Reporter Dye Research Articles

Electric Destabilization of Supramolecular Lipid Vesicles Subjected to Fast Electric Pulses.

Biological membranes are weakly permeable to hydrophilic molecules and ions and electric pulses can induce their transient permeabilization, but this process is not well characterized. We directly assay the electropermeabilization process, on the minimum model of lipid vesicles, by using a highly sensitive fluorescence method based on manganese ion transport. The approach gives access, at the single-lipid self-assembly level, to the transmembrane potential needed to detect divalent ion permeabilization on supramolecular giant unilamellar lipid vesicles. The critical values are strongly dependent on the lipid composition and are observed to vary from 10 to 150 mV. These values appear to be much lower than those previously reported in the literature for cells and vesicles. The detection method appears to be a decisive parameter as it is controlled by the transport of the reporter dye. We also provide evidence that the electropermeabilization process is a transient transition of the lipid self-organization due to the loss of assembly cohesion induced by bioelectrochemical perturbations of the zwitterionic interface with the solution.

Membrane Potential and Calcium Dynamics in Beta Cells from Mouse Pancreas Tissue Slices: Theory, Experimentation, and Analysis.

Beta cells in the pancreatic islets of Langerhans are precise biological sensors for glucose and play a central role in balancing the organism between catabolic and anabolic needs. A hallmark of the beta cell response to glucose are oscillatory changes of membrane potential that are tightly coupled with oscillatory changes in intracellular calcium concentration which, in turn, elicit oscillations of insulin secretion. Both membrane potential and calcium changes spread from one beta cell to the other in a wave-like manner. In order to assess the properties of the abovementioned responses to physiological and pathological stimuli, the main challenge remains how to effectively measure membrane potential and calcium changes at the same time with high spatial and temporal resolution, and also in as many cells as possible. To date, the most wide-spread approach has employed the electrophysiological patch-clamp method to monitor membrane potential changes. Inherently, this technique has many advantages, such as a direct contact with the cell and a high temporal resolution. However, it allows one to assess information from a single cell only. In some instances, this technique has been used in conjunction with CCD camera-based imaging, offering the opportunity to simultaneously monitor membrane potential and calcium changes, but not in the same cells and not with a reliable cellular or subcellular spatial resolution. Recently, a novel family of highly-sensitive membrane potential reporter dyes in combination with high temporal and spatial confocal calcium imaging allows for simultaneously detecting membrane potential and calcium changes in many cells at a time. Since the signals yielded from both types of reporter dyes are inherently noisy, we have developed complex methods of data denoising that permit for visualization and pixel-wise analysis of signals. Combining the experimental approach of high-resolution imaging with the advanced analysis of noisy data enables novel physiological insights and reassessment of current concepts in unprecedented detail.

Rapid Detection of Escherichia coli via Enzymatically Triggered Reactions in Self-Reporting Chitosan Hydrogels.

In this work, a self-reporting hydrogel for the rapid in situ detection of bacterial enzymes is reported. To implement the reporting function for the bacterium Escherichia coli into a film-based sensing format, chitosan hydrogel films on solid backing supports were equipped with a reporting function for the enzyme β-glucuronidase (β-GUS), which is secreted by >98% of all known E. coli strains. Covalent coupling of the fluorogenic substrate 4-methylumbelliferyl-β-D-glucuronide or the complementary chromogenic substrate 4-nitrophenyl-β-D-glucuronide via amide bond formation afforded an attachment that is stable for >24 h under physiological conditions. By contrast, in the presence of β-GUS, the reporter dyes were very rapidly cleaved and produced a signal for the presence of the enzyme, which was detectable by bare eye under appropriate illumination. Detailed investigations of the enzymatic reaction for both types of substrates in neat enzyme solution as well as in bacterial supernatant revealed the apparent reaction kinetics and allowed us to determine the concentration of β-GUS in the supernatant. Under optimized conditions, the 4-methylumbelliferyl-β-D-glucuronide-functionalized hydrogel reported the presence of β-GUS within 15 min with a limit of detection of <1 nM. Finally, the function of the generally applicable hydrogel-film-based sensing approach, which is compatible with polymer-film-based applications, including wound dressings and packaging materials, and is also amenable to address noncultivatable pathogenic bacteria by using appropriate fluorogenic or chromogenic substrates, was demonstrated by direct application with bacterial medium.

