Simultaneous Detection of Multiple Pathogenic Targets with Stem-Tagged Primer Sets.

Simultaneous multiple gene detection is indispensable for the detection of various genes in a small sample obtained by an invasive method. A typical detection method is probe-based fluorescence melting curve analysis by means of real-time PCR. It is very limited because, for each target, a probe sequence with at least a different Tm must be designed. To overcome this limitation, we developed a simultaneous multiple gene detection method based on a giant amplicon molecular beacon. PCR was performed by attaching stem sequences with different Tm values to each primer set, and the melting Tm was measured by hybridizing the stem sequences at both ends of the amplified amplicon; this generated well-separated Tm signals. The important point here is that the stem sequence that produces the Tm signal is an arbitrarily selectable sequence unrelated to the target gene. Because it is arbitrarily selectable, the desired Tm can be freely adjusted. As a result, we succeeded in the simultaneous detection of four samples with the use of only one fluorophore. Theoretically, a combination of five fluorophores could detect more than 20 multiple genes simultaneously.

Simultaneous genotyping of multiple somatic mutations by using a clamping PNA and PNA detection probes.

It has been very difficult to detect and quantify multiple somatic mutations simultaneously in single-tube qPCR. Here, a novel method for simultaneous detection of multiple mutations and a melting curve analysis was developed by using clamping PNA and detection PNA probes. Each PNA probe was designed to have a specific melting temperature by the introduction of γ-PNA monomer. This technique was successfully applied to the detection of six genotypes in two different mutations of K-RAS at the same time. Such simultaneous analysis of an amplified curve and a melting curve in qPCR can be widely used for the early diagnosis of cancer and determining the prognosis of drug treatments.

Sequence selective tagging of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) using PNAs.

8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) is a commonly formed DNA lesion that is useful as a biomarker for oxidative stress. Methods for detecting 8-oxodGuo at specific positions within DNA could be useful for correlating DNA damage with mutational hotspots and repair enzyme accessibility. We describe a method for covalently linking ('tagging') peptide nucleic acids (PNAs) containing terminal nucleophiles under oxidative conditions to 8-oxodGuo at specific sites within DNA. Several nucleophiles were examined and the ε-amine of lysine was selected for further studies. As little as 10 fmol of 8-oxodGuo were detected by gel shift using (32)P-labeled target DNA and no tagging of dG at the same site or 8-oxodGuo at a distal site was detected when potassium ferricyanide was used as oxidant in substrates as long as 221 bp.

Quantitative detection of 8-Oxo-7,8-dihydro-2'-deoxyguanosine using chemical tagging and qPCR.

8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) is a commonly formed DNA lesion that is useful as a biomarker for oxidative stress. Although methods for selective quantification of 8-oxodGuo exist, there is room for additional methods that are sensitive and utilize instrumentation that is widely available. We previously took advantage of the reported reactivity of 8-oxodGuo to develop a method for detecting the lesion by selectively covalently tagging it with a molecule equipped with a biotin label that can be used subsequently with a reporting method ( Xue , L. and Greenberg , M. M. ( 2007 ) J. Am. Chem. Soc. 129 , 7010 ). We now report a method that can detect as little as 14 amol of 8-oxodGuo by tagging DNA with a reagent containing a disulfide that reduces background due to nonspecific binding. The reagent also contains biotin that enables capturing target DNA on streptavidin-coated magnetic beads. The captured DNA is quantified using quantitative PCR. The method is validated by comparing the amount of 8-oxodGuo detected as a function of Fe(2+)/H2O2/ascorbate-dose to that reported previously using mass spectrometry.

Facile synthesis, cytotoxicity and bioimaging of Fe(3+) selective fluorescent chemosensor.

