Influence of salt concentration on the formation of Pickering emulsions.

Here we study emulsification in a model experimental system comprised of water, an oil and colloidal particles. The particles are charge-stabilised colloidal silica; unsurprisingly, by varying the concentration of salt the degree of flocculation of the particles can be modified. The influence of salt on the formation of particle-stabilised oil droplets goes well beyond considerations of the colloidal stability of the particles. Our results demonstrate that the influence of salt on the particle-particle interaction is less important for emulsion formation than the influence of salt on both the particle wettability and the particle-interface interaction.

Development of HyBeacon® probes for specific mRNA detection using body fluids as a model system.

HyBeacons are linear oligonucleotides which incorporate fluorescent dyes covalently linked to internal nucleotides. They have previously been used with PCR and isothermal amplification to interrogate SNPs and STRs in fields as diverse as clinical diagnostics, food authentication, and forensic DNA profiling. This work explores their use for the identification of expressed gene sequences through mRNA profiling. The use of mRNA is becoming increasingly common in forensic casework to identify body fluids on evidence items, as it offers higher specificity and fewer false positives than current chemical presumptive testing methods. The work presented here details the development of a single-step one-tube RT-PCR assay to detect the presence of body fluids of forensic interest (saliva, blood, seminal fluid, vaginal fluid and menstrual blood) using HyBeacon® probes and melt curve analysis. Each assay shows a high degree of specificity to the target body fluid mRNA suggesting there is no requirement to remove genomic DNA prior to analysis. Of the five assays developed, four were able to detect between 10 and 100 copies of target cDNA, the fifth 1000 copies of target. The results presented here demonstrate that such an approach can be optimised for non-expert users and further areas of work are discussed.

Sprouting Droplets Driven by Physical Effects Alone.

Combining a partially miscible three-liquid system with interfacially trapped silica colloids, we show that small droplets can exhibit dramatic growth phenomena driven by physical effects alone. The mass dense droplets sprout tubes which grow vertically upward in a gravitational field and respond to the presence of other droplets in their path. Two of the liquids in our system are water and toluene. By varying the third liquid, we are able to relate the growth behavior to the details of the underlying three-fluid phase diagram and the changes to the interfacial tension. Additionally, we introduce a pendant drop in the path of our growing drop. We use this to confirm that growth is driven by the partitioning of solvents, that exchange of solvents between droplets is chemically selective, and that the exchange behavior can itself generate further growth phenomena.

Temperature- and pH-Dependent Shattering: Insoluble Fatty Ammonium Phosphate Films at Water-Oil Interfaces.

We study the films formed by tetradecylamine (TDA) at the water-dodecane interface in the presence of hydrogen phosphate ions. Using Fourier transform infrared spectroscopy (FTIR), interfacial shear rheology, confocal fluorescence microscopy, cryo-scanning electron microscopy (cryo-SEM), and small-angle neutron scattering (SANS), we find that between pH 5 and 8 tetradecylammonium cations bind to hydrogen phosphate anions to form needle-shaped crystallites of tetradecylammonium hydrogen phosphate (TAHP). These crystallites self-assemble into films with a range of morphologies; below pH 7, they form brittle, continuous sheets, and at pH 8, they form lace-like networks that deform plastically under shear. They are also temperature-responsive: when the system is heated, the film thins and its rheological moduli drop. We find that the temperature response is caused by dissolution of the film in to the bulk fluid phases. Finally, we show that these films can be used to stabilize temperature-responsive water-in-oil emulsions with potential applications in controlled release of active molecules.

Synthesis and use of universal sequence probes in fluorogenic multi-strand hybridisation complexes for economical nucleic acid testing.