Development and application of a ray-based model of light propagation through a spherical acousto-optic lens.

A spherical acousto-optic lens (AOL) consists of four acousto-optic deflectors (AODs) that can rapidly and precisely control the focal position of an optical beam in 3D space. Development and application of AOLs has increased the speed at which 3D random access point measurements can be performed with a two-photon microscope. This has been particularly useful for measuring brain activity with fluorescent reporter dyes because neuronal signalling is rapid and sparsely distributed in 3D space. However, a theoretical description of light propagation through AOLs has lagged behind their development, resulting in only a handful of simplified principles to guide AOL design and optimization. To address this we have developed a ray-based computer model of an AOL incorporating acousto-optic diffraction and refraction by anisotropic media. We extended an existing model of a single AOD with constant drive frequency to model a spherical AOL: four AODs in series driven with linear chirps. AOL model predictions of the relationship between optical transmission efficiency and acoustic drive frequency including second order diffraction effects closely matched experimental measurements from a 3D two-photon AOL microscope. Moreover, exploration of different AOL drive configurations identified a new simple rule for maximizing the field of view of our compact AOL design. By providing a theoretical basis for understanding optical transmission through spherical AOLs, our open source model is likely to be useful for comparing and improving different AOL designs, as well as identifying the acoustic drive configurations that provide the best transmission performance over the 3D focal region.

Detection of silent cells, synchronization and modulatory activity in developing cellular networks.

Developing networks in the immature nervous system and in cellular cultures are characterized by waves of synchronous activity in restricted clusters of cells. Synchronized activity in immature networks is proposed to regulate many different developmental processes, from neuron growth and cell migration, to the refinement of synapses, topographic maps, and the mature composition of ion channels. These emergent activity patterns are not present in all cells simultaneously within the network and more immature "silent" cells, potentially correlated with the presence of silent synapses, are prominent in different networks during early developmental periods. Many current network analyses for detection of synchronous cellular activity utilize activity-based pixel correlations to identify cellular-based regions of interest (ROIs) and coincident cell activity. However, using activity-based correlations, these methods first underestimate or ignore the inactive silent cells within the developing network and second, are difficult to apply within cell-dense regions commonly found in developing brain networks. In addition, previous methods may ignore ROIs within a network that shows transient activity patterns comprising both inactive and active periods. We developed analysis software to semi-automatically detect cells within developing neuronal networks that were imaged using calcium-sensitive reporter dyes. Using an iterative threshold, modulation of activity was tracked within individual cells across the network. The distribution pattern of both inactive and active, including synchronous cells, could be determined based on distance measures to neighboring cells and according to different anatomical layers.

Array of Synthetic Oligonucleotides to Generate Unique Multi-Target Artificial Positive Controls and Molecular Probe-Based Discrimination of Liposcelis Species