The designing and development of fluorescent chemosensors have recently been intensively explored for sensitive and specific detection of environmentally and biologically relevant metal ions in aqueous solution and living cells. Herein, we report the photophysical results of alanine substituted rhodamine B derivative 3 having specific binding affinity toward Fe(3+) with micro molar concentration level. Through fluorescence titration at 599nm, we were confirmed that ligand 3 exhibited ratiometric fluorescence response with remarkable enhancement in emission intensity by complexation between 3 and Fe(3+) while it appeared no emission in case of the competitive ions (Sc(3+), Yb(3+), In(3+), Ce(3+), Sm(3+), Cr(3+), Sn(2+), Pb(2+), Ni(2+), Co(2+), Cu(2+), Ba(2+), Ca(2+), Mg(2+), Ag(+), Cs(+), Cu(+), K(+)) in aqueous/methanol (60:40, v/v) at neutral pH. However, the fluorescence as well as colorimetric response of ligand-iron complex solution was quenched by addition of KCN which snatches the Fe(3+) from complex and turn off the sensor confirming the recognition process was reversible. Furthermore, bioimaging studies against L-929 cells (mouse fibroblast cells) and BHK-21 (hamster kidney fibroblast), through confocal fluorescence microscopic experiment indicated that ligand showed good permeability and minimum toxicity against the tested cell lines.

5-Phenylselenyl- and 5-methylselenyl-methyl-2'-deoxyuridine induce oxidative stress, DNA damage, and caspase-2-dependent apoptosis in cancer cells.

In the present study, we investigated the signaling pathways implicated in the induction of apoptosis by two modified nucleosides, 5-phenylselenyl-methyl-2'-deoxyuridine (PhSe-T) and 5-methylselenyl-methyl-2'-deoxyuridine (MeSe-T), using human cancer cell lines. The induction of apoptosis was associated with proteolytic activation of caspase-3 and -9, PARP cleavage, and decreased levels of IAP family members, including c-IAP-1 and c-IAP-2, but had no effect on XIAP and survivin. PhSe-T and MeSe-T also enhanced the activities of caspase-2 and -8, Bid cleavage, and the conformational activation of Bax. Additionally, nucleoside derivative-induced apoptosis was inhibited by the selective inhibitors of caspase-2, -3, -8, and -9 and also by si-RNAs against caspase-2, -3, -8, and -9; however, inhibition of caspase-2 and -3 was more effective at preventing apoptosis than inhibition of caspase-8 and -9. Moreover, the inhibition of caspase-2 activation by the pharmacological inhibitor z-VDVAD-fmk or by the knockdown of protein expression using siRNA suppressed nucleoside derivative-induced caspase-3 activation, but not vice versa. PhSe-T and MeSe-T also induced a Δψ(m) loss via a CsA-insensitive mechanism, ROS production, and DNA damage, including strand breaks. Moreover, ROS scavengers such as NAC, tiron, and quercetin inhibited nucleoside derivative-induced ROS generation and apoptosis by blocking the sequential activation of caspase-2 and -3, indicating the role of ROS in caspase-2-mediated apoptosis. Taken together, these results indicate that caspase-2 acts upstream of caspase-3 and that caspase-2 functions in response to DNA damage in both PhSe-T- and MeSe-T-induced apoptosis. Our results also suggest that ROS are critical regulators of the sequential activation of caspase-2 and -3 in nucleoside derivative-treated cancer cells.

p38 mitogen-activated protein kinase is a key regulator of 5-phenylselenyl- and 5-methylselenyl-methyl-2'-deoxyuridine-induced apoptosis in human HL-60 cells.

Two novel, modified thymidine nucleosides, 5-phenylselenyl-methyl-2'-deoxyuridine (PhSe-T) and 5-methylselenyl-methyl-2'-deoxyuridine (MeSe-T), trigger reactive oxygen species (ROS) generation and DNA damage and thereby induce caspase-mediated apoptosis in human HL-60 cells; however, the mechanism leading to caspase activation and apoptotic cell death remains unclear. Therefore, we investigated the signaling molecules involved in nucleoside derivative-induced caspase activation and apoptosis in HL-60 cells. PhSe-T/MeSe-T treatment activated two mitogen-activated protein kinases (MAPKs), extracellular-receptor kinase (ERK) and p38, and induced the phosphorylation of two downstream targets of p38, ATF-2 and MAPKAPK2. In addition, the selective p38 inhibitor SB203580 suppressed PhSe-T/MeSe-T-induced apoptosis and activation of caspase-3, -9, -8, and -2, whereas the jun amino-terminal kinase (JNK) inhibitor SP600125 and the ERK inhibitor PD98059 had no effect. SB203580 and an ROS scavenger, tiron, inhibited PhSe-T/MeSe-T-induced histone H2AX phosphorylation, which is a DNA damage marker. Moreover, tiron inhibited PhSe-T/MeSe-T-induced phosphorylation of p38 and enhanced p38 MAP kinase activity, indicating a role for ROS in PhSe-T/MeSe-T-induced p38 activation. Taken together, our results suggest that PhSe-T/MeSe-T-induced apoptosis is mediated by the p38 pathway and that p38 serves as a link between ROS generation and DNA damage/caspase activation in HL-60 cells.

