Multiplexed and spatiotemporal measurements of glutamate secreted by neurons and bacteria.

By applying an in vivo biotinylation platform, glutamate-sensing protein can be easily immobilized on streptavidin-functionalized magnetic microbeads, which expands the detection modality for the spatiotemporal measurements of glutamate secreted by adherent neuronal cells and suspension microbial cells using fluorescence microscopy and microplate photometers.

BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types.

BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource.

Investigation of patient, tumour and treatment variables affecting residual motion for respiratory-gated radiotherapy.

Respiratory gating can reduce the apparent respiratory motion during imaging and treatment; however, residual motion within the gating window remains. Respiratory training can improve respiratory reproducibility and, therefore, the efficacy of respiratory-gated radiotherapy. This study was conducted to determine whether residual motion during respiratory gating is affected by patient, tumour or treatment characteristics. The specific aims of this study were to: (1) identify significant characteristics affecting residual motion, (2) investigate time trends of residual motion over a period of days (inter-session) and (3) investigate time trends of residual motion within the same day (intra-session). Twenty-four lung cancer patients were enrolled in an Institutional Review Board (IRB)-approved protocol. For approximately five sessions, 331 four-minute, respiratory motion traces were acquired with free breathing, audio instructions and audio-visual biofeedback for each patient. The residual motion was quantified by the standard deviation of the displacement within the gating window. The generalized linear model was used to obtain coefficients for each variable within the model and to evaluate the clinical and statistical significance. The statistical significance was determined by a p-value<0.05, while effect sizes of 0.1 cm (one standard deviation) were considered clinically significant. This data analysis was applied to patient, tumour and treatment variables. Inter- and intra-session variations were also investigated. The only variable that was significant for both inhale- and exhale-based gating was disease type. In addition, visual-training displacement, breathing type and Karnofsky performance status (KPS) values were significant for inhale-based gating, and dose-per-fraction was significant for exhale-based gating. Temporal respiratory variations within and between sessions were observed for individual patients. However inter- and intra-session analyses did not show significant time trends on average for any of the variables considered. The lack of significant time trends within and between sessions indicates that on average (1) there is no significant learning period for breathing training, (2) the patients did not experience training-related fatigue and (3) the margin component to account for residual motion during gated radiotherapy appears to remain constant throughout the treatment.

Hypericum perforatum L. extract - novel photosensitizer against human bladder cancer cells.

The polar methanolic fraction (PMF) of the Hypericum perforatum L. extract has recently been developed and tested as a novel, natural photosensitizer for use in the photodynamic therapy (PDT), and photodynamic diagnosis (PDD). PMF has been tested on HL-60 leukemic cells and cord blood hemopoietic progenitors. In the present study, the efficacy of PMF as a phototoxic agent against urinary bladder carcinoma has been studied using the T24 (high grade metastatic cancer), and RT4 (primary low grade papillary transitional cell carcinoma) human bladder cancer cells. Following cell culture incubation, PMF was excited using 630 nm laser light. The photosensitizer exhibited significant photocytotoxicity in both cell lines at a concentration of 60microg/ml, with 4-8 J/cm(2) light dose, resulting in cell destruction from 80% to 86%. At the concentration of 20microg/ml PMF was not active in either cell line. These results were compared with the results obtained in the same cell lines, under the same conditions with a clinically approved photosensitizer, Photofrin. Photofrin was used in the maximum clinically tolerable dose of 4microg/ml, and it was also excited with 630 nm laser light. In the T24 cell Photofrin exhibited slightly less photocytotocixity, compared with PMF, resulting in 77% cell death with 8J/cm(2) light dose. However, against the RT4 cells Photofrin resulted in minimal cell death (9%) with even 8J/cm(2) light dose. Finally, the type of cell death induced by PMF photoactivation was studied using flow cytometry and DNA laddering. Cell death by PMF photodynamic action in these two bladder cell lines is caused predominently by apoptosis. The reported significant photocytotoxicity, selective localization, natural abundance, easy, and inexpensive preparation, underscore that the PMF extract hold the promise of being a novel, effective PDT photosensitizer.

The application of the sinusoidal model to lung cancer patient respiratory motion.

