Single nucleotide polymorphism genotyping of aldehyde dehydrogenase 2 gene using a single bacterial magnetic particle

Bacterial magnetosome and its potential application

Bacterial magnetosome, synthetized by magnetosome-producing microorganisms including magnetotactic bacteria (MTB) and some non-magnetotactic bacteria (Non-MTB), is a new type of material comprising magnetic nanocrystals surrounded by a phospholipid bilayer. Because of the special properties such as single magnetic domain, excellent biocompatibility and surface modification, bacterial magnetosome has become an increasingly attractive for researchers in biology, medicine, paleomagnetism, geology and environmental science. This review briefly describes the general feature of magnetosome-producing microorganisms. This article also highlights recent advances in the understanding of the biochemical and magnetic characteristics of bacterial magnetosome, as well as the magnetosome formation mechanism including iron ions uptake, magnetosome membrane formation, biomineralization and magnetosome chain assembly. Finally, this review presents the potential applications of bacterial magnetosome in biomedicine, wastewater treatment, and the significance of mineralization of magnetosome in biology and geology.

High-throughput SNP genotyping based on solid-phase PCR on magnetic nanoparticles with dual-color hybridization

Single-nucleotide polymorphisms (SNPs) are one-base variations in DNA sequence that can often be helpful when trying to find genes responsible for inherited diseases. In this paper, a microarray-based method for typing single nucleotide polymorphisms (SNPs) using solid-phase polymerase chain reaction (PCR) on magnetic nanoparticles (MNPs) was developed. One primer with biotin-label was captured by streptavidin coated magnetic nanoparticles (SA-MNPs), and PCR products were directly amplified on the surface of SA-MNPs in a 96-well plate. The samples were interrogated by hybridization with a pair of dual-color probes to determine SNP, and then genotype of each sample can be simultaneously identified by scanning the microarray printed with the denatured fluorescent probes. The C677T polymorphisms of methylenetetrahydrofolate reductase (MTHFR) gene from 126 samples were interrogated using this method. The results showed that three different genotypes were discriminated by three fluorescence patterns on the microarray. Without any purification and reduction procedure, and all reactions can be performed in the same vessel, this approach will be a simple and labor-saving method for SNP genotyping and can be applicable towards the automation system to achieve high-throughput SNP detection.

Detection of epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC) using a fully automated system with a nano-scale engineered biomagnetite

A fully automated system using nano-scale engineered biomagnetite was developed to detect mutations in the epidermal growth factor receptor (EGFR) gene in non-small cell lung cancer (NSCLC). Bacterial magnetic particles (BacMPs) were isolated from the magnetic bacterium Magnetospirillum magneticum AMB-1 and conjugated to streptavidin. Biotin-labeled target PCR products were then captured with the BacMPs, hybridized with the detection probe and detected by fluorescence signaling. The process was performed using a newly designed automated processor equipped with an XYZ mobile arm containing a 96-way automated pipetter, reagent dispenser and fluorescence detector. Two types of somatic mutations (in-frame deletions and point substitutions) in the EGFR gene were successfully identified within 3.5h using this system, suggesting that this system could be used in clinical tests of EGFR gene mutations in lung cancer, and potentially other cancer, patients. Additionally, a very low mutation rate could be detected in these samples.

Efficient and stable display of functional proteins on bacterial magnetic particles using mms13 as a novel anchor molecule

Magnetic particles are increasingly used for various biomedical applications because they are easy to handle and separate from biological samples. In this work, a novel anchor molecule was used for targeted protein display onto magnetic nanoparticles. The magnetic bacterium Magnetospirillum magneticum AMB-1 synthesizes intracellular bacterial magnetic particles (BMPs) covered with a lipid bilayer membrane. In our recent research, an integral BMP membrane protein, Mms13, was isolated and used as an anchor molecule to display functional proteins onto BMPs. The anchoring properties of Mms13 were confirmed by luciferase fusion studies. The C terminus of Mms13 was shown to be expressed on the surface of BMPs, and Mms13 was bound to magnetite directly and tightly permitting stable localization of a large protein, luciferase (61 kDa), on BMPs. Consequently, luminescence intensity obtained from BMPs using Mms13 as an anchor molecule was >400 or 1,000 times higher than Mms16 or MagA, which previously were used as anchor molecules. Furthermore, the immunoglobulin G-binding domain of protein A (ZZ) was displayed uniformly on BMPs using Mms13, and antigen was detected by transmission electron microscopy using antibody-labeled gold nanoparticles on a single BMP displaying the ZZ-antibody complex. The results of this study demonstrated the utility of Mms13 as a molecular anchor, which will facilitate the assembly of other functional proteins onto BMPs in the near feature.