Nano-engineered optimal templates for surface-plasmon enhanced Raman scattering.

We investigated the critical conditions to realize reliable and nano-engineered templates for surface-plasmon enhanced Raman scattering (SERS). Ultra-sensitive SERSs of thymine oligonucleotides were successfully realized on the template of Au nanoparticle arrays which were prepared by the combination of electron-beam lithography and post-chemical modification techniques. Drastic enhancement of Raman signal from the thymine oligonucleotides was only observed on the optimized templates, where the tuning of the plasmon resonance condition and the formation of the hot spots were both critical. Our results suggest that the artificial generation of reproducible and controlled hot spots can be achieved by our approach.

Potent radiosensitizing agents: 5-methylselenyl- and 5-phenylselenyl-methyl-2'-deoxyuridine.

This Letter describes the novel radiosensitizing agents based on nucleoside base modification. In addition to the known 5-phenylselenide derivative, 5-methylselenide modified thymidine, which has a van der Waals radius smaller than the phenyl group, was newly synthesized. The similar monomer activity of 5-methylselenide derivative under oxidation condition was confirmed by NMR experiments. The cytotoxicity tests and radiosensitizing experiments of both compounds were carried out using the H460 lung cancer cell line. Both the 5-phenylselenide and the 5-methylselenide derivatives showed a relatively low toxicity to the cells. However, in combination with γ-radiolysis, both exerted good radiosensitizing effects to the lung cancer cell lines in vitro. This result confirms that 5-methylselenide modified thymidine could be a useful candidate as a potential radiosensitizing agent in vivo.

Synthesis and evaluation of cytotoxic effects of hanultarin and its derivatives.

One of the known cytotoxic lignans is (-)-1-O-feruloyl-secoisolariciresinol designated as hanultarin, which was isolated from the seeds of Trichosanthes kirilowii. In this Letter, we described the first synthesis of 1-O-feruloyl-secoisolariciresinol, 1,4-O-diferuloyl-secoisolariceresinol and their analogues. The cytotoxicities of these compounds were evaluated against several cancer cell lines. Interestingly, we found that the feruloyl diester derivative of secoisolariciresinol was the most active cytotoxic compound against all the cancer cells tested in this experiment. The IC(50) values of the1,4-O-diferuloyl-secoisolariceresinol were in the range of 7.1-9.8µM except one cell line. In considering that both ferulic acid and secoisolariciresinol are commonly found in many plants and have no cytotoxicity, this finding is remarkable in that simple covalent bonds between the ferulic acid and secoisolariciresinol cause a cytotoxic effect.

Treatment of velopharyngeal insufficiency in a patient with a submucous cleft palate using a speech aid: the more treatment options, the better the treatment results.

