Yang-Hoon Kim

Bacterial communities in the initial stage of marine biofilm formation on artificial surfaces

Succession of bacterial communities during the first 36 h of biofilm formation in coastal water was investigated at 3∼15 h intervals. Three kinds of surfaces (i.e., acryl, glass, and steel substratum) were submerged in situ at Sacheon harbor, Korea. Biofilms were harvested by scraping the surfaces, and the compositions of bacterial communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of 16S rRNA genes. While community structure based on T-RFLP analysis showed slight differences by substratum, dramatic changes were commonly observed for all substrata between 9 and 24 h. Identification of major populations by 16S rRNA gene sequences indicated that γ-Proteobacteria (Pseudomonas, Acinetobacter, Alteromonas, and uncultured γ-Proteobacteria) were predominant in the community during 0∼9 h, while the ratio of α-Proteobacteria (Loktanella, Methylobacterium, Pelagibacter, and uncultured α-Proteobacteria) increased 2.6∼4.8 folds during 24∼36 h of the biofilm formation, emerging as the most predominant group. Previously, α-Proteobacteria were recognized as the pioneering organisms in marine biofilm formation. However, results of this study, which revealed the bacterial succession with finer temporal resolution, indicated some species of γ-Proteobacteria were more important as the pioneering population. Measures to control pioneering activities of these species can be useful in prevention of marine biofilm formation.

Arsenic removal from Vietnamese groundwater using the arsenic-binding DNA aptamer.

Single-stranded DNA aptamers were generated from a random library to remove arsenic from Vietnamese groundwater. On the basis of significant arsenic contamination levels, three areas in Ha Nam province (Vinh Tru, Bo De, and Hoa Hau) and five areas near the Mekong River Delta (MR1-5) were selected as study areas. The aptamers were in vitro selected using an arsenic aptamer affinity column created by immobilizing arsenic on Affi-gel 10 resin. Quantitative analyses of the aptamer candidates Ars-1 to Ars-8 by surface plasmon resonance (SPR) revealed the Ars-3 aptamer to have the highest affinity to arsenate [(As(V)] and arsenite [As(III)] with a dissociation constant (K(d)) of 4.95 +/- 0.31 and 7.05 +/- 0.91 nM, respectively. The specific affinity interactions of the Ars-3 aptamer to arsenic were verified against other heavy metals. After obtaining successful removal results with a laboratory-prepared aqueous arsenic solution, Ars-3 was applied for removal of any arsenic present in the groundwater samples collected from the studied areas in Vietnam. Field results were also successful: various arsenic concentrations ranging from 28.1 to 739.2 microg/L were completely removed after 5 min of incubation with the arsenic-binding aptamer Ars-3.

Immobilization of lysozyme-CLEA onto electrospun chitosan nanofiber for effective antibacterial applications.

Chitosan (CS) nanofibers with a diameter of 150-200nm were fabricated from a mixed chitosan/poly (vinyl alcohol) (PVA) solution by the electrospinning method. The nascent CS/PVA nanofibers were treated with 0.5M NaOH solution to make stable CS nanofibers by removing PVA under aqueous conditions. Hen egg-white lysozyme was immobilized on electrospun CS nanofibers via cross-linked enzyme aggregates (CLEAs) and used for effective and continuous antibacterial applications. The maximum amount of lysozyme immobilized on the CS nanofibers was determined to be 62.3mg/g of nanofibers under the optimum conditions. The immobilized lysozyme-CLEA retained more than 75.4% of its initial activity after 80 days of storage at room temperature, while the free lysozyme lost all of its activity under the same conditions. In addition, the immobilized lysozyme-CLEA retained more than 76% of its activity after 100 consecutive uses. Finally, the durability of the lysozyme-CLEA immobilized CS nanofibers showed bacteriostasis ratios of 82.4%, 79.8%, 83.4%, and 84.1% after 10 cycles against 4 pathogenic bacteria, viz. Staphylococcus aureus, Bacillus subtilis, Shigella flexneri, and Psedomonas aeruginosa, respectively. These results demonstrated that lysozyme-CLEA immobilized CS nanofibers could be used as a promising material for enhanced and continuous antibacterial applications.

Effects of glyphosate and methidathion on the expression of the Dhb, Vtg, Arnt, CYP4 and CYP314 in Daphnia magna.