Analysis of nucleic acid amplification products has become the gold standard for applications such as pathogen detection and characterisation of single nucleotide polymorphisms and short tandem repeat sequences. The development of real-time PCR and melting curve analysis using fluorescent probes has simplified nucleic acid analyses. However, the cost of probe synthesis can be prohibitive when developing large panels of tests. We describe an economic two-stage method for probe synthesis, and a new method for nucleic acid sequence analysis which together considerably reduce costs. The analysis method utilises three-strand and four-strand hybridisation complexes for the detection and identification of nucleic acid target sequences by real-time PCR and fluorescence melting.

Rapid detection of diagnostic targets using isothermal amplification and HyBeacon probes--a homogenous system for sequence-specific detection.

Isothermal amplification is a rapid, simple alternative to PCR, with amplification commonly detected using fluorescently labelled oligonucleotide probes, intercalating dyes or increased turbidity as a result of magnesium pyrophosphate generation. SNP identification is possible but requires either allele-specific primers or multiple dye-labelled probes, but further downstream processing is often required for allelic identification. Here we demonstrate that modification of common isothermal amplification methods by the addition of HyBeacon probes permits homogeneous sequence detection and discrimination by melting or annealing curve analysis. Furthermore, we demonstrate that isothermal amplification and sequence discrimination is possible directly from a crude sample such as an expressed buccal swab.

Pioneering BRCA1/2 Point-Of-Care Testing for Integration of Germline and Tumor Genetics in Breast Cancer Risk Management: A Vision for the Future of Translational Pharmacogenomics.

Research performed in South African (SA) breast, ovarian and prostate cancer patients resulted in the development of a rapid BRCA point-of-care (POC) assay designed as a time- and cost-effective alternative to laboratory-based technologies currently used for first-tier germline DNA testing. In this study the performance of the new assay was evaluated for use on a portable screening device (ParaDNA), with the long-term goal to enable rollout at POC as an inventive step to meet the World Health Organization's sustainable development goals for Africa. DNA samples for germline testing were obtained retrospectively from 50 patients with early-stage hormone receptor-positive breast cancer referred for genomic tumor profiling (MammaPrint). Currently, SA patients with the luminal-type breast cancer are not routinely selected for BRCA1/2 testing as is the case for triple-negative disease. An initial evaluation involved the use of multiple control samples representing each of the pathogenic founder/recurrent variants included in the BRCA 1.0 POC Research Assay. Comparison with a validated laboratory-based first-tier real-time polymerase chain reaction (PCR) assay demonstrated 100% concordance. Clinical utility was evident in five patients with the founder BRCA2 c.7934delG variant, identified at the 10% (5/50) threshold considered cost-effective for BRCA1/2 testing. BRCA2 c.7934delG carrier status was associated with a significantly younger age (p=0.03) at diagnosis of breast cancer compared to non-carriers. In three of the BRCA2 c.7934delG carriers a high-risk MammaPrint 70-gene profile was noted, indicating a significantly increased risk for both secondary cancers and breast cancer recurrence. Initiating germline DNA testing at the POC for clinical interpretation early in the treatment planning process, will increase access to the most common pathogenic BRCA1/2 variants identified in SA and reduce loss to follow-up for timely gene-targeted risk reduction intervention. The ease of using cheek swabs/saliva in future for result generation within approximately one hour assay time, coupled with low cost and a high BRCA1/2 founder variant detection rate, will improve access to genomic medicine in Africa. Application of translational pharmacogenomics across ethnic groups, irrespective of age, family history, tumor subtype or recurrence risk profile, is imperative to sustainably implement preventative healthcare and improve clinical outcome in resource-constrained clinical settings.

HyBeacon probes for rapid DNA sequence detection and allele discrimination.

