Detection of single-nucleotide polymorphisms using gold nanoparticles and single-strand-specific nucleases

The current study reports an assay approach that can detect single-nucleotide polymorphisms (SNPs) and identify the position of the point mutation through a single-strand-specific nuclease reaction and a gold nanoparticle assembly. The assay can be implemented via three steps: a single-strand-specific nuclease reaction that allows the enzyme to truncate the mutant DNA; a purification step that uses capture probe-gold nanoparticles and centrifugation; and a hybridization reaction that induces detector probe-gold nanoparticles, capture probe-gold nanoparticles, and the target DNA to form large DNA-linked three-dimensional aggregates of gold nanoparticles. At high temperature (63 degrees C in the current case), the purple color of the perfect match solution would not change to red, whereas a mismatched solution becomes red as the assembled gold nanoparticles separate. Using melting analysis, the position of the point mutation could be identified. This assay provides a convenient colorimetric detection that enables point mutation identification without the need for expensive mass spectrometry. To our knowledge, this is the first report concerning SNP detection based on a single-strand-specific nuclease reaction and a gold nanoparticle assembly.     

Effects of dietary probiotic supplementations on prevention/treatment of yersiniosis disease

Aims:  To evaluate Enterobacter cloacae and Bacillus mojavensis , isolated from rainbow trout gut in the present study, as a probiotic to control yersiniosis disease.
Methods and Results:  A strain of Ent. cloacae and B. mojavensis , isolated from the digestive tract of rainbow trout had an antagonistic effect to Yersinia ruckeri , which causes yersiniosis. After feeding fish with 1 × 10⁸ cells g⁻¹ probiotic containing feed for 60 days, the fish survival rate increased to 99·2% following challenge with Y. ruckeri compared with controls that had 35% survival rate. Effects of Ent. cloacae and B. mojavensis on weight gains and stimulation of red blood cells, white blood cells, platelets and hemoglobin were also evaluated in separate groups of fish fed probiotic containing feed for 2 months. Probiotic significantly affected white blood cells, hemoglobin and weight gains of the experimental fish.
Conclusions:  Enterobacter cloacae and B. mojavensis , can be used to prevent and control yersiniosis disease.
Significance and Impact of the Study:  In conclusion, concomitant use of Ent. cloacae and B. mojavensis as a feed supplement is beneficial to rainbow trout. Use of these organisms can protect fish from yersiniosis and enhance digestibility and utilization of feed. Use of such probiotics may also limit the use of antibiotics and other chemicals in control and treatment of diseases, and thus contribute to the effort to reduce environmental contamination by residual antibiotics and chemicals .     

Investigation of Gold and Silver Nanoparticles on Absorption Heating and Scattering Imaging

Efficient conversion of absorbed light to heat energy and strong scattering by gold and silver nanoparticles suggest these nanoparticles as the agents of heating and imaging. Absorption efficiency and scattering efficiency of gold and silver nanoparticles were studied through numerical simulation using the discrete dipole approximation method. This study shows that the size of gold and silver nanoparticles can effect gold and silver nanoparticles’ absorption efficiency and scattering efficiency. The gold nanoparticle is found to possess the maximum absorption efficiency when the size of gold nanoparticle is 50 nm and the incident wavelength is 540 nm, and the increasing scattering efficiency with the increasing size of gold nanoparticle in the medium, and refractive index of the medium is around 1.33. However, the silver nanoparticle owns the maximum absorption efficiency when the size of silver nanoparticle is 20 nm and the incident wavelength is 396 nm, and the maximum scattering efficiency when the size of silver nanoparticle is 30 nm and the incident wavelength is 410 nm in the same medium. The conditions for achieving the maximum adsorption efficiency and scattering efficiency of gold and silver nanoparticle can be used for heating and imaging using visible and near-infrared light.     

Extensive evaluations of the cytotoxic effects of gold nanoparticles

Background

Many in vitro studies have revealed that the interference of dye molecules in traditional nanoparticle cytotoxicity assays results in controversial conclusions. The aim of this study is to establish an extensive and systematic method for evaluating biological effects of gold nanoparticles in mammalian cell lines.

