Monitoring of the Binding Between EGFR Protein and EGFR Aptamer Using In-Situ Total Internal Reflection Ellipsometry.

The epidermal growth factor receptor (EGFR) protein has received significant attention in medical biotechnology because it is an important component in cell growth and division. We report the results of a study on the binding between the EGFR protein and the associated aptamer, measured in real time. Aptamers can be used for clinical purposes including macromolecular medicine and basic research. In particular, EGFR aptamers are promising molecular agents for targeting cancer. The data were obtained in-situ with total internal reflection ellipsometry (TIRE), which combines the analytic capability of spectroscopic ellipsometry with the high surface sensitivity of surface plasmon resonance measurements. Our results show that TIRE can be used to determine adsorption of nanoscale biomolecules. Our results are supported by additional data obtained by liquid atomic-force-microscopy.

Dynamics and stability of lipid bilayers modulated by thermosensitive polypeptides, cholesterols, and PEGylated lipids.

Lipid bilayers, which consist of dipalmitoylglycerophosphocholines (DPPCs), PEGylated lipids, cholesterols, and elastin-like polypeptides (ELPs; [VPGVG]3) at different molar ratios, were simulated. Simulations were carried out for 2 µs using the coarse-grained (CG) model that had captured the experimentally observed phase behavior of PEGylated lipids and lateral diffusivity of DPPC bilayers. Starting with the initial position of ELPs on the bilayer surface, ELPs insert into the hydrophobic region of the bilayer because of their interaction with lipid tails, consistent with previous all-atom simulations. Lateral diffusion coefficients of DPPCs significantly increase in the bilayer composed of more ELPs and less cholesterols, showing their opposite effects on the bilayer dynamics. In particular, ELPs modulate the dynamics and phase for the disordered liquid bilayer, but not for the ordered gel bilayer, indicating that ELPs can destabilize only the disordered bilayer. In the ordered bilayer, ELP chains tend to have a spherical shape and slowly diffuse, while they are extended and diffuse faster in the disordered bilayer, indicating the effect of the bilayer phase on the conformation and diffusivity of ELPs. These findings explain the experimental observation that the ELP-conjugated liposomes are stable at 310 K (ordered phase) but become unstable and release the encapsulated drugs at 315 K (disordered phase), which suggests the effects of ELPs and cholesterols. Since the cholesterol-stabilized bilayer can be destabilized by the extended shaped ELPs only in the disordered phase (not in the ordered phase), the inclusion of cholesterols is required to safely shield drugs at 310 K as well as allow ELPs to disrupt lipids and destabilize the liposomes at 315 K.

Characterization of Saccharomyces cerevisiae promoters for heterologous gene expression in Kluyveromyces marxianus.

Kluyveromyces marxianus is now considered one of the best choices of option for industrial applications of yeast because the strain is able to grow at high temperature, utilizes various carbon sources, and grows fast. However, the use of K. marxianus as a host for industrial applications is still limited. This limitation is largely due to a lack of knowledge on the characteristics of the promoters since the time and amount of protein expression is strongly dependent on the promoter employed. In this study, four well-known constitutive promoters (P(CYC), P(TEF), P(GPD), and P(ADH)) of Saccharomyces cerevisiae were characterized in K. marxianus in terms of protein expression level and their stochastic behavior. After constructing five URA3-auxotrophic K. marxianus strains and a plasmid vector, four cassettes each comprising one of the promoters--the gene for the green fluorescence protein (GFP)--CYC1 terminator (T(CYC)) were inserted into the vector. GFP expression under the control of each one of the promoters was analyzed by reverse transcription PCR, fluorescence microscopy, and flow cytometer. Using these combined methods, the promoter strength was determined to be in the order of P(GPD) > P(ADH) ∼ P(TEF) >> P(CYC). All promoters except for the P(CYC) exhibited three distinctive populations, including non-expressing cells, weakly expressing cells, and strongly expressing cells. The relative ratios between populations were strongly dependent on the promoter and culture time. Forward scattering was independent of GFP fluorescence intensity, indicating that the different fluorescence intensities were not just due to different cell sizes derived from budding. It also excluded the possibility that the non-expressing cells resulted from plasmid loss because plasmid stability was maintained at almost 100 % over the culture time. The same cassettes, cloned into a single copy plasmid pRS416 and transformed into S. cerevisiae, showed only one population. When the cassettes were integrated into the chromosome, the stochastic behavior was markedly reduced. These combined results imply that the gene expression stochasticity should be overcome in order to use this strain for delicate metabolic engineering, which would require the co-expression of several genes.