Several species of the genus Liposcelis are common insect pests that cause serious qualitative and quantitative losses to various stored grains and processed grain products. They also can contaminate foods, transmit pathogenic microorganisms and cause allergies in humans. The common occurrence of multi-species infestations and the fact that it is difficult to identify and discriminate Liposcelis spp. make accurate, rapid detection and discriminatory tools absolutely necessary for confirmation of their identity. In this study, PCR primers and probes specific to different Liposcelis spp. were designed based on nucleotide sequences of the cytochrome oxidase 1 (CO1) gene. Primer sets ObsCo13F/13R, PeaCo15F/14R, BosCO7F/7R, BruCo5F/5R, and DecCo11F/11R were used to specifically detect Liposcelis obscura Broadhead, Liposcelis pearmani Lienhard, Liposcelis bostrychophila Badonnel, Liposcelis brunnea Motschulsky and Liposcelis decolor (Pearman) in multiplex endpoint PCRs, which amplified products of 438-, 351-, 191-, 140-, and 87-bp, respectively. In multiplex TaqMan qPCR assays, orange, yellow, red, crimson and green channels corresponding to reporter dyes 6-ROXN, HEX, Cy5, Quasar705 and 6-FAM specifically detected L. obscura, L. brunnea, L. bostrychophila, L. pearmani and L. decolor, respectively. All developed primer and probe sets allowed specific amplification of corresponding targeted Liposcelis species. The development of multiplex endpoint PCR and multiplex TaqMan qPCR will greatly facilitate psocid identification and their management. The use of APCs will streamline and standardize PCR assays. APC will also provide the opportunity to have all positive controls in a single tube, which reduces maintenance cost and labor, but increases the accuracy and reliability of the assays. These novel methods from our study will have applications in pest management, biosecurity, quarantine, food safety, and routine diagnostics.

Identification of an Antimicrobial Agent Effective against Methicillin-Resistant Staphylococcus aureus Persisters Using a Fluorescence-Based Screening Strategy.

Persisters are a subpopulation of normal bacterial cells that show tolerance to conventional antibiotics. Persister cells are responsible for recalcitrant chronic infections and new antibiotics effective against persisters would be a major development in the treatment of these infections. Using the reporter dye SYTOX Green that only stains cells with permeabilized membranes, we developed a fluorescence-based screening assay in a 384-well format for identifying compounds that can kill methicillin-resistant Staphylococcus aureus (MRSA) persisters. The assay proved robust and suitable for high throughput screening (Z`-factor: >0.7). In screening a library of hits from a previous screen, which identified compounds that had the ability to block killing of the nematode Caenorhabditis by MRSA, we discovered that the low molecular weight compound NH125, a bacterial histidine kinase inhibitor, kills MRSA persisters by causing cell membrane permeabilization, and that 5 μg/mL of the compound can kill all cells to the limit of detection in a 108 CFU/mL culture of MRSA persisters within 3h. Furthermore, NH125 disrupts 50% of established MRSA biofilms at 20 μg/mL and completely eradicates biofilms at 160 μg/mL. Our results suggest that the SYTOX Green screening assay is suitable for large-scale projects to identify small molecules effective against MRSA persisters and should be easily adaptable to a broad range of pathogens that form persisters. Since NH125 has strong bactericidal properties against MRSA persisters and high selectivity to bacteria, we believe NH125 is a good anti-MRSA candidate drug that should be further evaluated.

Dual Enzyme-Responsive Capsules of Hyaluronic Acid-block-Poly(Lactic Acid) for Sensing Bacterial Enzymes.

The synthesis of novel amphiphilic hyaluronic acid (HYA) and poly(lactic acid) (PLA) block copolymers is reported as the key element of a strategy to detect the presence of pathogenic bacterial enzymes. In addition to the formation of defined HYA-block-PLA assemblies, the encapsulation of fluorescent reporter dyes and the selective enzymatic degradation of the capsules by hyaluronidase and proteinase K are studied. The synthesis of the dual enzyme-responsive HYA-b-PLA is carried out by copper-catalyzed Huisgen 1,3-dipolar cycloaddition. The resulting copolymers are assembled in water to form vesicular structures, which are characterized by scanning electron microscopy, transmission electron microscopy, dynamic light scattering (DLS), and fluorescence lifetime imaging microscopy (FLIM). DLS measurements show that both enzymes cause a rapid decrease in the hydrodynamic diameter of the nanocapsules. Fluorescence spectroscopy data confirm the liberation of encapsulated dye, which indicates the disintegration of the capsules and validates the concept of enzymatically triggered payload release. Finally, cytotoxicity assays confirm that the HYA-b-PLA nanocapsules are biocompatible with primary human dermal microvascular endothelial cells.

On the effect of serum on the transport of reactive oxygen species across phospholipid membranes.

