ESI MS for Microsized Bioparticles.

An ESI ion trap mass spectrometer was designed for high-throughput and rapid mass analysis of large bioparticles. Mass calibration of the instrument was performed using commercially available polystyrene (PS) microparticles with a size comparable to cancer cells. Different sizes of MCF-7 breast cancer cells (8 to 15 µm) were used in this study. The masses of different cancer cells were measured. This system allows for the analysis of all types of particles.

Recent Advances in Anticancer Activities and Drug Delivery Systems of Tannins.

Tannins, polyphenols in medicinal plants, have been divided into two groups of hydrolysable and condensed tannins, including gallotannins, ellagitannins, and (-)-epigallocatechin-3-gallate (EGCG). Potent anticancer activities have been observed in tannins (especially EGCG) with multiple mechanisms, such as apoptosis, cell cycle arrest, and inhibition of invasion and metastases. Furthermore, the combinational effects of tannins and anticancer drugs have been demonstrated in this review, including chemoprotective, chemosensitive, and antagonizing effects accompanying with anticancer effect. However, the applications of tannins have been hindered due to their poor liposolubility, low bioavailability, off-taste, and shorter half-life time in human body, such as EGCG, gallic acid, and ellagic acid. To tackle these obstacles, novel drug delivery systems have been employed to deliver tannins with the aim of improving their applications, such as gelatin nanoparticles, micelles, nanogold, liposomes, and so on. In this review, the chemical characteristics, anticancer properties, and drug delivery systems of tannins were discussed with an attempt to provide a systemic reference to promote the development of tannins as anticancer agents.

Selective killing of cancer cells by nanoparticle-assisted ultrasound.

BACKGROUND: Intense ultrasound, such as that used for tumor ablation, does not differentiate between cancerous and normal cells. A method combining ultrasound and biocompatible gold or magnetic nanoparticles (NPs) was developed under in vitro conditions using human breast and lung epithelial cells, which causes ultrasound to preferentially destroy cancerous cells. RESULTS: Co-cultures of BEAS-2B normal lung cells and A549 cancerous lung cells labeled with green and red fluorescent proteins, respectively, were treated with focused ultrasound beams with the addition of gold and magnetic nanoparticles. There were significantly more necrotic A549 cells than BEAS-2 cells when gold nanoparticles were added to the culture medium [(50.6 ± 15.1) vs. (7.4 ± 2.9) %, respectively, P < 0.01]. This selective damage to cancer cells was also observed for MDA-MB231 breast cancer cells relative to MCF-10A normal breast cells after treatment with magnetic nanoparticles. CONCLUSIONS: The data obtained for different cell lines indicate that nanoparticle-assisted ultrasound therapy (NAUT) could be an effective new tool for cancer-specific treatment and could potentially be combined with conventional methods of cancer diagnosis and therapy to further increase the overall cancer cure rate.

Uniqueness: skews bit occurrence frequencies in randomly generated fingerprint libraries.

Requiring that randomly generated chemical fingerprint libraries have unique fingerprints such that no two fingerprints are identical causes a systematic skew in bit occurrence frequencies, the proportion at which specified bits are set. Observed frequencies (O) at which each bit is set within the resulting libraries systematically differ from frequencies at which bits are set at fingerprint generation (E). Observed frequencies systematically skew toward 0.5, with the effect being more pronounced as library size approaches the compound space, which is the total number of unique possible fingerprints given the number of bit positions each fingerprint contains. The effect is quantified for varying library sizes as a fraction of the overall compound space, and for changes in the specified frequency E. The cause and implications for this systematic skew are subsequently discussed. When generating random libraries of chemical fingerprints, the imposition of a uniqueness requirement should either be avoided or taken into account.

Differentiation of neural stem/progenitor cells using low-intensity ultrasound.