Controlling chemical reactivity at solid-solution interfaces by means of hydrophobic magnetic nanoparticles

Hydrophobic magnetic nanoparticles are employed to reversibly regulate the hydrophobic/hydrophilic properties of surfaces and to control the electrochemistry and bioelectochemistry at chemically modified electrodes. Selective bioelectrocatalytic transformations at relay-functionalized electrodes are accomplished by the magnetic attractions of the hydrophobic magnetic nanoparticles with coadsorbed hydrophobic redox relays to the electrode. The selective activation of one of two biocatalysts solubilized in the aqueous electrolyte solution in the absence or presence of hydrophobic magnetic nanoparticles results in the specific activation of bioelectrocatalytic processes. The magnetic attraction and retraction of hydrophobic magnetic nanoparticles to and from semiconductor nanoparticle (CdS)-functionalized electrodes enable the control of the photocurrent directions at the electrode from cathodic to anodic directions, respectively. The magnetic attraction of the hydrophobic magnetic nanoparticles to the surfaces is also employed to control biorecognition and biocatalytic transformations at solid supports. The magnetic attraction and retraction of the hydrophobic magnetic nanoparticles to and from the surfaces allow the blockage and activation of DNA hybridization, polymerization, and enzymatic digestion, respectively.

Integrated nanoparticle-biomolecule hybrid systems: synthesis, properties, and applications

Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.

Mutation detection using ligase chain reaction in passivated silicon-glass microchips and microchip capillary electrophoresis

The ligase chain reaction (LCR) following PCR is one of the most sensitive and specific methods for detecting mutations, especially single nucleotide polymorphisms (SNPs). Performing LCR in microchips remains a challenge because of the inhibitory effect of the internal surfaces of silicon-glass microchips. We have tested a dynamic polymer-based surface passivation method for LCR conducted in oxide-coated silicon-glass microchips. The combination of polyvinylpyrrolidone 40 (PVP-40) at 0.75% (w/v) with an excess of the ligase produced successful LCR in the silicon-glass microchips, with yields of ligated primers comparable to reactions performed in conventional reaction tubes. Ligated primers were detected and quantified simply and conveniently using microchip capillary electrophoresis.

Spontaneous integration of transmembrane peptides into a bacterial magnetic particle membrane and its application to display of useful proteins

An antimicrobial peptide, temporin L, and its derivative (TL-A2) were employed as anchor peptides and displayed streptavidin on a bacterial magnetic particle (BMP) membrane. The ribotoxin L3 loop (L3) and the arginine-chain peptide (R(12)), which are carrier peptides permeable to eukaryotic cell membranes, were also used. The peptides were labeled with a fluorescent dye, 4-fluoro-7-nitrobenzofurazan (NBD), at the N-terminal region (NBD-peptides) and mixed with BMPs. A specific integration of NBD-temporin L into a BMP membrane was observed. The basic amino acids in temporin L played an important role in the integration into BMPs. Biotin conjugated to the N-terminus of temporin L was integrated into a BMP membrane. The C-terminus of temporin L was incorporated into a BMP membrane, and the N-terminus was located on the BMP membrane surface. The present study shows that temporin L is a stable molecular anchor on BMPs by the binding of soluble protein to the N-terminus.

Association between endometriosis and genetic polymorphisms of the estradiol-synthesizing enzyme genes HSD17B1 and CYP19

BACKGROUND

Endometriosis, an estrogen-dependent disease, is believed to be influenced by multiple genetic and environmental factors. Here, we evaluated whether the risk and severity of endometriosis are associated with polymorphisms in estradiol-synthesizing enzyme genes: the Ser312Gly polymorphism in 17-beta-hydroxysteroid dehydrogenase type 1 (HSD17B1) and the Arg264Cys polymorphism in cytochrome P450, subfamily XIX (CYP19).