Accurate modeling of the respiratory cycle is important to account for the effect of organ motion on dose calculation for lung cancer patients. The aim of this study is to evaluate the accuracy of a respiratory model for lung cancer patients. Lujan et al. [Med. Phys. 26(5), 715-720 (1999)] proposed a model, which became widely used, to describe organ motion due to respiration. This model assumes that the parameters do not vary between and within breathing cycles. In this study, first, the correlation of respiratory motion traces with the model f(t) as a function of the parameter n (n = 1, 2, 3) was undertaken for each breathing cycle from 331 four-minute respiratory traces acquired from 24 lung cancer patients using three breathing types: free breathing, audio instruction, and audio-visual biofeedback. Because cos2 and cos4 had similar correlation coefficients, and cos2 and cos1 have a trigonometric relationship, for simplicity, the cos1 value was consequently used for further analysis in which the variations in mean position (z0), amplitude of motion (b) and period (tau) with and without biofeedback or instructions were investigated. For all breathing types, the parameter values, mean position (z0), amplitude of motion (b), and period (tau) exhibited significant cycle-to-cycle variations. Audio-visual biofeedback showed the least variations for all three parameters (z0, b, and tau). It was found that mean position (z0) could be approximated with a normal distribution, and the amplitude of motion (b) and period (tau) could be approximated with log normal distributions. The overall probability density function (pdf) of f(t) for each of the three breathing types was fitted with three models: normal, bimodal, and the pdf of a simple harmonic oscillator. It was found that the normal and the bimodal models represented the overall respiratory motion pdfs with correlation values from 0.95 to 0.99, whereas the range of the simple harmonic oscillator pdf correlation values was 0.71 to 0.81. This study demonstrates that the pdfs of mean position (z0), amplitude of motion (b), and period (tau) can be used for sampling to obtain more realistic respiratory traces. The overall standard deviations of respiratory motion were 0.48, 0.57, and 0.55 cm for free breathing, audio instruction, and audio-visual biofeedback, respectively.

Cytometry microchip using polymer-based saltbridge electrodes.

We developed a cytometry glass chip using polymer-based saltbridge electrodes. Saltbridge electrodes were placed at lateral sides of channel to increase the sensitivity and robustness of detection. The dimension of saltbridge electrodes which are exposed to channel was 50mum by 20mum (width, height). The saltbridge electrode was formed at a specific position in a predefined shape by photopolymerization technique. UV light sensitive monomer DMAC (dially dimethyl ammonium chloride) was used for polymerization. Polymer-based saltbridge electrode enabled the DC impedance analysis of the channel for cytometry. Moreover, the lateral positioning of saltbridge electrode is easily accomplished by photopolymerization technique. We validated the detection sensitivity of developed chip using 10mum fluorescent bead.

Identification of inhibitors of bacterial transcription/translation machinery utilizing a miniaturized 1536-well format screen.

This report presents the miniaturization of a HTS screen to identify inhibitors of prokaryotic transcription-translation in a 1536-well format. The in vitro assay design utilized the bacterial expression machinery to drive expression of a firefly luciferase reporter gene, which was read as an endpoint luminesence measurement. This multicomponent system permits identification of inhibitors at different steps in this pathway. Successful miniaturization required integration of homogeneous assay formats, robust liquid-handling workstations, and second-generation imaging systems. Comparison of data from a triplicate 1536-well screen of a subset of a target library that had been previously validated and followed up for hit confirmation in a 384-well plate format confirmed that triplicate screening yields data of higher confidence and quality, eliminates the time-consuming and potentially error-prone step of cherry-picking, and reduces the number of false positives and negatives. The substantial savings of reagents and reduction of the numbers of plates to process obtained in a 1536-well format as compared to a 384-well format allowed a full triplicate evaluation of the entire library of 183,000 compounds at lower cost and in less time. The triplicate-screen statistics are consistent with a highly reliable data set with a coefficient of variation of 14.8% and Z' and Z values of 0.57 and 0.25, respectively. This screen resulted in the identification of 1,149 hits (0.63% hit rate), representing a compound population at 2.5 standard deviations from the mean cutoff. Furthermore, the data demonstrate good agreement between IC(50) values derived for this assay in a 1536-well format and 384-well format.

Reproducible fabrication of miniaturized glucose sensors: preparation of sensing membranes for continuous monitoring.

The immobilization process of glucose oxidase(GOx) in the poly(1,3-diaminobenzene) (poly(1,3-DAB)) network was closely investigated in situ using an electrochemical quartz crystal microbalance(EQCM). GOx captured in approximately 50 nm thick poly-1,3-DAB layer causes a 514 Hz frequency increase, corresponding to 541 ng, and distributes mostly in the outer part of the polymer film. The presence of poly-L-lysine and glutaraldehyde during electropolymerization of poly(1,3-DAB) improves sensitivity by raising the amount of GOx immobilized. Adding a protective membrane on to the enzyme layer from poly(tetrafluoroethylene) (PTFE) dispersed in aqueous media lets the entire fabrication procedure finish perfectly without nonaqueous solvent. The finalized needle-type glucose sensors show competent functions in sensitivity, stability, biocompatibility, lifetime, interference and reproducibility.