Herein, we report the evaluation of apoptosis, cell differentiation, neurite outgrowth and differentiation of neural stem/progenitor cells (NSPCs) in response to low-intensity ultrasound (LIUS) exposure. NSPCs were cultured under different conditions, with and without LIUS exposure, to evaluate the single and complex effects of LIUS. A lactic dehydrogenase assay revealed that the cell viability of NSPCs was maintained with LIUS exposure at an intensity range from 100 to 500 mW/cm(2). Additionally, in comparison with no LIUS exposure, the cell survival rate was improved with the combination of medium supplemented with nerve growth factor and LIUS exposure. Our results indicate that LIUS exposure promoted NSPC attachment and differentiation on a glass substrate. Neurite outgrowth assays revealed the generation of longer, thicker neurites after LIUS exposure. Furthermore, LIUS stimulation substantially increased the percentage of differentiating neural cells in NSPCs treated with nerve growth factor in comparison with the unstimulated group. The high percentage of differentiated neural cells indicated that LIUS induced neuronal networks denser than those observed in the unstimulated groups. Furthermore, the release of nitric oxide, an important small-molecule neurotransmitter, was significantly upregulated after LIUS exposure. It is therefore reasonable to suggest that LIUS promotes the differentiation of NSPCs into neural cells, induces neurite outgrowth and regulates nitric oxide production; thus, LIUS may be a potential candidate for NSPC induction and neural cell therapy.

Structural Key Bit Occurrence Frequencies and Dependencies in PubChem and Their Effect on Similarity Searches.

Little published literature exists on the 881 bit structural keys used by PubChem for categorizing and comparing the compounds present in its database. We characterized these structural keys by examining their frequencies of occurrence within the PubChem compound database. In addition, bit dependencies, defined as the universal presence of a bit given the presence of another, were determined. We show that the vast majority of bits are rarely set and that substantial numbers of dependencies exist. A comparison of similarity searches with five United States Food and Drug Administration approved drugs as reference compounds using the full structural keys versus a variant in which all dependent bits were removed was performed using the Tanimoto coefficient. These bit dependencies not only affect similarity scores, but also alter the compounds returned in similarity searching. Judicious selection of bits is needed to maintain sufficient ability to differentiate related compounds.

Rapid and direct microRNA quantification by an enzymatic luminescence assay.

A quantitative bioluminescence assay for rapid and sensitive microRNA (miRNA) expression analysis was developed. The assay uses miRNA directly as a primer for binding to a circular single-stranded DNA template, followed by rolling circle amplification. The detection of inorganic pyrophosphate (PPi) molecules released during the DNA polymerization and amplification process is performed by a multi-enzyme system. PPi is converted to ATP by ATP-sulfurylase, which provides energy for luciferase to oxidize luciferin and produce light. Experimental results show that the assay has a dynamic range exceeding three orders of magnitude and the ability to discriminate miRNAs with high-homology sequences. Quantification of nine miRNAs in human heart tissues demonstrated high cross-platform consistency between this assay and the TaqMan real-time polymerase chain reaction (PCR) assay with R(2)=0.941. The assay requires fewer reagents, can be performed at an isothermal condition without thermal cycling, and is capable of detecting miRNAs in less than 1h. Compared with the real-time PCR and microarray-based detection methods, this assay provides a simpler, faster, and less expensive platform for miRNA quantification in life science research, drug discovery, and clinical diagnosis.

Transient model of thermal deactivation of enzymes.

The kinetics of enzyme deactivation provide useful insights on processes that determine the level of biological function of any enzyme. Photinus pyralis (firefly) luciferase is a convenient enzyme system for studying mechanisms and kinetics of enzyme deactivation, refolding, and denaturation caused by various external factors, physical or chemical by nature. In this report we present a study of luciferase deactivation caused by increased temperature (i.e., thermal deactivation). We found that deactivation occurs through a reversible intermediate state and can be described by a Transient model that includes active and reversibly inactive states. The model can be used as a general framework for analysis of complex, multiexponential transient kinetics that can be observed for some enzymes by reaction progression assays. In this study the Transient model has been used to develop an analytical model for studying a time course of luciferase deactivation. The model might be applicable toward enzymes in general and can be used to determine if the enzyme exposed to external factors, physical or chemical by nature, undergoes structural transformation consistent with thermal mechanisms of deactivation.

Real-time bioluminescent assay for inhibitors of RNA and DNA polymerases and other ATP-dependent enzymes.