In this study, the expression of five stress responsive genes was quantified and analyzed using a semi-quantitative RT-PCR to study the changes in their expression in Daphnia magna after exposure to known pesticides, glyphosate and methidathion. Hemoglobin (Dhb), which was used to show the effect of the oxygen level in the aquatic system, was significantly expressed in D. magna after exposure to glyphosate and methidathion. Additionally, aryl hydrocarbon receptor nuclear translocator (Arnt), a gene related to the metabolism of aryl hydrocarbons, had lower expression levels in D. magna than within the control. CYP4, which was used among cytochrome P450s (CYPs) to show the effects on the fatty acid and steroids metabolisms, was down-regulated in D. magna exposed to glyphosate. However, methidathion affected the expression of CYP314, which was used to show effects of ecdysis, not CYP4 in D. magna. Therefore, glyphosate and methidathion probably caused physiological effects with different patterns in D. magna, especially metabolisms related to CYPs. On the other hand, only vitellogenin (Vtg), which was responsive to the estrogenic potency, did not show any differences in D. magna after exposure to glyphosate or methidathion.

Analytical bioconjugates, aptamers, enable specific quantitative detection of Listeria monocytogenes

As a major human pathogen in the Listeria genus, Listeria monocytogenes causes the bacterial disease listeriosis, which is a serious infection caused by eating food contaminated with the bacteria. We have developed an aptamer-based sandwich assay (ABSA) platform that demonstrates a promising potential for use in pathogen detection using aptamers as analytical bioconjugates. The whole-bacteria SELEX (WB-SELEX) strategy was adopted to generate aptamers with high affinity and specificity against live L. monocytogenes. Of the 35 aptamer candidates tested, LMCA2 and LMCA26 reacted to L. monocytogenes with high binding, and were consequently chosen as sensing probes. The ABSA platform can significantly enhance the sensitivity by employing a very specific aptamer pair for the sandwich complex. The ABSA platform exhibited a linear response over a wide concentration range of L. monocytogenes from 20 to 2×10(6) CFU per mL and was closely correlated with the following relationship: y=9533.3x+1542.3 (R(2)=0.99). Our proposed ABSA platform also provided excellent specificity for the tests to distinguish L. monocytogenes from other Listeria species and other bacterial genera (3 Listeria spp., 4 Salmonella spp., 2 Vibrio spp., 3 Escherichia coli and 3 Shigella spp.). Improvements in the sensitivity and specificity have not only facilitated the reliable detection of L. monocytogenes at extremely low concentrations, but also allowed for the development of a 96-well plate-based routine assay platform for multivalent diagnostics.

Proteomic analysis of curdlan-producing Agrobacterium sp. in response to pH downshift

During batch cultivation of Agrobacterium sp. ATCC 31750, proteome analysis in response to a pH downshift from 7.0 to 5.5 was carried out using two-dimensional electrophoresis and matrix-assisted laser desorption-ionization-time of flight mass spectrometry. When the pH of the exponentially growing Agrobacterium sp. culture was downshifted to pH 5.5, the synthesis level of 27 intracellular proteins showed significant changes in level over a prolonged period of time compared with the batch culture controlled at pH 7.0. In particular, the intracellular protein level of the beta-1,3-glucan synthase catalytic subunit, UTP-glucose-1-phosphate uridylyltransferase, and phosphoglucomutase, which are key metabolic enzymes in the curdlan biosynthesis pathway, were more than 10-, 3- and 17-times higher in the low pH culture. On the other hand, the level of orotidine5-phosphate decarboxylase (conversion of OMP to UMP) was significantly up-regulated after pH downshift. The accumulation of UMP may direct the metabolic flow towards the biosynthetic route of UTP, which is a key metabolic precursor for UDP-glucose. Therefore, it is possible that increase of cellular metabolic enzymes during pH downshift culture can enhance the metabolic flux of the biosynthesis of key precursor, such as UTP- and UDP-glucose, resulting in an increase in curdlan biosynthesis.

Aptamer-based Sandwich Assay and its Clinical Outlooks for Detecting Lipocalin-2 in Hepatocellular Carcinoma (HCC)

We validated a single-stranded, DNA aptamer-based, diagnostic method capable of detecting Lipocalin-2 (LCN2), a biomarker from clinically relevant hepatocellular carcinoma (HCC) patient serum, in the sandwich assay format. Nine aptamers (LCN2_apta1 to LCN2_apta9) for LCN2 were screened with SELEX processes, and a sandwich pair (LCN2_apta2 and LCN2_apta4) was finally chosen using surface plasmon resonance (SPR) and dot blotting analysis. The result of the proposed aptamer sandwich construction shows that LCN2 was sensitively detected in the concentration range of 2.5–500 ng mL−1 with a limit of detection of 0.6 ng mL−1. Quantitative measurement tests in HCC patients were run on straight serum and were compared with the performance of the conventional antibody-based ELISA kit. The aptamer sandwich assay demonstrated an excellent dynamic range for LCN2 at clinically relevant serum levels, covering sub-nanogram per mL concentrations. The new approach offers a simple and robust method for detecting serum biomarkers that have low and moderate abundance. It consists of functionalization, hybridization and signal read-out, and no dilution is required. The results of the study demonstrate the capability of the aptamer sandwich assay platform for diagnosing HCC and its potential applicability to the point-of-care testing (POCT) system.