The transport of plasma generated reactive oxygen species (ROS) across a simple phospholipid membrane mimic of a (real) cell was investigated. Experiments were performed in cell culture media (Dulbecco's modified Eagle's medium, DMEM), with and without 10% serum. A (broad spectrum) ROS reporter dye, 2,7-dichlorodihydrofluorescein (DCFH), was used to detect the generation of ROS by a helium (He) plasma jet in DMEM using free DCFH and with DCFH encapsulated inside phospholipid membrane vesicles dispersed in DMEM. The authors focus on the concentration and on the relative rates (arbitrary units) for oxidation of DCFH [or the appearance of the oxidized product 2,7-dichlorofluorescein (DCF)] both in solution and within vesicles. In the first 1 h following plasma exposure, the concentration of free DCF in DMEM was ~15× greater in the presence of serum (cf. to the serum-free DMEM control). The DCF in vesicles was ~2× greater in DMEM containing serum compared to the serum-free DMEM control. These data show that serum enhances plasma ROS generation in DMEM. As expected, the role of the phospholipid membrane was to reduce the rate of oxidation of the encapsulated DCFH (with and without serum). And the efficiency of ROS transport into vesicles was lower in DMEM containing serum (at 4% efficiency) when compared to serum-free DMEM (at 32% efficiency). After 1 h, the rate of DCFH oxidation was found to have significantly reduced. Based upon a synthesis of these data with results from the open literature, the authors speculate on how the components of biological fluid and cellular membranes might affect the kinetics of consumption of plasma generated ROS.

Improved properties of gold nanorods coated with thin multilayer of small organic molecules by fast and facile method for surface enhanced Raman scattering

We introduce a thin multilayer-shell-coated gold nanorods (GNRs) that we have been able to achieve by way of coating them with two thin layers of small organic molecules in a new, efficient, effective, time-saving, and easy-to-control multilayer coating method. Compared to the thick shell, due to the small size of the coating molecules, this new type of GNR, by simply mixed with the sample solution, has shown that it can act as a highly effective and improved surface enhanced Raman scattering (SERS) enhancement agent without the need of any sample connecting or doping. This enhancement is found not only related to the off-resonance surface enhancement, but also to the increased signal-to-noise ratio brought by the low level of fluorescence emission. It showed excellent stability in strong acids, bases and some organic solvents as examined by comparing the longitudinal surface plasmon resonance peak values. A living body experiment on a tumor-bearing nude mouse injected with the Raman reporter dye loaded onto our new GNRs showed strong surface enhanced Raman scattering signal in the tumor, suggesting its high potential use in many related optical applications.

Enzyme Degradable Polymersomes from Hyaluronic Acid-block-poly(ε-caprolactone) Copolymers for the Detection of Enzymes of Pathogenic Bacteria

We introduce a new hyaluronidase-responsive amphiphilic block copolymer system, based on hyaluronic acid (HYA) and polycaprolactone (PCL), that can be assembled into polymersomes by an inversed solvent shift method. By exploiting the triggered release of encapsulated dye molecules, these HYA-block-PCL polymersomes lend themselves as an autonomous sensing system for the detection of the presence of hyaluronidase, which is produced among others by the pathogenic bacterium Staphylococcus aureus. The synthesis of the enzyme-responsive HYA-block-PCL block copolymers was carried out by copper-catalyzed Huisgen 1,3-dipolar cycloaddition of ω-azide-terminated PCL and ω-alkyne-functionalized HYA. The structure of the HYA-block-PCL assemblies and their enzyme-triggered degradation and concomitant cargo release were investigated by dynamic light scattering, fluorescence spectroscopy, confocal laser-scanning microscopy, scanning and transmission electron, and atomic force microscopy. As shown, a wide range of reporter dye molecules as well as antimicrobials can be encapsulated into the vesicles during formation and are released upon the addition of hyaluronidase.

Rapid and simple method of qPCR primer design.