Viral polymerases are important targets for drug development. However, current methods used to identify and characterize inhibitors of polymerases are time-consuming, use radiolabeled reagents, and are cost-inefficient. Here we present a bioluminescent assay for the identification and characterization of inhibitors of polymerases, as well as other ATP-dependent enzymes, that monitors the decrease of ATP or dATP in real time, allowing detection of enzyme inhibition based on differences in ATP/dATP consumption. The assay works with a variety of RNA and DNA polymerases, using both RNA and DNA templates. The assay measures changes in substrate concentration in real time and provides a faster alternative for kinetic studies of inhibition. Michaelis-Menten plots were obtained from a single reaction, yielding K(m) values that compared well with literature values. The assay could identify the mechanism of inhibition and determine inhibition constants (K(i)) for a weak competitive inhibitor of Klenow fragment and two strong noncompetitive inhibitors of HIV-1 reverse transcriptase with one series of inhibitor concentrations, reducing the total number of experiments that would normally be needed. The assay is also sensitive enough to detect a weak inhibitor with K(i)>100 µM, making it a viable technique for fragment-based drug discovery.

Ultrasound ionization of biomolecules.

To date, mass spectrometric analysis of biomolecules has been primarily performed with either matrix-assisted laser desorption/ionization (MALDI) or electrospray ionization (ESI). In this work, ultrasound produced by a simple piezoelectric device is shown as an alternative method for soft ionization of biomolecules. Precursor ions of proteins, saccharides and fatty acids showed little fragmentation. Cavitation is considered as a primary mechanism for the ionization of biomolecules.

Rapid 3D imaging of contrast flow: demonstration of a dual beam technique.

Perfusion imaging in a 3D volume using ultrasound contrast agent may improve vascular characterization compared with 2D imaging. Conventional 3D acquisition requires excessive scan time. A dual transducer technique using conventional systems has been introduced that allows 3D imaging of contrast dynamics with drastically reduced scan times (LeCarpentier et al. 2003). Two transducers are translated across a volume where the leading transducer effects contrast clearance and the following transducer images at desired contrast refill times. With 2D arrays that allow simultaneous clearance and imaging pulses, scan times could be further reduced and the need for two transducers eliminated. The dual transducer technique was demonstrated on a tube phantom, with observed contrast profiles matching those expected. Measured center velocities of (+/- std dev) 1.46 +/- 0.21 and 2.25 +/- 0.5 did not statistically differ from expected values of 1.75 and 2.50 (all mm/s), (p > 0.05). This technique is introduced for rapid acquisition of 3D contrast refill images.

An observer study comparing spot imaging regions selected by radiologists and a computer for an automated stereo spot mammography technique.

We are developing an automated stereo spot mammography technique for improved imaging of suspicious dense regions within digital mammograms. The technique entails the acquisition of a full-field digital mammogram, automated detection of a suspicious dense region within that mammogram by a computer aided detection (CAD) program, and acquisition of a stereo pair of images with automated collimation to the suspicious region. The latter stereo spot image is obtained within seconds of the original full-field mammogram, without releasing the compression paddle. The spot image is viewed on a stereo video display. A critical element of this technique is the automated detection of suspicious regions for spot imaging. We performed an observer study to compare the suspicious regions selected by radiologists with those selected by a CAD program developed at the University of Michigan. True regions of interest (TROIs) were separately determined by one of the radiologists who reviewed the original mammograms, biopsy images, and histology results. We compared the radiologist and computer-selected regions of interest (ROIs) to the TROIs. Both the radiologists and the computer were allowed to select up to 3 regions in each of 200 images (mixture of 100 CC and 100 MLO views). We computed overlap indices (the overlap index is defined as the ratio of the area of intersection to the area of interest) to quantify the agreement between the selected regions in each image. The averages of the largest overlap indices per image for the 5 radiologist-to-computer comparisons were directly related to the average number of regions per image traced by the radiologists (about 50% for 1 region/image, 84% for 2 regions/image and 96% for 3 regions/image). The average of the overlap indices with all of the TROIs was 73% for CAD and 76.8% +/- 10.0% for the radiologists. This study indicates that the CAD determined ROIs could potentially be useful for a screening technique that includes stereo spot mammography imaging.