Genome sequence of the thermotolerant yeast Kluyveromyces marxianus var. marxianus KCTC 17555.

Kluyveromyces marxianus is a thermotolerant yeast that has been explored for potential use in biotechnological applications, such as production of biofuels, single-cell proteins, enzymes, and other heterologous proteins. Here, we present the high-quality draft of the 10.9-Mb genome of K. marxianus var. marxianus KCTC 17555 (= CBS 6556 = ATCC 26548).

Pediatricians' perception of factors concerning the clinical application of blockchain technology to pediatric health care: a questionnaire survey.

BACKGROUND: Interest in digital medical information has increased because it allows doctors to easily access a patient's medical records and provide appropriate medical care. Blockchain technology ensures data safety, reliability, integrity, and transparency by distributing medical data to all users over a peer-to-peer network. This study attempted to assess pediatricians' thoughts and attitudes toward introducing blockchain technology into the medical field. METHODS: This study used a questionnaire survey to examine the thoughts and attitudes of 30- to 60-year-old pediatricians regarding the introduction of blockchain technology into the medical field. Responses to each item were recorded on a scale ranging from 1 (never agree) to 7 (completely agree). RESULTS: The scores for the intentions and expectations of using blockchain technology were 4.0 to 4.6. Pediatricians from tertiary hospitals responded more positively (4.5-4.9) to the idea of using blockchain technology for hospital work relative to the general population (4.3-4.7). However, pediatricians working in primary and secondary hospitals had a slightly negative view of the application of blockchain technology to hospital work (p=0.018). CONCLUSION: When introducing the medical records of related pediatric and adolescent patients using blockchain technology in the future, it would be better to conduct a pilot project that prioritizes pediatricians in tertiary hospitals. The cost, policy, and market participants' perceptions are essential factors to consider when introducing technology in the medical field.

Sensitive and simultaneous detection of cardiac markers in human serum using surface acoustic wave immunosensor.

We present a rapid and sensitive surface acoustic wave (SAW) immunosensor that utilizes gold staining as a signal enhancement method. A sandwich immunoassay was performed on sensing area of the SAW sensor, which could specifically capture and detect cardiac markers (cardiac troponin I (cTnI), creatine kinase (CK)-MB, and myoglobin). The analytes in human serum were captured on gold nanoparticles (AuNPs) that were conjugated in advance with detection antibodies. Introduction of these complexes to the capture antibody-immobilized sensor surface resulted in a classic AuNP-based sandwich immunoassay format that has been used for signal amplification. In order to achieve further signal enhancement, a gold staining method was performed, which demonstrated that it is possible to obtain gold staining-mediated signal augmentation on a mass-sensitive device. The sensor response due to gold staining varied as a function of cardiac marker concentration. We also investigated effects of increasing operating frequency on sensor responses. Results showed that detection limit of the SAW sensor could be further improved by increasing the operating frequency.

Improved galactose fermentation of Saccharomyces cerevisiae through inverse metabolic engineering.