Methods

We establish the cell-impedance measurement system, a label-free, real-time cell monitoring platform that measures electrical impedance, displaying results as cell index values, in a variety of mammalian cell lines. Cytotoxic effects of gold nanoparticles are also evaluated with traditional in vitro assays.

Results

Among the six cell lines, gold nanoparticles induce a dose-dependent suppression of cell growth with different levels of severity and the suppressive effect of gold nanoparticles was indirectly associated with their sizes and cellular uptake. Mechanistic studies revealed that the action of gold nanoparticles is mediated by apoptosis induction or cell cycle delay, depending on cell type and cellular context. Although redox signaling is often linked to the toxicity of nanoparticles, in this study, we found that gold nanoparticle-mediated reactive oxygen species generation was not sustained to notably modulate proteins involved in antioxidative defense system.

Conclusion

The cell-impedance measurement system, a dye-free, real-time screening platform, provides a reliable analysis for monitoring gold nanoparticle cytotoxicity in a variety of mammalian cell lines. Furthermore, gold nanoparticles induce cellular signaling and several sets of gene expression to modulate cellular physical processes.

General significance

The systematic approach, such as cell-impedance measurement, analyzing the toxicology of nanomaterials offers convincing evidence of the cytotoxicity of gold nanomaterials.     

The Effect of Ag Nanoparticles on Surface-Enhanced Luminescence from Au Nanovoid Arrays

Studies comparing the effect of adding two different nanoparticle compositions on the plasmonic properties of Au nanovoid arrays were undertaken. Surface-enhanced resonance luminescence and surface-enhanced resonance Raman studies comparing dispersed Ag nanoparticles and Ag nanoparticle aggregates on gold nanovoid arrays were undertaken. These studies showed that using Ag nanoparticle aggregates increased both luminescence and Raman efficiency relative to when dispersed nanoparticles were used; in addition, these studies also showed that adding dispersed Ag nanoparticles supported a more reproducible enhancement in luminescence and Raman across the substrate compared to using Ag nanoparticle aggregates. Finite element analysis simulations indicated that surface plasmon polariton distribution in the sample was affected by the presence of the Ag nanoparticles on the Au nanovoid array.     

Investigation of Biophysical Mechanisms in Gold Nanoparticle Mediated Laser Manipulation of Cells Using a Multimodal Holographic and Fluorescence Imaging Setup

Laser based cell manipulation has proven to be a versatile tool in biomedical applications. In this context, combining weakly focused laser pulses and nanostructures, e.g. gold nanoparticles, promises to be useful for high throughput cell manipulation, such as transfection and photothermal therapy. Interactions between laser pulses and gold nanoparticles are well understood. However, it is still necessary to study cell behavior in gold nanoparticle mediated laser manipulation. While parameters like cell viability or perforation efficiency are commonly addressed, the influence of the manipulation process on other essential cell parameters is not sufficiently investigated yet. Thus, we set out to study four relevant cell properties: cell volume and area, ion exchange and cytoskeleton structure after gold nanoparticle based laser manipulation. For this, we designed a multimodal imaging and manipulation setup. 200 nm gold nanoparticles were attached unspecifically to canine cells and irradiated by weakly focused 850 ps laser pulses. Volume and area change in the first minute post laser manipulation was monitored using digital holography. Calcium imaging and cells expressing a marker for filamentous actin (F-actin) served to analyze the ion exchange and the cytoskeleton, respectively. High radiant exposures led to cells exhibiting a tendency to shrink in volume and area, possibly due to outflow of cytoplasm. An intracellular raise in calcium was observed and accompanied by an intercellular calcium wave. This multimodal approach enabled for the first time a comprehensive analysis of the cell behavior in gold nanoparticle mediated cell manipulation. Additionally, this work can pave the way for a better understanding and the evaluation of new applications in the context of cell transfection or photothermal therapy.     