METHODS

All participants underwent diagnostic laparoscopy, and the stage of endometriosis was determined according to the Revised American Fertility Society classification. Of the 138 women enrolled, 59 had no endometriosis, 21 had stage I, 10 had stage II, 23 had stage III and 25 had stage IV. SNPs were discriminated by allele-specific oligonucleotide hybridization.

RESULTS

Individuals having at least one A-allele (A/G or A/A genotype) of HSD17B1 showed a significantly increased risk of endometriosis (A/G genotype: adjusted OR, 3.06; 95%CI 1.21-7.74; A/A genotype: adjusted OR, 3.02; 95%CI 1.08-8.43). There was a significant trend associating A/G + A/A genotypes with severity of endometriosis (P for trend < 0.01). No statistically significant association was found for the CYP19 polymorphism.

CONCLUSIONS

Evidence for association between the Ser312Gly polymorphism in HSD17B1 and endometriosis was found in a Japanese population. The A-allele of HSD17B1 appears to confer higher risk for endometriosis.

Neisseria meningitidis: an overview of the carriage state

During periods of endemic disease, about 10 % of the general population harbour Neisseria meningitidis in the nasopharynx. Since N. meningitidis is a strict human pathogen and most patients have not been in contact with other cases, asymptomatic carriers are presumably the major source of the pathogenic strains. Most carrier isolates are shown to lack capsule production. The capsule deficient state of meningococcal strains in the nasopharynx may aid evasion of the human immune defence and hence be selected to survive nasopharyngeal colonization. Carriage itself can be an immunizing process resulting in systemic protective antibody responses. Frequent nasopharyngeal colonization with related bacteria like Neisseria lactamica improves natural immunity to meningococci by the formation of cross-reacting antibodies. While most meningococcal strains recovered from patients belong to a limited number of clonal groups worldwide, strains isolated from carriers comprise numerous genotypes, with only a small proportion of the strains representing invasive clones. During the carriage state, co-colonization with other pathogenic and non-pathogenic bacteria may lead to genetic exchange, which may result in the emergence of new meningococcal clones. The high diversity of meningococcal carrier strains, compared with hypervirulent strains, supports the idea that transmissibility, not invasion, is essential in the life cycle of N. meningitidis.

Single nucleotide polymorphism detection in aldehyde dehydrogenase 2 (ALDH2) gene using bacterial magnetic particles based on dissociation curve analysis

Single nucleotide polymorphism (SNP) detection for aldehyde dehydrogenase 2 (ALDH2) gene based on DNA thermal dissociation curve analysis was successfully demonstrated using an automated system with bacterial magnetic particles (BMPs) by developing a new method for avoiding light scattering caused by nanometer-size particles when using commercially available fluorescent dyes such as FITC, Cy3, and Cy5 as labeling chromophores. Biotin-labeled PCR products in ALDH2, two allele-specific probes (Cy3-labeled detection probe for ALDH2*1 and Cy5-labeled detection probe for ALDH2*2), streptavidin-immobilized BMPs (SA-BMPs) were simultaneously mixed. The mixture was denatured at 70 degrees C for 3 min, cooled slowly to 25 degrees C, and incubated for 10 min, allowing the DNA duplex to form between Cy3- or Cy5-labeled detection probes and biotin-labeled PCR products on SA-BMPs. Then duplex DNA-BMP complex was heated to 58 degrees C, a temperature determined by dissociation curve analysis and a dissociated single-base mismatched detection probe was removed at the same temperature under precise control. Furthermore, fluorescence signal from the detection probe was liberated into the supernatant from completely matched duplex DNA-BMP complex by heating to 80 degrees C and measured. In the homozygote target DNA (ALDH2*1/*1 and ALDH2*2/*2), the fluorescence signals from single-base mismatched were decreased to background level, indicating that mismatched hybridization was efficiently removed by the washing process. In the heterozygote target DNA (ALDH2*1/*2), each fluorescence signals was at a similar level. Therefore, three genotypes of SNP in ALDH2 gene were detected using the automated detection system with BMPs.