HyBeacon probes are single-stranded oligonucleotides with one or more internal base(s) labeled with a fluorescent dye. When a probe forms a duplex with its target sequence, the level of fluorescence emission increases considerably. HyBeacons have been developed as new tools for rapid sequence detection and discrimination and have been employed in a wide variety of applications including infectious diagnostics and analysis of human polymorphisms. Single-labeled (FVG1) and dual-labeled (FVG11) probes were designed to analyze the factor V Leiden (R506Q) polymorphism which causes an increased risk of deep vein thrombosis and pulmonary embolism. Detection and identification of factor V alleles is performed by melting curve analysis and determination of probe melting temperature (T(m)). HyBeacon hybridization to the glutamine allele (Q) causes the formation of mismatched DNA duplexes that are detected through decreases in T(m). HyBeacon probes are included in homogeneous PCR assays to genotype samples with respect to the factor V polymorphism within 20 min, using purified DNAs and unpurified saliva/blood samples. This paper describes the preparation of homogeneous PCR assays, LightCycler target amplification, and subsequent melting curve analysis. This chapter also describes the use of homologous oligonucleotides and melting curve analysis as a method for probe evaluation.

Rapid typing of STRs in the human genome by HyBeacon melting.

A new method based on DNA melting has been developed for the rapid analysis of STRs in the human genome. The system is based on homogeneous PCR followed by fluorescence melting analysis and utilises a HyBeacon probe combined with a PCR primer-blocker oligonucleotide. The use of blockers of different length permits identification of the full range of common D16S539 repeats enabling detection of 99.8% of known alleles. The interrogation of STRs can be carried out on standard genetic analysis platforms and could be applied to other loci to form the basis of a bespoke high-throughput system for use in forensic analysis, particularly as fluorescent genetic analysis platforms are now available for high-resolution melting. This methodology may be suitable for rapid forensic DNA analysis at the point-of-arrest or in a custody suite where it is important to identify an individual from a small group of suspects/detainees.

Analysis of multiple single nucleotide polymorphisms closely positioned in the ovine PRNP gene using linear fluorescent probes and melting curve analysis.

BACKGROUND: Resistance and susceptibility to scrapie has been associated with single nucleotide polymorphisms located within codons 136, 154 and 171 of the ovine prion protein gene (PRNP). Dual-labelled HyBeacon probes were developed to analyse single and clustered polymorphisms within these and neighbouring codons. METHODS: Extracted DNAs and unpurified blood samples were genotyped with respect to polymorphisms in PRNP codons 136, 141, 154 and 171. PCR amplicons were investigated using a LightTyper instrument, measuring the stability of probe/target hybridisation through peak melting temperatures and determining the sequence of nucleotides at polymorphic sites. RESULTS: The performance of HyBeacon assays was evaluated in a validation study comparing genotypes with those obtained using a primer extension assay (Sequenom MassEXTEND) analysed on a MALDI-ToF mass spectrometer. Over 12,000 sheep samples were successfully genotyped, reliably detecting A136, V136, T136, T137, L141, F141 R154, H154, L168, R171, Q171, H171 and K171 sequence variants using only 4 HyBeacon probes. CONCLUSION: HyBeacon assays provide an extremely robust and accurate method for the analysis of single and clustered PRNP polymorphisms in a high-throughput format. The flexibility of the diagnostic tests ensures that samples are correctly genotyped even in the presence of additional sequence variations that flank the polymorphisms of interest. Such sequence variations may also be neutralised using universal bases such as 5-nitroindole if required.

The secret life of Pickering emulsions: particle exchange revealed using two colours of particle.

Emulsion droplets stabilised by colloidal particles (Pickering emulsions) can be highly stable, so it is unsurprising that they are beginning to be exploited industrially. The individual colloidal particles have interfacial attachment energies that are vastly larger than the thermal energy, hence they are usually thought of as being irreversibly adsorbed. Here we show, for the first time, particles being exchanged between droplets in a Pickering emulsion. This occurs when the emulsion contains droplets that share particles, often called bridging. By starting with two emulsions showing bridging, each stabilised by a different colour of particle, the dynamics can be studied as they are gently mixed together on a roller bank. We find that particle exchange occurs by two routes: firstly, during a period of unbridging and rebridging whose duration can be tuned by varying the wettability of the particles, and secondly, during very rare events when particles are ejected from one droplet and re-adsorbed onto another.