The estimation of pooled-sample sensitivity for detection of Salmonella in turkey flocks

Aims:  To investigate the effectiveness of pooled sampling methods for detection of Salmonella in turkey flocks.
Methods and Results:  Individual turkey droppings were taken from 43 flocks, with half the dropping tested for S almonella as an individual sample and the other half included in a pool of five. A pair of boot swabs and a dust sample were also taken from each flock. The results were analysed using Bayesian methods in the absence of a gold standard. This showed a dilution effect of mixing true-positive with negative samples, but even with this the pooled faecal samples were found to be a highly efficient method of testing compared with individual faecal samples. The more samples included in the pool, the more sensitive the pooled sampling method was predicted to be. The sensitivity of dust sampling was much more sensitive than faecal sampling at low prevalence.
Conclusions:  Pooled faecal sampling is an efficient method of Salmonella detection in turkey flocks. The additional testing of a dust sample greatly increased the effectiveness of sampling, especially at low prevalence.
Significance and Impact of the Study:  This is the first study to relate the sensitivity of the sampling methods to the within-flock prevalence.     

Biosynthesis of silver and gold nanoparticles using thermophilic bacterium Geobacillus stearothermophilus

Nanomaterials have assumed a great deal of importance as they often display unique and considerably modified physical, chemical and biological properties as compared to their counterparts of the macroscale. In this study, biogenic synthesis of silver and gold nanoparticles by Geobacillus stearothermophilus has been attempted. The exposure of G. stearothermophilus cell free extract to the metal salts leads to the formation of stable silver and gold nanoparticles in the solution. These nanoparticles were characterized by UV–Vis spectra, FTIR, TEM, and XRD. The silver and gold nanoparticles have absorption maxima at 423 nm and 522 nm respectively. The TEM micrograph revealed the formation of polydispersed particles in the case of silver nanoparticles and monodispersed particles with respect to the gold nanoparticles. High stability of the nanoparticle solution could be attributed to the secretion of certain capping proteins by the bacterium in the reaction mixture. The involvement of these proteins was confirmed by FTIR and SDS PAGE.     

Manipulation of Microscale Fluid Using Laser-Irradiated Nanoparticle Arrays

The manipulation of microscale fluid has been widely used in biology, medicine, and chemistry. However, the traditional control systems are relatively large, complex, and costly. Optical driving micro- and nanofluid is a new trend of microfluidics, which combines the advantages of both optics and microfluidics in the micro-nano scale. In the present work, we investigated a method to drive microfluid by taking advantage of the localized surface plasmon resonance effect of gold nanoparticles, which can convert optical energy to fluid motion. First, numerical simulation was carried out to calculate the electromagnetic, temperature, and flow field around laser-irradiated gold nanoparticles. Then, the simplified heat source condition was verified. The nanoparticle array was regarded as heat source to induce convection flow. The influence of the spacing and number of nanoparticles in array was investigated. On this basis, the structural parameters of nanoparticle array that can be used to regulate the velocity of microfluidic were obtained.

     

A colorimetric method for point mutation detection using high-fidelity DNA ligase

The present study reported proof-of-principle for a genotyping assay approach that can detect single nucleotide polymorphisms (SNPs) through the gold nanoparticle assembly and the ligase reaction. By incorporating the high-fidelity DNA ligase (Tth DNA ligase) into the allele-specific ligation-based gold nanoparticle assembly, this assay provided a convenient yet powerful colorimetric detection that enabled a straightforward single-base discrimination without the need of precise temperature control. Additionally, the ligase reaction can be performed at a relatively high temperature, which offers the benefit for mitigating the non-specific assembly of gold nanoparticles induced by interfering DNA strands. The assay could be implemented via three steps: a hybridization reaction that allowed two gold nanoparticle-tagged probes to hybrid with the target DNA strand, a ligase reaction that generates the ligation between perfectly matched probes while no ligation occurred between mismatched ones and a thermal treatment at a relatively high temperature that discriminate the ligation of probes. When the reaction mixture was heated to denature the formed duplex, the purple color of the perfect-match solution would not revert to red, while the mismatch gave a red color as the assembled gold nanoparticles disparted. The present approach has been demonstrated with the identification of a single-base mutation in codon 12 of a K-ras oncogene that is of significant value for colorectal cancers diagnosis, and the wild-type and mutant type were successfully scored. To our knowledge, this was the first report concerning SNP detection based on the ligase reaction and the gold nanoparticle assembly. Owing to its ease of operation and high specificity, it was expected that the proposed procedure might hold great promise in practical clinical diagnosis of gene-mutant diseases.     