Although Saccharomyces cerevisiae is capable of fermenting galactose into ethanol, ethanol yield and productivity from galactose are significantly lower than those from glucose. An inverse metabolic engineering approach was undertaken to improve ethanol yield and productivity from galactose in S. cerevisiae. A genome-wide perturbation library was introduced into S. cerevisiae, and then fast galactose-fermenting transformants were screened using three different enrichment methods. The characterization of genetic perturbations in the isolated transformants revealed three target genes whose overexpression elicited enhanced galactose utilization. One confirmatory (SEC53 coding for phosphomannomutase) and two novel targets (SNR84 coding for a small nuclear RNA and a truncated form of TUP1 coding for a general repressor of transcription) were identified as overexpression targets that potentially improve galactose fermentation. Beneficial effects of overexpression of SEC53 may be similar to the mechanisms exerted by overexpression of PGM2 coding for phosphoglucomutase. While the mechanism is largely unknown, overexpression of SNR84, improved both growth and ethanol production from galactose. The most remarkable improvement of galactose fermentation was achieved by overexpression of the truncated TUP1 (tTUP1) gene, resulting in unrivalled galactose fermentation capability, that is 250% higher in both galactose consumption rate and ethanol productivity compared to the control strain. Moreover, the overexpression of tTUP1 significantly shortened lag periods that occurs when substrate is changed from glucose to galactose. Based on these results we proposed a hypothesis that the mutant Tup1 without C-terminal repression domain might bring in earlier and higher expression of GAL genes through partial alleviation of glucose repression. mRNA levels of GAL genes (GAL1, GAL4, and GAL80) indeed increased upon overexpression of tTUP. The results presented in this study illustrate that alteration of global regulatory networks through overexpression of the identified targets (SNR84 and tTUP1) is as effective as overexpression of a rate limiting metabolic gene (PGM2) in the galactose assimilation pathway for efficient galactose fermentation in S. cerevisiae. In addition, these results will be industrially useful in the biofuels area as galactose is one of the abundant sugars in marine plant biomass such as red seaweed as well as cheese whey and molasses.

A visible light-induced photocatalytic silver enhancement reaction for gravimetric biosensors.

We have developed a novel microgravimetric immunosensor using a WO(3) nanoparticle-modified immunoassay and a silver enhancement reaction. When the nanoparticles in silver ion solution (i.e.  AgNO(3)) are exposed to visible light, the silver ions are photocatalytically reduced and form a metallic silver coating on the nanoparticles. This silver coating consequently induces changes in the mass and light absorption spectrum. Although photocatalytic reduction reactions can be achieved using ultraviolet (UV) light and TiO(2) nanoparticles as described in our previous publication (Seo et al 2010 Nanotechnology 21 505502), the use of UV light in biosensing applications has drawbacks in that UV light can damage proteins. In addition, conventional quartz crystal substrates must be passivated to prevent undesirable silver ion reduction on their gold-coated sensing surfaces. We addressed these problems by adopting a visible light-induced photocatalytic silver enhancement method using WO(3) nanoparticles and lateral field excited (LFE) quartz crystals. As a proof-of-concept demonstration of the technique, streptavidin was adsorbed onto an LFE quartz crystal, and its mass was enhanced with biotinylated WO(3) nanoparticles, this being followed by a photocatalytic silver enhancement reaction. The mass change due to the enhancement was found to be > 30 times greater than the mass change obtained with the streptavidin alone.

Electrochemical cell lysis device for DNA extraction.

We present a novel electrochemical cell lysis device to prepare DNA samples for lab-on-a-chip (LOC) applications. It utilizes the electrolysis of saline solution to generate hydroxide ions (OH(-)) at the cathode as alkaline lytic agents. Cathode and anode chambers are separated by a negatively-charged ion exchangeable polymer diaphragm to maintain the high pH level for efficient cell lysis in the cathode chamber, to prevent inflow of PCR-amplification inhibitors from the anode chamber, and to minimize binding of DNA molecules. Electric current flow and pH maintenance, which depended on the device design, were two important parameters of the device performance. After optimizing the design and visually confirming cell lysis of Chinese hamster ovary (CHO) cells in a very short amount of time, we directly electrolyzed four bacterial cell types suspended in saline solution. Real-time PCR (qPCR) analysis showed that our device could lyse both gram-positive and gram-negative bacterial cells with higher efficiency than other common methods and could detect DNA on the microlitre scale. Our data demonstrate several advantages of the proposed device: absence of cell lysis chemicals and heating; no adverse effects on PCR amplification; low DNA loss; low voltage and power consumption; and rapid processing. The device could potentially be applied as an on-chip DNA extraction component.