Quantitative real-time polymerase chain reaction (qPCR) is a powerful tool for analysis and quantification of gene expression. It is advantageous compared to traditional gel-based method of PCR, as gene expression can be visualized "real-time" using a computer. In qPCR, a reporter dye system is used which intercalates with DNA's region of interest and detects DNA amplification. Some of the popular reporter systems used in qPCR are the following: Molecular Beacon(®), SYBR Green(®), and Taqman(®). However, success of qPCR depends on the optimal primers used. Some of the considerations for primer design are the following: GC content, primer self-dimer, or secondary structure formation. Freely available software could be used for ideal qPCR primer design. Here we have shown how to use some freely available web-based software programs (such as Primerquest(®), Unafold(®), and Beacon designer(®)) to design qPCR primers.

Quantitative structural information from single-molecule FRET.

Single-molecule studies can be used to study biological processes directly and in real-time. In particular, the fluorescence energy transfer between reporter dye molecules attached to specific sites on macromolecular complexes can be used to infer distance information. When several measurements are combined, the information can be used to determine the position and conformation of certain domains with respect to the complex. However, data analysis schemes that include all experimental uncertainties are highly complex, and the outcome depends on assumptions about the state of the dye molecules. Here, we present a new analysis algorithm using Bayesian parameter estimation based on Markov Chain Monte Carlo sampling and parallel tempering termed Fast-NPS that can analyse large smFRET networks in a relatively short time and yields the position of the dye molecules together with their respective uncertainties. Moreover, we show what effects different assumptions about the dye molecules have on the outcome. We discuss the possibilities and pitfalls in structure determination based on smFRET using experimental data for an archaeal transcription pre-initiation complex, whose architecture has recently been unravelled by smFRET measurements.

Optimizing the Roche LightCycler(R) for Single-Tube Multiplexed RT-PCR Assays.

The Roche Diagnostics LightCycler® (LC) Carousel-Based Systems are a single-source thermocycler capable of detecting light emissions from fluorescing molecules released during RT-PCR. This technology utilizes a single light source at 470 nm to excite fluorophores for read-out in one of three channels (530, 640 and 705 nm) for older 1.5 models and up to six channels (530, 560, 610, 640, 670, and 705nm) for the 2.0 model. The persistent challenge of LC technology is multiplexing, the ability to discriminate more than one target with different fluorophores in a single capillary tube that can be excited at the same 470-nm wavelength and read on 3 or 6 different channels without cross-talk or “bleed-over”. The most commonly employed fluorescent probe is 6-carboxyfluorescein (FAM), fluorescing in channel 1 (530 nm), with bleed-over into the other channels, which is currently compensated for by surrendering valuable carousel space for extraction controls, amplification controls, and duplicate sample runs to assure the generated answer is correct. Using the 705 nm channel requires resonance transfer probes, as few fluorescent molecules exist with Stokes’ shifts wide enough to achieve detection in this channel. In 2009, a fluorescence resonance energy transfer (FRET)-based method was developed which, when combined with TaqMan style probes, provides a linker that emits a signal that can be read in the unused third channel of the LC 1.5 [1]. This “FRET-MAN” technology works well; however, designing assays with dual probes and quenchers can be challenging. To address this challenge, Biosearch Technologies designed a probe called the Pulsar® 650, which is a fluorescent reporter dye based on a Ru (bpy)3 complex with a large Stokes shift, (λex = 460 nm, λem = 650 nm) that can be used in place of a two-dye FRET construct. Importantly, this dye is stable under oligonucleotidesynthesis conditions, strong acids, and strong bases (Biosearch Technologies, http://www.biosearchtech.com). We present here an extension of a duplexed assay originally developed for the LC 1.2 [2] to an RNA-based viral target with the inclusion of an internal control for robust quantitation. Here, the primary target was one of two strains of influenza A, chosen due to the increase of awareness of public health in recent years. The third-channel duplex probe was designed based on the human RNase P (hRP), GAPDH, 18S ribosomal RNA, β-actin, cyclophilin or gyrase [3–8]. To demonstrate the ability of duplexed detection, inclusion of the internal controls (ICs) is shown herein to function in both laboratory buffered samples and in clinical matrices. Theoretically, the second probe could instead be used as a detector for a second target organism.