Proteomic analysis in Daphnia magna exposed to As(III), As(V) and Cd heavy metals and their binary mixtures for screening potential biomarkers.

In this study, the effects of three widespread heavy metals, As(III), As(V) and Cd, and their binary mixtures on the proteomic profile in D. magna were examined to screen novel protein biomarkers using the two-dimensional gel electrophoresis method (2DE). Ten 20d daphnia were exposed to the LC20 concentrations for each of a total of 8 treatments, including the control, As(III), As(V), Cd, [As(III)+As(V)], [As(III)+Cd], [As(V)+Cd], and [As(III), As(V), Cd], for 24h before protein isolation. Three replicates were performed for each treatment. These protein samples were employed for 2DE experiments with a pH gradient gel strip from pH 3 to pH 10. The protein spots were detected by a silver staining process and their intensities were analyzed by Progenesis software to discover the differentially expressed proteins (DEPs) in response to each heavy metal. A total of 117 differentially expressed proteins (DEPs) were found in daphnia responding to the 8 treatments and mapped onto a 2D proteome map, which provides some information of the molecular weight (MW) and pI value for each protein. All of these DEPs are considered as potential candidates for protein biomarkers in D. magna for detecting heavy metals in the aquatic ecosystem. Comparing the proteomic results among these treatments suggested that exposing D. magna to binary mixtures of heavy metals may result in some complex interactive molecular responses within them, rather than just the simple sum of the proteomic profiles of the individual chemicals, (As(III), As(V), and Cd).

Electrochemically oriented immobilization of antibody on poly-(2-cyano-ethylpyrrole)-coated gold electrode using a cyclic voltammetry.

Using quartz crystal microbalance (QCM) as an immunosensor, this work investigates the contribution of a cyclic voltammetry (CV) on the proper immobilization of antibodies with the aim of enhancing its target recognition and binding ability. Primarily, CV in the range of -0.1 to 0.9 V was applied to form a layer of poly-(2-cyano-ethylpyrrole) (PCEPy) on gold quartz crystal electrode. Then the efficiencies of antibodies (anti-IgG, AIgG) immobilized electrochemically with CV applied in 0-0.65 V were compared to those immobilized via physical adsorption, by observing relative affinity towards AIgG-Fab and AIgG-Fc fragments. The results showed antibody-AIgG-Fab interaction could be enhanced about 4 times when CV is applied (11.2 ± 1.3 vs 41.6 ± 3.4 relative fluorescence unit). On the contrary, physisorbed antibodies showed a higher degree of affinity towards AIgG-Fc indicating inappropriate orientations of physisorbed antibodies. AIgG immobilized PCEPy-gold QC electrode was characterized further for its sensitivity towards a new target bovine albumin with both a QCM and fluorescence measurement. Such electrode exhibited a good sensitivity as well as a large linear dynamic range, from 0.4 μg/ml to 1.0 μg/ml and from 0.5 μg/ml to 10.0 μg/ml, at QCM and fluorescence measurement, respectively.

Increased In Vitro Lysosomal Function in Oxidative Stress-Induced Cell Lines

Exposure of mammalian cells to oxidative stress alters lysosomal enzymes. Through cytochemical analysis of lysosomes with LysoTracker, we demonstrated that the number and fluorescent intensity of lysosome-like organelles in HeLa cells increased with exposure to hydrogen peroxide (H2O2), 6-hydroxydopamine (6-OHDA), and UVB irradiation. The lysosomes isolated from HeLa cells exposed to three oxidative stressors showed the enhanced antimicrobial activity against Escherichia coli. Further, when lysosomes that were isolated from HeLa cells exposed by oxidative stress were treated to normal HeLa cells, the viability of the HeLa cells was drastically reduced, suggesting increased in vitro lysosomal function (i.e., antimicrobial activity, apoptotic cell death). In addition, we also found that cathepsin B and D were implicated in increased in vitro lysosomal function when isolated from HeLa cells exposed by oxidative stress. Decrease in cathepsin B activity and increase in cathepsin D activity were observed in lysosomes isolated from HeLa cells after treatment with H2O2, 6-ODHA, or UVB, but cathepsin B and D were not the sole factors to induce cell death by in vitro lysosomal function. Therefore, these studies suggest a new approach to use lysosomes as antimicrobial agents and as new materials for treating cancer cell lines.