Gene expression analysis for high throughput screening applications

To meet growing needs for high throughput gene expression profiling, we established a new automated high throughput TaqMan RT-PCR method for quantitative mRNA expression analysis. In this method, the Allegro( trade mark ) (Zymark) system conducts all sample tracking and liquid handling steps, and ABI PRISM 7900 HT (Applied Biosystems) is used to conduct real-time determination of the C(t) value when amplification of PCR products is first detected and accumulation of inhibitory PCR products is unlikely to occur. The ABI PRISM 7900 HT Sequence Detection System features a real-time PCR instrument with 384-well-plate compatibility and robotic loading, and continuous wavelength detection, which enables the use of multiple fluorophores in a single reaction. The Allegro System offers an assembly line approach with a modular design that allows reconfiguration of the components to accommodate variations in the assay flow. In the present study, we have established and validated a new automated High Throughput (HT) TaqMan RT-PCR- based method for quantitative mRNA expression analysis. The data demonstrate that HT-Taqman PCR is a powerful tool that can be used for measuring low concentrations of mRNA, and is highly accurate, reproducible, and amenable to high throughput analysis. Results suggest that HT-TaqMan is a reliable method for the quantification of low-expression genes and a powerful tool with HT capability for target identification/validation, structure-activity relationship (SAR) study, compound selection for efficacy studies, and biomarker identification in drug discovery and development.     

Determination of erythrocyte deformability and its correlation to cellular ATP release using microbore tubing with diameters that approximate resistance vessels in vivo

A novel method is described for measuring the deformability of red blood cells (RBCs) in tubing whose diameters approximate forces encountered in vivo. Here, RBCs from rabbits are loaded into a 50 cm section of 75 microm id microbore tubing and connected to a syringe pump. This section of tubing is then connected to a 15 cm section of 25 microm id tubing. As buffer is pumped through the flow system, the RBCs are evacuated from both sections of tubing. However, the inability of the RBCs to move freely through the 25 mirom id section of tubing results in a buildup of cells at the inlet of this portion of tubing. The continued force output by the syringe pump results in a deformation of the RBCs until all of the cells are eventually evacuated from the flow system. It was found that a measurement of the time required to reach half of the maximum pressure (1/2 P(max)) may be used as an indicator of the RBC deformability. For a given sample, a simple buffer results in less time to reach 1/2 P(max) (6.9 +/- 0.2 s) than deformable RBCs (21.6 +/- 0.8 s). To verify that the increased amount of time to reach 1/2 P(max) is indeed due to the RBCs, various hematocrits of an RBC sample were investigated and, as expected, it was found that a 12% RBC hematocrit had a higher 1/2 P(max) value (26.0 s +/- 2.2 s) when compared to a 7% hematocrit (19.1 +/- 0.3 s). In addition, RBCs chemically stiffened with glutaraldehyde were shown to be 25% less deformable than normal RBCs. Finally, a study was performed to examine the relationship between RBC deformability and ATP release and it was found that ATP release increased as a function of RBC deformability. This method greatly simplifies deformability measurements, employing only a syringe pump and microbore tubing, and may lead to a more complete understanding of the physiological significance of erythrocyte deformability.     

On the Effects of UV Radiation on the Release Ability of Glucose Embedded in Hydroxypropyl Cellulose Films

New drug delivery systems based on hydroxypropyl cellulose (HPC) and different percents of glucose were prepared and characterized to check their suitability as UV resistant patches. The spectral absorption properties of the HPC and HPC-glucose blends before and after UV irradiation were analyzed. The surface polarity and hydrophilicity were correlated with the morphology of the films and analyzed with respect to the UV exposure time and the embedded amount of glucose. The effects of UV radiation on in vitro evaluation of glucose release from the HPC films are reported. The mechanism involved in the drug release process, evaluated using the Korsmeyer-Peppas equation, was dependent on the introduced amount of glucose and less on the UV exposure time. A more polar, smoother, and less dense surface releases the glucose over larger periods of time, making the system with lower percents of glucose more adequate for the pursued purpose.     

Automated chemical resonance generation and structure filtration for kinetic modeling

This work discusses efficient and automated methods for constructing a set of representative resonance structures for arbitrary chemical species, including radicals and biradicals, consisting of the elements H, C, O, N, and S. Determining the representative reactive structures of chemical species is crucial for identification of reactive sites and consequently applying the correct reaction templates to generate the set of important reactions during automated chemical kinetic model generation. We describe a fundamental set of resonance pathway types, accounting for simple resonating structures, as well as global approaches for polycyclic aromatic species. Automatically discovering potential localized structures along with filtration to identify the representative structures was shown to be robust and relatively fast. The algorithms discussed here were recently implemented in the Reaction Mechanism Generator (RMG) software. The final structures proposed by this method were found to be in reasonable agreement with quantum chemical computation results of localized structure contributions to the resonance hybrid.     