Fabrication of silver nanoparticles by Phoma glomerata and its combined effect against Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus

Aims:  We report extracellular synthesis of silver nanoparticles (Ag-NPs) from Phoma glomerata and its efficacy against Escherichia coli , Staphylococcus aureus and Pseudomonas aeruginosa . The bacteria exhibiting resistance to various antibiotics showed remarkable sensitivity, when used in combination of antibiotics and Ag-NPs.
Methods and Results:  Biosynthesis of Ag-NPs was carried out by challenging the fungal cell filtrate with 1 mmol l⁻¹ silver nitrate. The Ag-NPs were characterized with the help of UV–Visible spectrophotometer and Fourier transform infrared spectroscopy. Scanning electron microscopy was carried out to detect the size of Ag-NPs. Evaluation of the combined effect(s) was studied by disc diffusion method against E. coli , Staph. aureus and Ps. aeruginosa .
Conclusions:  The biosynthesis route seems to be eco-friendly and easy to scale up the process. Thus, these Ag-NPs may prove as a better candidate for drugs and can potentially eliminate the problem of chemical agents because of their biogenic nature.
Significance and Impact of the Study:  The bacterial resistance against antibiotics has been increasing with alarming rate. To overcome this problem, there is a pressing need to develop bactericidal agents. Ag-NPs may prove to be an answer to drug-resistant bacteria.     

Ligand density effect on biorecognition by PEGylated gold nanoparticles: regulated interaction of RCA120 lectin with lactose installed to the distal end of tethered PEG strands on gold surface

PEGylated gold nanoparticles (diameter: 20 nm) possessing various functionalities of lactose ligand on the distal end of tethered PEG ranging from 0 to 65% were prepared to explore the effect of ligand density of the nanoparticles on their lectin binding property. UV-visible spectra of the aqueous solution of the nanoparticles revealed that the strong steric stabilization property of the PEG layer lends the nanoparticles high dispersion stability even under the physiological salt concentration (ionic strength, I = 0.15 M). The number of PEG strands on a single particle was determined to be 520 from thermogravimetric analysis (TGA). Scanning electron microscopy (SEM) observation under controlled acceleration voltage revealed the thickness of the PEG layer on the nanoparticle to be approximately 7 nm. The area occupied by a single lactose molecule on the surface of PEGylated gold nanoparticles was then calculated based on TGA and SEM results and was varied in the range of 10-34 nm2 depending on the lactose functionality (65 approximately 20%). PEGylated gold nanoparticles with 40% and 65% lactose functionality showed a selective and time-dependent aggregation in phosphate buffer with the addition of Ricinus communis agglutinin (RCA120) lectin, a bivalent galactose-specific protein. The aggregates can be completely redispersed by adding an excess amount of galactose. Time-lapse monitoring of UV-visible spectra at 600-750 nm revealed that the aggregation of PEGylated gold nanoparticles was accelerated with an increase in both RCA120 concentration in the solution and the lactose density of the nanoparticles. Furthermore, the sensitivity of lectin detection could be controlled by the regulation of lactose density on the particle surface. Interestingly, there was a critical lactose density (>20%) observed to induce detectable particle aggregation, indicating that the interaction between the particles is triggered by the multimolecular bridging via lectin molecules.     

Capacity of robot handling for Epstein-Barr virus transformation

Objectives:  Epstein-Barr virus (EBV) transformation has been described as a routine method to establish human B lymphoblastoid cell lines. Each established lymphoblastoid cell line represents one unique genetic information carrier and can produce unlimited quantities of DNA materials available for downstream applications and research. Undoubtedly, it is of great value to human clinical and experimental genetic studies. However, the current process of EBV transformation requires much manpower in the routine renewal of medium, which is time-consuming. This situation can become a serious problem especially when establishing a human B lymphoblastoid cell bank. A modified and cost-effective protocol for EBV transformation should be considered.
Materials and methods:  In the present study, process in EBV transformation was modified to fit the requirements of robot handling.
Results:  1 mL of whole blood was demonstrated to be sufficient to perform EBV transformation. Additionally, EBV transformation can performed in 96-deep-well plates that are directly and widely used with automatic work platforms.
Conclusions:  Based on these facts, a process of EBV transformation can be modified to fit the requirements of robot handling.     