Development of aggressive squamous cell carcinoma in epidermodysplasia verruciformis associated with human papillomavirus type 22b.

Epidermodysplasia verruciformis (EV) is a rare genetic disease characterized by abnormal susceptibility to infection with EV-related human papillomavirus (HPV), now known as the beta-papillomavirus (beta-PV). Clinically specific beta-PV-type-associated EV, especially HPV-5 and -8, shows a high rate of progression to squamous cell carcinoma (SCC). In this report, we describe a 39-year-old Korean man with HPV-22b-associated EV who developed a rapidly progressing SCC. The patient presented with a huge destructive mass on the nose. Histopathological evaluation of the mass was compatible with well-differentiated SCC. HPV typing results from both EV and SCC specimens demonstrated HPV-22b which has not been considered to be associated with SCC in EV patients so far. The patient underwent surgical excision and postoperative radiotherapy for locoregional control. This is the first report presenting the association of an SCC arising from previous EV with HPV-22b infection only.

Circulating Tumor Cell Counts in Patients With Localized Prostate Cancer Including Those Under Active Surveillance.

AIM: To evaluate the clinical efficacy of a circulating tumor cell (CTC) test by comparison between healthy volunteers and patients with localized prostate cancer including those under active surveillance. MATERIALS AND METHODS: CTC counts in peripheral blood were compared between patients with prostate cancer (n=45) and healthy volunteers (n=17). CTCs were identified based on the expression of epithelial cell adhesion molecule (EpCAM) and counted using a SMART BIOPSY™ SYSTEM. RESULTS: The number of EpCAM+ cells was significantly higher in patients with cancer than in healthy volunteers. Among the low-risk patients (n=9), two had up-staging and six had up-grading. Among those up-staged, there was one case which was EpCAM+ Among those cases up-graded, three were EpCAM+ In those with stage T2 tumors, the presence of Gleason pattern 5 was positively correlated with EpCAM positivity (rho=0.59, p<0.001). CONCLUSION: CTC counts in localized prostate cancer were associated with Gleason pattern 5. Active treatment should be considered for patients with low-risk disease during active surveillance who are found to have EpCAM+ CTCs because of a risk of up-staging and up-grading.

Bacterial DNA sample preparation from whole blood using surface-modified Si pillar arrays.

A novel bacterial DNA sample preparation device for molecular diagnostics has been developed. On the basis of optimized conditions for bacterial adhesion, surface-modified silicon pillar arrays for bacterial cell capture were fabricated, and their ability to capture bacterial cells was demonstrated. The capture efficiency for bacterial cells such as Escherichia coli, Staphylococcus epidermidis, and Streptococcus mutans in buffer solution was over 75% with a flow rate of 400 microL/min. Moreover, the proposed method captured E. coli cells present in 50% whole blood effectively. The captured cells from whole blood were then in- situ lyzed on the surface of the microchip, and the eluted DNA was successfully amplified by qPCR. These results demonstrate that the full process of pathogen capture to DNA isolation from whole blood could be automated in a single microchip.

Improvement of Antitumor Efficacy by Combination of Thermosensitive Liposome with High-Intensity Focused Ultrasound.

High intensity focused ultrasound (HIFU), allowing for precise heating of the deep and local area, is emerging as the source of mild hyperthermia for delivery of doxorubicin (DOX) using thermosensitive liposomes (TSLs). Conventionally, HIFU has been used for intravascular drug release at tumor tissue by inducing mild hyperthermia immediately upon systemic administration of DOX-TSLs. This immediate heating approach (IHA), however, limits the deep penetration of DOX for high anticancer efficacy. In an attempt to maximize the accumulation of DOX at tumor, the delayed heating approach (DHA) has been explored. In this approach, DOX-TSLs were intravenously administered into the tumor-bearing mice after pre-treatment of tumor tissue with HIFU to increase vascular permeability. We developed the fatty acid-cojugated elastinlike polypeptide bearing TSL (FTSL). The DOX-loaded FTSLs had a hydrodynamic size of 142 nm. In vivo biodistribution study demonstrated that DOX-FTSLs were selectively accumulated at tumor tissue with the maximum amount of DOX at 6 h post-injection. Thereafter, the tumor tissue was heated to 42 °C to induce rapid release of DOX from FTSLs. The results have demonstrated that, compared to IHA, DHA significantly enhances the antitumor efficacy of DOX-FTSLs because of their effective penetration to tumor tissue via the enhanced permeation retention effect, followed by rapid release of DOX.

