfide with gamma-Al2O3.

A new method to study the diffusion properties of molecules into porous materials using transmission IR spectroscopy is employed. A measurement of the diffusion of the 2-chloroethylethyl sulfide (2-CEES) molecule into two types of gamma-Al2O3 powder is performed, showing that the diffusion rate into subnanometer crystallite particle size gamma-Al2O3 powders (subnano-Al2O3) is higher than that into the larger crystallite particle size powder. It is shown that a surface diffusion mechanism can be used to model the diffusion process giving good agreement with the experimental results, where Dsubnano-Al2O3 is approximately 5 times larger than Dmultinano-Al2O3 at 170 K for the 2-CEES molecule.

Journal Article↗

PubMed2006

Perturbation of adsorbed CO by amine derivatives coadsorbed on the gamma-Al2O3 surface: FTIR and first principles studies.

The coadsorption of CO and triethylenediamine (TEDA) (also called 1,4-diazabicyclo[2.2.2]octane, DABCO) on a high-area gamma-Al2O3 surface has been investigated with use of transmission FTIR spectroscopy. It has been found that TEDA binds more strongly to both Lewis acid sites and to Brønsted Al-OH sites than does CO. Competition experiments indicate that TEDA displaces CO to less strong binding sites. Evidence for weak CO...TEDA interactions is found in which small nu(CO) redshifts are produced. Comparison between different amines such as triethylenemonoamine (TEMA) (also called 1-azabicyclo[2.2.2]octane, ABCO), trimethylamine (TMA), and ammonia indicates that the nu(CO) redshift increases with increasing amine polarizability, indicating that the redshift is mainly due to dipole image damping effects on the CO oscillator frequency. The direct bonding between the exposed N lone pair electrons of the TEDA molecule and CO does not occur. First principles theoretical studies have characterized the bonding of CO with gamma-Al2O3 Lewis acid sites of various types as well as TEDA bonding to both Lewis acid sites and to Al-OH groups. The theoretical studies also indicate that strong bonding of adsorbed CO with TEDA molecules does not occur, and that the observed decrease in the binding energy of CO when coadsorbed with TEDA on gamma-Al2O3 is expected.

Journal Article↗

PubMed2005

Adsorption of triethylenediamine on Al2O3-III: Bonding to Lewis acid Al3+ sites.

The adsorption of triethylenediamine (TEDA) on Lewis acid (Al(3+)) sites of the highly dehydroxylated Al(2)O(3) surface has been observed by FT-IR spectroscopy. This was done by monitoring the competitive adsorption of TEDA and CO on the Al(3+) sites. A stoichiometric replacement of Al(3+)-CO species was observed as Al(3+)-TEDA surface species were formed.

Journal Article↗

PubMed2005

The adsorption of triethylenediamine on Al(2)O(3)-II: hydrogen bonding to Al-OH groups.

The hydrogen bonding of the triethylenediamine (TEDA) molecule to isolated Al-OH groups on partially dehydroxylated high area gamma-Al(2)O(3) powder has been studied using transmission IR spectroscopy. It has been found that TEDA adsorbs both singly and as multiple species to single Al-OH groups in clearly separable equilibrium stages of adsorption at 300 K. The reversible adsorption of a single TEDA molecule to Al-OH fits the Langmuir adsorption isotherm well, and the enthalpy of adsorption is found to be -15.6 +/- 0.5 kJ mol(-1) in the range of fractional coverage of 0.5-0.6. Red shifts of the Al-OH frequency from approximately -200 cm(-1) to approximately -1000 cm(-1) are observed as a result of -OH bonding to the N lone pair in the TEDA molecule.

Journal Article↗

PubMed2005

The adsorption of triethylenediamine on Al(2)O(3)-I: a vibrational spectroscopic and desorption kinetic study of surface bonding.

The adsorption of triethylenediamine (TEDA) at 300 K is observed to occur via hydrogen bonding to isolated Al-OH groups on the surface of partially dehydroxylated high area gamma-Al(2)O(3) powder. This form of bonding results in +0.3 to +0.4% blue shifts in the CH(2) scissor modes at 1455 cm(-1) and a -0.4% red shift in the CN skeletal mode at 1060 cm(-1), compared to the gas-phase frequencies. Other modes are red shifted less than 0.1%. The isolated OH modes are red shifted by -200 to -1000 cm(-1) due to the strong hydrogen bonding association of Al-OH groups with an N atom in TEDA. Thermal desorption of adsorbed TEDA from the surface occurs in the range 300-700 K. Mass spectral and infrared studies indicate that the decomposition of TEDA occurs on Al(2)O(3) above 725 K, and that C-H bonds are broken, forming adsorbed species with N-H bonds which are stable to 1000 K or above. In contrast to adsorption at 300 K, adsorption of TEDA at 85 K results in the formation of a condensed ice of TEDA, which covers the outer surface of the porous Al(2)O(3) and which does not interact with Al-OH groups inside the porous powder due to immobility.