Guidelines for optimisation of a multiplex oligonucleotide ligation-PCR for characterisation of microbial pathogens in a microsphere suspension array.

With multiplex oligonucleotide ligation-PCR (MOL-PCR) different molecular markers can be simultaneously analysed in a single assay and high levels of multiplexing can be achieved in high-throughput format. As such, MOL-PCR is a convenient solution for microbial detection and identification assays where many markers should be analysed, including for routine further characterisation of an identified microbial pathogenic isolate. For an assay aimed at routine use, optimisation in terms of differentiation between positive and negative results and of cost and effort is indispensable. As MOL-PCR includes a multiplex ligation step, followed by a singleplex PCR and analysis with microspheres on a Luminex device, several parameters are accessible for optimisation. Although MOL-PCR performance may be influenced by the markers used in the assay and the targeted bacterial species, evaluation of the method of DNA isolation, the probe concentration, the amount of microspheres, and the concentration of reporter dye is advisable in the development of any MOL-PCR assay. Therefore, we here describe our observations made during the optimisation of a 20-plex MOL-PCR assay for subtyping of Salmonella Typhimurium with the aim to provide a possible workflow as guidance for the development and optimisation of a MOL-PCR assay for the characterisation of other microbial pathogens.

In-Cell Detection By Flow Cytometry of JAK2 V617F Mutation Using Gold Nanoflares

Today’s conventional technology has to overcome many challenging aspects for integrating expressional analysis of a mutation into the cellular function of a living cell. It is very striking to detect the expressional status of a mutation in a living cell without compromising its cellular function as well as its viability that allows to perform subsequent functional analysis. This has been a long time goal for most of the biological studies.Myeloproliferative neoplasms (MPN) originate at the level of hematopoietic stem cell with a single nucleotide mutation in the cytosolic tyrosine kinase, Janus kinase 2 (JAK2) named as JAK2V617F which facilitates the constitutive intracellular activation of JAK2 and found in 95% of Polycythemia Vera (PV) patients. Detection of this mutation is a major criteria for diagnosis of the malignancy and changes in the expression levels of JAK2V617F is valued for the prognosis as well as response to the treatment.Here, we have utilized the nanotechnology’s new development, entitled as "multiplexed nanoflares", a gold nanoparticle agent that is capable of simultaneously detecting two distinct mRNA targets inside a living cell. These probes are highly oriented oligonucleotide sequences, which are hybridized to a reporter dye such as Cy3 and Cy5 and each complementary to its corresponding mRNA target. When multiplexed nanoflares are exposed to their targets, they provide a sequence specific signal in both extra and intracellular environments. Thus, this signal could be easily detected by flow cytometry or confocal microscopy.We have employed JAK2 V617F specific nanoflare probes labeled with Cy3 (JAK2V617F-Cy3) and JAK2 wild type (wtJAK2) nanoflare probe labeled with Cy5 (JAK2-Cy5) including negative and positive control probes to distinguish and isolate mRNA’s of JAK2V617F and wtJAK2 in live cells by measuring subsequent fluorescence with flow cytometry. The initial testing of the nanoflares has been performed by treating cell lines such as K562 (wtJAK2), SET-2 (JAK2V617F heterozygote), HEL (JAK2V617F homozygote) cells with nanoflare probes which did not alter cell viability and morphology with the applied concentrations during 18 hours of cell culture. We measured the levels of two mRNA targets, JAK2V617F and JAK2, and detected 90±6 % positivity with JAK2V617F-Cy3 treated HEL cells and no positivity in K562 cells, meanwhile wtJAK2 probe treated cells succeeded staining of SET and K562 cells. Real time reverse transcription PCR (RT-PCR) was performed on the same cells to compare the relative amounts of target RNA in each cell type by calculating relative changes in mRNA expression using the ΔΔCt (cycle threshold) method and comfirmed the results of flow cytometry with sensitivity of 0.001. Subsequently, we have tested mononuclear cells (MNC) received from peripheral blood of 5 patients with PV, one of which has JAK2V617F heterozygote allele (patient 5) and 4 patients had JAK2V617F homozygote allele (patients 1-4)which were tested with nested allel specific PCR. Flow cytomeyric analysis of the patients‘ MNC treated with the wtJAK2 and JAK2V617F probes demonstrated distinct populations of wtJAK2+ and JAK2V617F+. Populations of wtJAK2+/JAK2V617F+ (2.9%), wtJAK2-/JAK2V617F- ( 21.4%), wtJAK2+/JAK2V617F-( 0%), wtJAK2-/JAK2V617F+ ( 79%) of patient 5 and populations of JAK2V617F+ (36,8%± 5 ), JAK2V617F- of patients 1-4 were sorted by cell sorter with ~ 90% purity following detection and analysis of each populations for relative changes in mRNA expressions . The data revealed distinct ΔCt values between each populations.In this study, we have aimed for a new approach by utilizing nanotechnology aligned with the conventional techniques in order to save time, money and outcome. The capability of in-cell detection and isolation of the JAK2V617F and wtJAK2 first time by performing the expression analysis, changes the routine protocols backwards, enables the detecting direct effect of the mutation to the cells as well as other genes. This study creates a platform where functional analysis regarding to the more detailed understanding of the initiation of malignancy as well as responses to the therapies could be performed. DisclosuresNo relevant conflicts of interest to declare.