In vivo and in vitro antitumor effects of platycodin d, a saponin purified from platycodi radix on the h520 lung cancer cell.

Platycodin D is a major pharmacological constituent of Platycodi radix and has showed various pharmacological activities through oxidative stress defense mechanisms. Here, possible antitumor, anticachexia, and immunomodulatory activities of platycodin D were observed on the H520 tumor cell-bearing athymic nude mice after confirming the in vitro cytotoxicity. Platycodin D was orally administered at dose levels of 200, 100, and 50 mg/kg, once a day for 35 days from 15 days after implantation. The results were compared with gemcitabine 160 mg/kg intraperitoneally treated mice (7-day intervals). Platycodin D showed favorable cytotoxic effects on the H520 cells, and also dose-dependently decreased the tumor volumes and weights with increases of apoptotic cells (caspase-3 and PARP immunopositive cells), iNOS and TNF-α immunoreactivities, decreases of COX-2 immunoreactivities in tumor masses. Platycodin D also showed dose-dependent immunostimulatory and anticachexia effects. Gemcitabine showed favorable cytotoxity against H520 tumor cell and related in vivo antitumor effects but aggravated the cancer related cachexia and immunosuppress in H520 tumor cell-bearing athymic nude mice. Taken together, it is considered that oral treatment of platycodin D has potent antitumor activities on H520 cells through direct cytotoxic effects, increases of apoptosis in tumor cells, and immunostimulatory effects and can be control cancer related cachexia.

Directed evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter.

Human immunoglobulin heavy chain variable domains (VH) are promising scaffolds for antigen binding. However, VH is an unstable and aggregation-prone protein, hindering its use for therapeutic purposes. To evolve the VH domain, we performed in vivo protein solubility selection that linked antibiotic resistance to the protein folding quality control mechanism of the twin-arginine translocation pathway of E. coli. After screening a human germ-line VH library, 95% of the VH proteins obtained were identified as VH3 family members; one VH protein, MG2x1, stood out among separate clones expressing individual VH variants. With further screening of combinatorial framework mutation library of MG2x1, we found a consistent bias toward substitution with tryptophan at the position of 50 and 58 in VH. Comparison of the crystal structures of the VH variants revealed that those substitutions with bulky side chain amino acids filled the cavity in the VH interface between heavy and light chains of the Fab arrangement along with the increased number of hydrogen bonds, decreased solvation energy, and increased negative charge. Accordingly, the engineered VH acquires an increased level of thermodynamic stability, reversible folding, and soluble expression. The library built with the VH variant as a scaffold was qualified as most of VH clones selected randomly were expressed as soluble form in E. coli regardless length of the combinatorial CDR. Furthermore, a non-aggregation feature of the selected VH conferred a free of humoral response in mice, even when administered together with adjuvant. As a result, this selection provides an alternative directed evolution pathway for unstable proteins, which are distinct from conventional methods based on the phage display.

Protein grafting of p53TAD onto a leucine zipper scaffold generates a potent HDM dual inhibitor.

Reactivation of the p53 pathway by a potential therapeutic antagonist, which inhibits HDM2 and HDMX, is an attractive strategy for drug development in oncology. Developing blockers towards conserved hydrophobic pockets of both HDMs has mainly focused on small synthetic compounds; however, this approach has proved challenging. Here we describe an approach to generate a potent HDM dual inhibitor, p53LZ2, by rational protein grafting of the p53 transactivation domain onto a homodimeric leucine zipper. p53LZ2 shows tight binding affinity to both HDMs compared with wild-type p53 in vitro. X-ray crystallographic, comparative modelling and small-angle X-ray scattering studies of p53LZ2-HDM complexes show butterfly-shaped structures. A cell-permeable TAT-p53LZ2 effectively inhibits the cancer cell growth in wild-type but not mutant p53 by arresting cell cycle and inducing apoptosis in vitro. Thus, p53LZ2, designed by rational grafting, shows a potential therapeutic approach against cancer.