Efficient Detection of Phthalate Esters in Human Saliva via Fluorescence Spectroscopy

The detection of phthalates in human biologic fluids remains an important research objective because it provides an important measure of an individual’s exposure to this class of compounds, which have known deleterious health effects. Moreover, the ability to accomplish such detection in fluids that are easy to collect, such as saliva and urine, provides additional practical advantages. Reported herein is the application of cyclodextrin-promoted fluorescence energy transfer and fluorescence modulation to accomplish precisely such detection: the development of sensitive and selective florescence-based detection methods for phthalates in saliva, an easily collectable human biologic fluid. Such saliva-based detection methods occur with high levels of selectivity (100% differentiation) and sensitivity (limits of detection as low as 0.089?µM), and provide significant potential in the development of practical phthalate detection devices.     

Colloidally Stable CdS Quantum Dots in Water with Electrostatically Stabilized Weak-Binding,Sulfur-Free Ligands

Colloidal quantum dot (QD) photocatalysts have the electrochemical and optical properties to be highly effective for a range of redox reactions. QDs are proven photo-redox catalysts for a variety of reactions in organic solvents but are less prominent for aqueous reactions. Aqueous QD photocatalysts require hydrophilic ligand shells that provide long-term colloidal stability but are not so tight-binding as to prevent catalytic substrates from accessing the QD surface. Common thiolate ligands, which also poison many co-catalysts and undergo photo-oxidative desorption, are therefore often not an option. This paper describes a framework for the design of water-solubilizing ligands that are in dynamic exchange on and off the QD surface, but still provide long-term colloidal stability to CdS QDs. The binding affinity and inter-ligand electrostatic interactions of a bifunctional ligand, aminoethyl phosphonic acid (AEP), are tuned with the pH of the dispersion. The key to colloidal stability is electrostatic stabilization of the monolayer. This work demonstrates a means of mimicking the stabilizing power of a thiolate-bound ligand with a zwitterionic tail group, but without the thiolate binding group.     

Remarkably large remote-stereocenter-induced chromatographic differences: azulenyl 1,5-diols

A series of four new azulene-1,5-diol diastereomers were prepared and found to exhibit large differences (ΔR_f 0.22–0.46) in silica TLC mobilities despite having stereocenters four bonds apart. The stereoisomers were identified by X-ray crystallography, and in all cases the RR/SS diastereomers were less strongly retained than the RS/SR diastereomers. The crystal structures suggested that this is due to a conformational preference for the CF₃ groups to be nearly perpendicular to the plane of the azulene ring, which caused the dihedral angle between the OH groups to be larger (in the RR/SS diastereomers) or smaller (in the RS/SR diastereomers). The smaller dihedral angles allow the RS/SR diastereomers to simultaneously bind to a silica surface and thus be more strongly retained. Two similar benzene derivatives and several cycloalkanediols with more proximate stereocenters showed little or no difference in mobilities between diastereomers, though the NMR differences were greater. Thus, the azulene ring is an important factor in enforcing the conformational preferences, either through steric interactions with the 4/8 substituents (H or methyl) or its significant dipole moment, or both.     

Surface energy gradient driven convection for generating nanoscale and microscale patterned polymer films using photosensitizers

The Marangoni effect describes how fluid flows in response to gradients in surface energy. This phenomenon could be broadly harnessed to pattern the surface topography of polymer films if generalizable techniques for programming surface energy gradients existed. Here, a near UV–visible light (NUV–vis) photosensitizer, 9,10‐dibromo‐anthracene (DBA), was doped into thin films of a model polymer, poly(isobutyl methacrylate). After exposure to light through a photomask and heating above the glass transition, thermolysis of photo‐oxidized DBA and grafting to the polymer promoted flow of the film material into the exposed regions. This mechanism did not significantly alter the molecular weight of PiBMA or the film's glass transition temperature, but resulted in an increase in film surface energy as indicated by a decrease in water contact angle. Film height variations of 580 nm were produced using a mask with 12.5 μm features; a mask with 800 nm features was also employed to generate topographic features of corresponding width without expensive contacting equipment. Due to the broad absorbance spectra of DBA, highly accessible and/or unconventional light sources may be employed in this process; this advantage was demonstrated by patterning with sunlight. The nonspecific radical‐mediated nature of the DBA grafting reaction makes this a promising approach for many classes of polymers. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52, 1195–1202     

Practical and efficient applications of novel dioxaborolanes and dioxaborinanes in the synthesis of corresponding boronates and their use in the palladium-catalyzed cross coupling reactions

The syntheses of boronates derived from the reaction of dioxaborolanes and dioxaborinanes with either organolithium or organomagnesium reagents are investigated along with their subsequent use in the palladium cross coupling reaction. The intrinsic stability of these cyclic esters contributes to their facile reaction with both lithium and magnesium nucleophiles at mild and safe conditions. We have found that many of the reactions proceed at room temperature which is a significant improvement over the traditional routes which require cryogenic temperatures. The scope of these reactions and their practical application to large scale process synthesis is described.