Abstract 4018: Development and analytical validation of a novel real-time multiplex RT-qPCR assay for the simultaneous quantification of ER, PR, HER-2 and EGFR mRNA expression in circulating tumor cells of breast cancer patients

Abstract Introduction: Circulating Tumor Cells (CTCs) represent an important biological link in the spread of breast cancer from primary to metastatic disease. CTCs have already been established as strong predictors of prognosis in patients with metastatic breast cancer. Triple-negative breast cancers have a more aggressive clinical outcome than other forms of breast cancer. The aim of our work was to develop a quantitative real-time multiplex RT-qPCR assay for studying the expression of ER, PR, HER-2 and EGFR in CTC of breast cancer patients. Materials and Methods: A quadruplex quantitative real time RT-qPCR assay for ER, PR, HER-2 and EGFR was developed based on the de novo in-silico design of eight primers and four dual hybridization probes. All primers and probes were designed to avoid cross-reactions and primer dimer formation and to match the assay conditions, such as amplicon sizes, and melting temperatures. The specificity of all primer and hybridization probe sequences was first tested by homology searches in the nucleotide database (NCBI, nucleotide BLAST). Each probe set included a 3′-fluorescein (F) donor probe and a 5′- LC acceptor probe that was different for each gene set: ER at 610nm, PR at 640nm, HER-2 at 670nm, EGFR at 705nm. A color compensation test was performed by using pure dye spectra so that spectral overlap between dyes was corrected. The LightCycler 2.0 platform, (Roche, Diagnostics) was used since it allows detection of six multiple reporter dyes in the same capillary. The assay was designed, so that only 1 μL of cDNA is used and the total reaction volume is 10 μL. Results: The assay sensitivity was evaluated by performing spiking experiments. For this reason known numbers of MCF7 and SKBR-3 cells, as well as external quantification calibrators ranging from 105 copies/μL to 10 copies/μL, were used. The specificity was evaluated by carefully designed cross reaction studies, performed for each gene target in the presence of all other targets. Our assay, under optimized conditions has shown a very high specificity for each analyte. Conclusions: We report for the first time a highly sensitive, specific and reproducible quantitative multiplex real-time RT-qPCR assay for the simultaneous quantification of ER, PR, HER-2 and EGFR. The assay is currently validated in CTC isolated from a large number of breast cancer patients. Citation Format: Areti D. Strati, Evi S. Lianidou. Development and analytical validation of a novel real-time multiplex RT-qPCR assay for the simultaneous quantification of ER, PR, HER-2 and EGFR mRNA expression in circulating tumor cells of breast cancer patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4018. doi:10.1158/1538-7445.AM2014-4018