BACKGROUND: The submucous cleft palate (SMCP) is a type of cleft palate that may result in velopharyngeal insufficiency (VPI). Palate muscles completely separate oral and nasal cavities by closing off the velopharynx during functional processes such as speech or swallow. Also, hypernasality may arise from anatomical or neurological abnormalities in these functions. Treatments of this issue involve a combination of surgical intervention, speech aid, and speech therapy. This case report demonstrates successfully treated VPI resulted from SMCP without any surgical intervention but solely with speech aid appliance and speech therapy. CASE PRESENTATION: A 13-year-old female patient with a speech disorder from velopharyngeal insufficiency that was caused by a submucous cleft palate visited to our OMFS clinic. In the intraoral examination, the patient had a short soft palate and bifid uvula. And the muscles in the palate did not contract properly during oral speech. She had no surgical history such as primary palatoplasty or pharyngoplasty except for tonsillectomy. And there were no other medical histories. Objective speech assessment using nasometer was performed. We diagnosed that the patient had a SMCP. The patient has shown a decrease in speech intelligibility, which resulted from hypernasality. We decided to treat the patient with speech aid (palatal lift) along with speech therapy. During the 7-month treatment, hypernasality measured by a nasometer decreased and speech intelligibility became normal. CONCLUSIONS: Surgery remains the first treatment option for patients with velopharyngeal insufficiencies from submucous cleft palates. However, there were few reports about objective speech evaluation pre- or post-operation. Moreover, there has been no report of non-surgical treatment in the recent studies. From this perspective, this report of objective improvement of speech intelligibility of VPI patient with SMCP by non-surgical treatment has a significant meaning. Speech aid can be considered as one of treatment options for management of SMCP.

Interstrand cross-link formation in duplex and triplex DNA by modified pyrimidines.

DNA interstrand cross-links have important biological consequences and are useful biotechnology tools. Phenylselenyl substituted derivatives of thymidine (1) and 5-methyl-2'-deoxycytidine (5) produce interstrand cross-links in duplex DNA when oxidized by NaIO4. The mechanism involves a [2,3]-sigmatropic rearrangement of the respective selenoxides to the corresponding methide type intermediates, which ultimately produce the interstrand cross-links. Determination of the rate constants for the selenoxide rearrangements indicates that the rate-determining step for cross-linking is after methide formation. Cross-linking by the thymidine derivative in duplex DNA shows a modest kinetic preference when flanked by pyrimidines as opposed to purines. In contrast, the rate constant for cross-link formation from 5 opposite dG in duplex DNA is strongly dependent upon the flanking sequence and, in general, is at least an order of magnitude slower than that for 1 in an otherwise identical sequence. Introduction of mispairs at the base pairs flanking 5 or substitution of the opposing dG by dI significantly increases the rate constant and yield for cross-linking, indicating that stronger hydrogen bonding between the methide derived from it and dG compared to dA and the respective electrophile derived from 1 limits reaction by increasing the barrier to rotation into the required syn-conformation. Incorporation of 1 or 5 in triplex forming oligonucleotides (TFOs) that utilize Hoogsteen base pairing also yields interstrand cross-links. The dC derivative produces ICLs approximately 10x faster than the thymidine derivative when incorporated at the 5'-termini of the TFOs and higher yields when incorporated at internal sites. The slower, less efficient ICL formation emanating from 1 is attributed to reaction at N1-dA, which requires local melting of the duplex. In contrast, 5 produces cross-links by reacting with N7-dG. The cross-linking reactions of 1 and 5 illustrate the versatility and utility of these molecules as mechanistic probes and tools for biotechnology.

PNA/DNA interstrand cross-links from a modified PNA base upon photolysis or oxidative conditions.

PNA/DNA interstrand cross-links (ICLs) were observed when peptide nucleic acids (PNAs) containing modified thymine derivatives were hybridized with the complementary or one-base mismatched DNA upon photolysis or treatments of oxidative agent. PNA/DNA ICL formation provides a useful method for biological applications such as antisense technologies or PNA chips.

A control system of a negative hydrogen ion sources by using an EPICS-based proportional-integral-derivative.

We have developed an EPICS-based control system for a multicusp negative ion source based on a VME IOC software, a sequencer controlling a closed proportional integral (PI) loop, and an interlock. The PI loop was tuned by a step input voltage, and tuning gains of the proportion and integral have been determined. The PI logics, developed by using standard proportional-integral-derivative records, can control the arc current within +/-1% of a given set value.

Development of a MeV proton beam irradiation system.