Molecular basis of action of HyBeacon fluorogenic probes: a spectroscopic and molecular dynamics study.

HyBeacons, novel DNA probes for ultra-rapid detection of single nucleotide polymorphisms, contain a fluorophore covalently attached via a linker group to an internal nucleotide. As the probe does not require a quencher or self-complementarity to function, this study investigates the molecular-level mechanism underlying the increase of fluorescence intensity on hybridization of HyBeacons with target DNA. Spectroscopic ultraviolet-visible and fluorimetric studies, combined with molecular dynamics simulations, indicate projection of the fluorophore moiety away from the target-probe duplex into aqueous solution, although specific linker-DNA interactions are populated. Based on evidence from this study, we propose that for HyBeacons, the mechanism of increased fluorescence on hybridization is due to disruption of quenching interactions in the single-stranded probe DNA between the fluorophore and nucleobases. Hybridization leads to an extended linker conformation, removing the fluorophore from the immediate vicinity of the DNA bases.

Making and breaking bridges in a Pickering emulsion.

HYPOTHESIS: Particle bridges form in Pickering emulsions when the oil-water interfacial area generated by an applied shear is greater than that which can be stabilised by the available particles and the particles have a slight preference for the continuous phase. They can subsequently be broken by low shear or by modifying the particle wettability. EXPERIMENTS: We have developed a model oil-in-water system for studying particle bridging in Pickering emulsions stabilised by fluorescent Stöber silica. A mixture of dodecane and isopropyl myristate was used as the oil phase. We have used light scattering and microscopy to study the degree to which emulsions are bridged, and how this is affected by parameters including particle volume fraction, particle wettability and shear rate. We have looked for direct evidence of droplets sharing particles using freeze fracture scanning electron microscopy. FINDINGS: We have created strongly aggregating Pickering emulsions using our model system. This aggregating state can be accessed by varying several different parameters, including particle wettability and particle volume fraction. Particles with a slight preference for the continuous phase are required for bridging to occur, and the degree of bridging increases with increasing shear rate but decreases with increasing particle volume fraction. Particle bridges can subsequently be removed by applying low shear or by modifying the particle wettability.

Synthesis of HyBeacons and dual-labelled probes containing 2'-fluorescent groups for use in genetic analysis.

An FMOC-protected 2'-hydroxyethyl uridine phosphoramidite has been used to synthesise fluorescein-labelled HyBeacon probes and "FAM-ROX" dual-labelled fluorogenic oligonucleotides.

Genotyping for CYP2C9 and VKORC1 alleles by a novel point of care assay with HyBeacon® probes.

BACKGROUND: Coumarin anticoagulants such as warfarin are used to treat and prevent thromboembolic events in patients. The required dosage is difficult to predict and the risk of over or under anticoagulation are dependent on several environmental and clinical factors, such as concurrent medication, diet, age and genotype for polymorphisms in two genes CYP2C9 and VKORC1. METHODS: A novel fluorescent PCR genotyping assay using HyBeacon® probes, was developed to enable clinical staff to genotype the CYP2C9*2 and CYP2C9*3 alleles and the VKORC1 G-1639A polymorphism directly from unextracted blood samples. A prototype PCR instrument, Genie 1, suitable for point of care use was developed to carry out the assays. The panel of tests was validated by analysing blood samples from 156 individuals and comparing genotypes with data obtained using DNA samples from the same individuals. The accuracy of genotypes obtained with the Genie 1 was compared against results from well validated real time PCR and PCR-restriction fragment length polymorphism analysis. RESULTS: Identical results were obtained for the newly developed HyBeacon® method and the validation method in all cases except for one where no result was obtained for the VKORC1 polymorphism on the Genie instrument. The samples used for validation represented all six possible *2 and *3 allele-related CYP2C9 genotypes and all three VKORC1 G-1639A genotypes. CONCLUSIONS: We observed excellent accuracy for the newly developed method which can determine genotype in less than 2 h.