Development of a Luminex assay for the simultaneous detection of human enteric viruses in sewage and river water

Real time PCR (qPCR) is increasingly being used for viral detection in aquatic environments because it enables high specificity and sensitivity of detection. However, the limited number of fluorescent reporter dyes restricts its multiplex application. In this study, a multiplex Luminex assay was established for the simultaneous detection of human adenovirus (HAdV), human polyomavirus (HPyV), enterovirus (EV), rotavirus (RoV), norovirus GI (NoVGI) and norovirus GII (NoVGII). Different river water and wastewater samples were tested for the viruses using both qPCR and the multiplex Luminex xMAP assay. HAdV and HPyV were the most abundant in all environmental samples. HAdV was detected in all river water and wastewater samples, and HPyV was detected in 79% of river water and 95.8% of wastewater samples. The multiplex xMAP assay revealed high specificity and no cross-reactivity. Using the multiplex Luminex assay, the viral detection rates in river water samples were lower than the rates obtained by qPCR for all viruses. Conversely, in wastewater samples, the viral detection rates were the same for both methods. In addition, the analytical sensitivity of the monoplex Luminex assay was comparable to or lower than qPCR. Results suggest that the multiplex Luminex assay could be a reliable method for the simultaneous detection of viral pathogens in wastewater.

Probing an Artificial Polypeptide Receptor Library Using a Series of Novel Histamine H3 Receptor Ligands

An artificial polypeptide receptor (APR) library was created by using the self-organization of N-lipidated peptides attached to cellulose via m-aminophenylamino-1,3,5-triazine. The response of the library was probed using a series of novel H3 receptor ligands. Since no guidelines on how to design an APRs selective vs certain receptor types exist, a diverse set of amino acids (Ala, Trp, Pro, Glu, His, Lys and Ser) were used and coupled with one of three gating fatty acids (palmitic, ricinoleic or capric). A competitive adsorption-desorption of an appropriate reporter dye was used for the indirect visualization of the interactions of guests with particular receptors. The resulted library response to individual inhibitors was then arranged in a matrix, preprocessed and analyzed using the principal component analysis (PCA) and partial least squares (PLS) method. The most important conclusion obtained from the PCA analysis is that the library differentiates the probed compounds according to the lipophilicity of the gating unit. The PC3 with a dominant absolute contribution of the receptors containing Glu allowed for the best separation of the ligands with respect to their activity. This conclusion is in agreement with the fact that Glu 206 is a genuine ligand counterpart in the natural histamine receptor.

Investigating the cellular fate of a DNA-targeted platinum-based anticancer agent by orthogonal double-click chemistry

Confocal fluorescence microscopy was used to study a platinum-based anticancer agent in intact NCI-H460 lung cancer cells. Orthogonal copper-catalyzed azide-alkyne cycloaddition (click) reactions were used to simultaneously determine the cell-cycle-specific localization of the azide-functionalized platinum-acridine agent 1 and monitor its effects on nucleic acid metabolism. Copper-catalyzed postlabeling showed advantages over copper-free click chemistry using a dibenzocyclooctyne (DIBO)-modified reporter dye, which produced high background levels in microscopic images and failed to efficiently label platinum adducts in chromatin. Compound 1 was successfully labeled with the fluorophore DIBO to yield 1* (characterized by in-line high-performance liquid chromatography/electrospray mass spectrometry). 1 and 1* show a high degree of colocalization in the confocal images, but the ability of 1* to target the (compacted) chromatin was markedly reduced, most likely owing to the steric bulk introduced by the DIBO tag. Nuclear platinum levels correlated inversely with the ability of the cells to synthesize DNA and cause cell cycle arrest, as confirmed by bivariate flow cytometry analysis. In addition, a decrease in the level of cellular transcription, shrinkage of the nucleolar regions, and redistribution of RNA into the cytosol were observed. Postlabeling in conjunction with colocalization experiments is a useful tool for studying the cell killing mechanism of this type of DNA-targeted agent.