Colonic stem cell data are consistent with the immortal model of stem cell division under non-random strand segregation

Objectives:  Colonic stem cells are thought to reside towards the base of crypts of the colon, but their numbers and proliferation mechanisms are not well characterized. A defining property of stem cells is that they are able to divide asymmetrically, but it is not known whether they always divide asymmetrically (immortal model) or whether there are occasional symmetrical divisions (stochastic model). By measuring diversity of methylation patterns in colon crypt samples, a recent study found evidence in favour of the stochastic model, assuming random segregation of stem cell DNA strands during cell division. Here, the effect of preferential segregation of the template strand is considered to be consistent with the 'immortal strand hypothesis', and explore the effect on conclusions of previously published results.
Materials and methods:  For a sample of crypts, it is shown how, under the immortal model, to calculate mean and variance of the number of unique methylation patterns allowing for non-random strand segregation and compare them with those observed.
Results:  The calculated mean and variance are consistent with an immortal model that incorporates non-random strand segregation for a range of stem cell numbers and levels of preferential strand segregation.
Conclusions:  Allowing for preferential strand segregation considerably alters previously published conclusions relating to stem cell numbers and turnover mechanisms. Evidence in favour of the stochastic model may not be as strong as previously thought.     

Oligonucleotide-coated metallic nanoparticles as a flexible platform for molecular imaging agents

Targeted metallic nanoparticles have shown promise as contrast agents for molecular imaging. To obtain molecular specificity, the nanoparticle surface must be appropriately functionalized with probe molecules that will bind to biomarkers of interest. The aim of this study was to develop and characterize a flexible approach to generate molecular imaging agents based on gold nanoparticles conjugated to a diverse range of probe molecules. We present two complementary oligonucleotide-based approaches to develop gold nanoparticle contrast agents which can be functionalized with a variety of biomolecules ranging from small molecules, to peptides, to antibodies. The size, biocompatibility, and protein concentration per nanoparticle are characterized for the two oligonucleotide-based approaches; the results are compared to contrast agents prepared using adsorption of proteins on gold nanoparticles by electrostatic interaction. Contrast agents prepared from oligonucleotide-functionalized nanoparticles are significantly smaller in size and more stable than contrast agents prepared by adsorption of proteins on gold nanoparticles. We demonstrate the flexibility of the oligonucleotide-based approach by preparing contrast agents conjugated to folate, EGF peptide, and anti-EGFR antibodies. Reflectance images of cancer cell lines labeled with functionalized contrast agents show significantly increased image contrast which is specific for the target biomarker. To demonstrate the modularity of this new bioconjugation approach, we use it to conjugate both fluorophore and anti-EGFR antibodies to metal nanoparticles, yielding a contrast agent which can be probed with multiple imaging modalities. This novel bioconjugation approach can be used to prepare contrast agents targeted with biomolecules that span a diverse range of sizes; at the same time, the bioconjugation method can be adapted to develop multimodal contrast agents for molecular imaging without changing the coating design or material.     

纳米粒子表面修饰对其与细胞膜相互作用的影响

纳米粒子在生物医学上的应用越来越广泛,其进入细胞的机制与规律是设计与开发的基础．已有研究发现,表面修饰不同亲疏水性基团的金纳米粒子,在内吞机制被抑制时,进入细胞的能力明显不同．更特别的是,粒子表面亲水性基团与疏水性基团呈间隔条纹规则排列的纳米粒子,与其他修饰成分相同仅排列不同的纳米粒子进入细胞的规律区别显著．这一特殊现象无法用已有的纳米粒子进入细胞的机制解释．本文针对该研究结果,将纳米粒子与细胞的体系简化,定量分析了3种不同纳米粒子进入细胞前后的不同状态,计算获得了表面修饰不同亲疏水性基团的纳米粒子与细胞膜之间相互作用的Flory．Huggins自由能．结果发现,修饰规则间隔排列亲疏水基团的纳米粒子,其作用自由能在与细胞接触前后变化最大．研究结果不仅解释了实验发现,同时预示了纳米粒子进入细胞的新机制．     