Effect of arginine-rich peptide length on the structure and binding strength of siRNA-peptide complexes.

Heparin decomplexation experiments, as well as all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations, were performed to determine the effect of the size of arginine(Arg)-rich peptides on the structure and binding strength of the siRNA-peptide complex. At a fixed peptide/siRNA mole ratio of 5:1 or 10:1, the siRNA complexes with peptides longer than nine Arg residues are more easily decomplexed by heparin than are those with nine Arg residues. At these mole ratios, peptides longer than nine Arg residues have cationic/anionic charge ratios in excess of unity, and produce more weakly bound complexes than nine Arg residue ones do. AA simulations of mixtures of peptides with a single siRNA show formation of an electrostatically induced complex, and the longer peptides produce a larger complex, but with no significant increase in the number of Arg residues bound to the siRNA. Larger-scale CG-MD simulations show that multiple siRNAs can be linked together by peptides into a large complex, as observed in the experiments. The peptides longer than nine residues, which at mole ratio 5:1 yield a peptide/siRNA charge ratio in excess of unity, include many noninteracting Arg residues, which repel each other electrostatically. This leads to a less dense complex than for 9-residue peptides, which can explain why these longer complexes are more easily decomplexed by heparin molecules, as observed in the experiments. The key role of the charge ratio is supported by simulations that show that, at a mole ratio of 2.5 peptides per siRNA, the longer 18-residue peptide has a charge ratio of roughly unity and also shows a tight complex, just as the 9-residue peptide does at a 5:1 mole ratio, where its charge ratio is also unity.

Continuous labeling of circulating tumor cells with microbeads using a vortex micromixer for highly selective isolation.

Circulating tumor cells (CTCs) are identified in transit within the blood stream of cancer patients and have been proven to be a main cause of metastatic disease. Current approaches for the size-based isolation of CTCs have encountered technical challenges as some of the CTCs have a size similar to that of leukocytes and therefore CTCs are often lost in the process. Here, we propose a novel strategy where most of the CTCs are coated by a large number of microbeads to amplify their size to enable complete discrimination from leukocytes. In addition, all of the microbead labeling processes are carried out in a continuous manner to prevent any loss of CTCs during the isolation process. Thus, a microfluidic mixer was employed to facilitate the efficient and selective labeling of CTCs from peripheral blood samples. By generating secondary vortex flows called Taylor-Gortler vortices perpendicular to the main flow direction in our microfluidic device, CTCs were continuously and successfully coated with anti-epithelial cell adhesion molecule-conjugated beads. After the continuous labeling, the enlarged CTCs were perfectly trapped in a micro-filter whereas all of the leukocytes escaped.

Simultaneous integration of multiple genes into the Kluyveromyces marxianus chromosome.

While Kluyveromyces marxianus is a promising yeast strain for biotechnological applications, genetic engineering of this strain is still challenging, especially when multiple genes are to be transformed. Sequential gene integration, which takes advantage of repetitive insertion/excision of the URA3 gene as a marker, has been the best option until now, because the URA3-deletion mutant is the only precondition for this method. However, we found that the introduced gene is co-excised during the URA3 excision step for next gene introduction, resulting in a very low cumulative probability (<1.57×10⁻6 % for 4 genes) of integrating all genes of interest. To overcome this extremely low probability, and to reduce labor and time, all 4 genes were simultaneously transformed. Surprisingly, the infamously high 'non-homologous end joining' activity of K. marxianus enabled simultaneous integration of all 4 genes in a single step, with a probability of 7.9%. Various K. marxianus strains could also be similarly transformed. Our finding not only reduces the labor and time required for such procedures, but also removes a number of preconditions, such as pre-made vectors, selection markers and knockout mutants, which are needed to introduce many genes into K. marxianus.