Journal Article↗

PubMed2005

Areolar-cutaneous junction injection boosts activity in sentinel node by more than 50 times compared to perilesional injection: implications for morbidity reduction.

The combination of concurrently administered perilesional radiotracer injections and areolar-cutaneous junction radiotracer injections during one imaging session in the detection of sentinel nodes (SN) in breast cancer is new. A case is presented where the perilesional injections of radiotracer produced a faint node. Subsequently, 45 minutes later, the same patient received an injection of radiotracer at the areolar-cutaneous junction, which "boosted" the activity in the original SN by more than 50 times. This case illustrates the marked improvement in SN counts that can occur with the addition of areolar-cutaneous junction injections to perilesional injections. The perilesional component of this hybrid injection technique maintains the ability to visualize internal mammary and extra-axillary SN. Even more importantly, these "hotter" nodes have significant implications for morbidity reduction, the main goal of sentinel lymph node biopsy in itself.

Adult↗

PubMed2004

Characterization of DNA immobilization and subsequent hybridization using in situ quartz crystal microbalance, fluorescence spectroscopy, and surface plasmon resonance.

We have characterized the immobilization of thiol-modified oligomers on Au surfaces and subsequent hybridization with a perfectly matched or single-base mismatched target using a quartz crystal microbalance (QCM) and fluorescence spectroscopy. The surface density of immobilized probe molecules and the hybridization efficiency depending on the type of buffer and salt concentration were investigated. We observed some ambiguities in surface coverage deduced from QCM measurement and adopted a complementary fluorescence displacement method. Direct comparison of surface coverage deduced from frequency change in QCM measurement and determined by the fluorescence exchange reaction revealed that QCM results are highly overestimated and the amount of overestimation strongly depends on the type of buffer and the structure of the film. Discrimination capability of the surface attached 15-mer probe was also examined using a single-base mismatched target at various hybridization temperatures. Hybridization efficiency depending on the type of single base mismatch was investigated using surface plasmon resonance (SPR).

DNA↗

PubMed2004

Influence of liquid medium and surface morphology on the response of QCM during immobilization and hybridization of short oligonucleotides.

With the goal of developing a quartz crystal microbalance (QCM)-based DNA sensor, we have conducted an in situ QCM study along with fluorescence measurements using oligonucleotides (15-mer) as a model single-stranded DNA (ss-DNA) in two different aqueous buffer solutions; the sequence of 15-mer is a part of iduronate-2-sulphate exon whose mutation is known to cause Hunter syndrome, and the 15-mer is thiolated to be immobilized on the Au-coated quartz substrate. The fluorescence data indicate that the initial immobilization as well as the subsequent hybridization with a complementary strand is hardly dependent on the kind of buffer solution. In contrast, the mass increases deducible from the decrease of QCM frequency via the Sauerbrey equation are 2.7-6.2 and 3.0-4.4 times larger than the actual mass increases, as reflected in the fluorescence measurements, for the immobilization and the subsequent hybridization processes, respectively. Such an overestimation is attributed to the trapping of solvent as well as the formation of quite a rigid hydration layer associated with the higher viscosities and/or densities of the buffer solutions. Another noteworthy observation is the excessively large frequency change that occurs when the gold electrode is deposited in advance with Au nanoparticles. This clearly illustrates that the QCM detection of DNA hybridization is also affected greatly by the surface morphology of the electrode. These enlarged signals are altogether presumed to be advantageous when using a QCM system as an in situ probing device in DNA sensors.

Adsorption↗

PubMed2003

Acquisition of heat shock tolerance by regulation of intracellular redox states.

In the yeast Saccharomyces cerevisiae, a mild heat treatment strongly induces Hsp104p which provides acquisition of thermotolerance. The mechanism by which Hsp104p protects cells from the severe heat shock has not yet been completely elucidated. In this study, a pivotal role of Hsp104p as an efficient scavenger of the reactive oxygen species (ROS) is investigated. In our previous study, we reported that Hsp104p acted as a regulator in the mitochondrial respiration pathway. In this report, the recombinant wild-type and hypersensitive ras mutants (ira2Delta) with the extrachromosomal plasmids wild-type and mutant hsp104 genes were studied. The resulting strains successfully expressed both wild-type and mutant Hsp104p and showed the thermotolerance phenotype in the strain with the functional wild-type Hsp104p expressed. Upon treatment with H2O2 and menadione, the strains with the functional Hsp104p expressed showed higher survival rates than the other mutants, indicating the protective role of Hsp104p from the oxidative stress. Fluorescence measurement of the oxidation-dependent probe, 2',7'-dichlorofluoroscein diacetate (H2DCFDA), also indicated that Hsp104p significantly reduced the amount of ROS. Resistance to the oxidative stress was independent of the amount of the glutathione in the hyperactivated ras mutants. Taken all together, this study confirms that Hsp104p plays a crucial role in keeping cells from being damaged by the oxidative stress, thus acting as a modulator of the intracellular redox state.

Cell Survival↗