Effect of Lactobacillus gasseri BNR17 on blood glucose levels and body weight in a mouse model of type 2 diabetes

Aims:  To investigate the effect of Lactobacillus gasseri BNR17 isolated from human breast milk on blood glucose and body weight in type 2 diabetic animals.
Methods and results:  db/db mice were divided into one control group and five sample groups; the sample groups received BNR17 (10⁷, 10⁸, 10⁹ and 10¹⁰ CFU) or rosiglitazone (8 mg kg⁻¹) orally twice a day for 12 weeks. BNR17 groups had a dose-dependent reduction in food, water intake and amount of excrement. Body weight loss was not seen in the BNR17 groups. Fasting and postprandial 2 h blood glucose levels were significantly lower in the BNR17 (10¹⁰ CFU) group compared with the control group. HbA1c decreased in the BNR17 group, although it was not statistically significant. During the oral glucose tolerance test, the BNR17 groups exhibited dose-dependent improvement in glucose sensitivity.
Conclusions:  Lactobacillus gasseri BNR17 has a suppressing effect on blood glucose levels and improved diabetic symptoms in db/db mice.
Significance and Impact of the Study:  Blood glucose-lowering lactic acid bacteria are expected to be useful as a therapeutic for treating type 2 diabetes in humans.     

Control of microbial contamination of Franz diffusion cell receptor phase in the development of transcutaneous breast cancer therapeutics

Aims:  To determine the micro-organism contamination of excised porcine (pig) ear, and evaluate the use of Cyclopore track-etched membranes (CTEM) for preventing ingress into Franz-type diffusion cells.
Methods:  Swabs were taken from four locations and used to inoculate Tryptone Soya Agar (TSA) and Sabouraud Dextrose Agar (SDA) plates. Diffusion cells were assembled to include porcine skin with and without CTEM, and the receptor phase sampled periodically and spread onto plates.
Results:  Five distinct colony types were isolated after incubation of all swabs on TSA plates at 37°C; on SDA plates, one fungal colony was found at 30°C and one at 37°C. The SDA agar plate incubated at 30°C resulted in the growth of a large diffused white fungal colony. No regional differences were observed. Without the CTEM, the receptor phase became contaminated within 6 h. With the CTEM present, microbial ingress was substantially retarded with visible presumptive fungal growth occurring at 24 h and detectable contamination on both microbiological media at 48 h.
Conclusions:  As expected, the native porcine ears were considerably contaminated. The ingress of contamination into the diffusion cell receptor phases can be largely, but not entirely, eliminated using CTEM. The addition of antimicrobial agents was necessary to eliminate micro-organisms that were observed at later time points.
Significance and Impact of the Study:  This article, while highlighting the presence of a high number of micro-organisms on native porcine skin, presents a practical means to reduce the risk of microbial contamination in transdermal/transcutaneous permeation studies, particularly in the study of cell cultures grown within Franz diffusion cell receptor compartments.     

Carotenoids' influence on radiotolerance of Pantoea agglomerans, a plant pathogen

Aim:  The aim of this study was to evaluate the effect of γ radiation on the carotenoid content of two strains of the Enterobacteriaceae : Pantoea agglomerans .
Methods and Results:  Pantoea agglomerans strains ATCC 49174 and RL1 were used for this study. Successive radiation treatments were performed to study the radiotolerance. Total carotenoids were obtained by multiple extraction using chloroform/methanol (2 : 1), quantified by measuring the optical density at 453 nm and their antioxidant activity measured by a colorimetric method. The D ₁₀ studies were conducted using a UC-15A irradiator loaded with ⁶⁰Co. Bacterial counts from various dilutions were carried out after irradiation. Strain ATCC 49174 irradiated at 1 kGy produced 4·3 times more carotenoids than the control, whereas carotenoid synthesis increased by 2·9-fold in the strain RL1. However, there was no significant difference in the D ₁₀ values.
Conclusion:  Carotenoid increased production is influenced by γ radiation but does not modify the tolerance to radiations.
Significance and Impact of the Study:  To our knowledge, this is the first study to demonstrate the effects of γ radiation on carotenoid production levels.