A proton beam irradiation system for the application of the MeV class proton beam, such as an implantation for a power semiconductor device and a smart-cut technology for a semiconductor production process, has been developed. This system consists of a negative ion source, an Einzel lens for a low energy beam transport, accelerating tubes, a gas stripper, a Cockroft-Walton high voltage power supply with 1 MV, a vacuum pumping system, and a high pressure insulating gas system. The negative hydrogen ion source is based on TRIUMF's design. Following the tandem accelerator, a pair of magnets is installed for raster scanning of the MeV proton beam to obtain a uniform irradiation pattern on the target. The system is 7 m long from the ion source to the target and is optimized for the proton beam irradiation. The details of the system development will be described.

Fast triggers for a proton injector at PEFP.

A fast timing system has been developed to control transistor transistor logic (TTL) trigger signals which are used to extract the pulsed proton beam from an ion source with the precision of less than submicro seconds. The system has been designed to set a delay and duty of the pulses, respectively, and prohibit the beam pulse by an external interlock signal. The system is based on VME which is composed of VME CPU and fast I/O boards with fan-out modules. The software of the system has been developed by the record/device supports and channel access in the core of the EPICS environments. In the paper, we describe software configurations and hardware drivers.

Development of superconducting magnets for RAON 28 GHz ECR ion source.

RAON, a 28 GHz electron cyclotron resonance ion source (ECR IS), was designed and tested as a Rare Isotope Science Project. It is expected that RAON would provide not only rare-isotope beams but also stable heavy ions ranging from protons to uranium. In order to obtain the steady heavy-ion beam required for ECR IS, we must use a 28 GHz microwave source as well as a high magnetic field. A superconducting magnet using a NbTi wire was designed and manufactured for producing the ECR IS and a test was conducted. In this paper, the design and fabrication of the superconducting magnet for the ECR IS are presented. Experimental results show that the quench current increases whenever quenching occurs, but it has not yet reached the designed current. The experiment is expected to reveal the ideal conditions required to reach the designed current.

Beam dynamics simulations of post low energy beam transport section in RAON heavy ion accelerator.

RAON (Rare isotope Accelerator Of Newness) heavy ion accelerator of the rare isotope science project in Daejeon, Korea, has been designed to accelerate multiple-charge-state beams to be used for various science programs. In the RAON accelerator, the rare isotope beams which are generated by an isotope separation on-line system with a wide range of nuclei and charges will be transported through the post Low Energy Beam Transport (LEBT) section to the Radio Frequency Quadrupole (RFQ). In order to transport many kinds of rare isotope beams stably to the RFQ, the post LEBT should be devised to satisfy the requirement of the RFQ at the end of post LEBT, simultaneously with the twiss parameters small. We will present the recent lattice design of the post LEBT in the RAON accelerator and the results of the beam dynamics simulations from it. In addition, the error analysis and correction in the post LEBT will be also described.

Prototyping of beam position monitor for medium energy beam transport section of RAON heavy ion accelerator.

A heavy ion accelerator, RAON is going to be built by Rare Isotope Science Project in Korea. Its target is to accelerate various stable ions such as uranium, proton, and xenon from electron cyclotron resonance ion source and some rare isotopes from isotope separation on-line. The beam shaping, charge selection, and modulation should be applied to the ions from these ion sources because RAON adopts a superconducting linear accelerator structure for beam acceleration. For such treatment, low energy beam transport, radio frequency quadrupole, and medium energy beam transport (MEBT) will be installed in injector part of RAON accelerator. Recently, development of a prototype of stripline beam position monitor (BPM) to measure the position of ion beams in MEBT section is under way. In this presentation, design of stripline, electromagnetic (EM) simulation results, and RF measurement test results obtained from the prototyped BPM will be described.

Emittance study of a 28 GHz electron cyclotron resonance ion source for the Rare Isotope Science Project superconducting linear accelerator.

A 28 GHz electron cyclotron resonance (ECR) ion source is being developed for use as an injector for the superconducting linear accelerator of the Rare Isotope Science Project. Beam extraction from the ECR ion source has been simulated using the KOBRA3-INP software. The simulation software can calculate charged particle trajectories in three dimensional complex magnetic field structures, which in this case are formed by the arrangement of five superconducting magnets. In this study, the beam emittance is simulated to understand the effects of plasma potential, mass-to-charge ratio, and spatial distribution. The results of these simulations and their comparison to experimental results are presented in this paper.