Self-assembled monolayer of a redox-active calix[4]arene: voltammetric recognition of the Ba2+ ion in aqueous media.

The Redox-active monolayer of a novel calix[4]arene recognizing redox-inactive ionic species by voltammetry is reported. Calix[4]arene-disulfide-diquinone, which is not only redox-active but is also a highly selective ionophore for the Ba2+ ion, spontaneously forms a stable and dense monolayer film on gold. The redox-active calixarene monolayer selectively recognizes Ba2+ ion in aqueous media, and the voltammetric signals are proportional to the ionic concentration. A new voltammetric peak can be detected by square-wave voltammetry upon adding a dilute solution containing Ba2+ ion having a concentration as low as 1.0 x 10(-6) M. The Langmuir plot (1/ip vs 1/[Ba2+]) shows a linear slope in the range from 1.0 x 10(-6) M to 1.0 x 10(-4) M. This modified electrode does not show any significant interference from alkali and alkaline earth metal ions except for Sr2+ and Ca2+. Only 100- and 500-fold concentrations of Sr2+ and Ca2+ ions, respectively, can lead to voltammetric responses comparable to that of Ba2+.

A scintillation proximity assay for rna detection.

A homogeneous scintillation proximity assay (SPA) for detection of RNA transcripts is described. 3H-labeled RNA transcripts are hybridized in solution to biotinylated oligodeoxynucleotides (ODNs), which are then bound by streptavidin-coated, scintillant-embedded beads. Only bound 3H-labeled RNA transcripts are brought in close enough proximity to stimulate light emission from the beads. The results from this novel homogeneous assay correlated well with those obtained using the traditional filter-binding methods to measure RNA polymerase activity. The assay has been miniaturized to a 384-well format compatible with automated high-throughput screening. This SPA method has also been successfully used to probe RNA-accessible sites to hybridization, and thus should provide a useful tool for selecting effective antisense ODNs in antisense research.

Electrochemical monitoring of proton transfer across liquid/liquid interfaces on the surface of graphite electrodes.

Equilibrium partitioning of HClO4 between aqueous solutions and benzonitrile (BN) or nitrobenzene (NB) was measured and used to evaluate the pKa of the acid in the two organic solvents. The potential drop across the BN/ H2O interface was evaluated from the known potential drop across the NB/H2O interface and the voltammetrically measured formal potential of a ferrocenium/ferrocene redox couple confined within thin layers of the two organic solvents. The voltammetric reduction of tetrachloro-1, 4-benzoquinone in thin layers of BN was used to monitor changes in the concentration of protons in the layer during proton-consuming faradaic reactions. The rate of proton transfer from the aqueous to the nonaqueous phase across the BN/H2O interface was shown to be adequate to sustain proton-consuming reactions at the electrode/BN interface.

Implementation of a continuous, enzyme-coupled fluorescence assay for high-throughput analysis of glutamate-producing enzymes.

Enzymatic formation of glutamate is critical to numerous biological pathways. However, current methods for assaying the activities of glutamate-forming enzymes are not particularly suitable for high-throughput screening in drug discovery. We present a continuous-read, fluorometric assay for high-throughput analysis of glutaminases. This assay is adapted to a microplate format and employs glutamate oxidase and horseradish peroxidase to couple glutamate formation to production of the fluorescent reporter molecule, resorufin, for enhancement of sensitivity (M. Zhou, Z. Diwu, N. Panchuk-Voloshina, and R. P. Haughland, 1997, Anal. Biochem. 253, 162-168). Described herein is the selection of suitable levels of coupling enzymes for optimal kinetic response and lag time of the reporter system, based on the kinetic characteristics of the individual coupling enzymes. Finally, implementation of the assay in a format for high-throughput kinetic analysis of glutaminases is demonstrated for Escherichia coli carbamoyl phosphate synthase. Derived kinetic constants are comparable to literature values determined using a variety of assay techniques.

Selective inhibition of bacterial dihydroorotate dehydrogenases by thiadiazolidinediones.

Dihydroorotate dehydrogenase is a critical enzyme of de novo pyrimidine biosynthesis in prokaryotic and eukaryotic cells. Differences in the primary structure of the enzymes from Gram-positive and -negative bacteria and from mammals indicate significant structural divergence among these enzymes. We have identified a class of small molecules, the thiadiazolidinediones, that inhibit prototypical enzymes from Gram-positive and -negative bacteria, but are inactive against the human enzyme. The most potent compound in our collection functioned as a time-dependent irreversible inactivator of the bacterial enzymes with k(inact)/K(i) values of 48 and 500 M(-1) sec(-1) for the enzymes from Escherichia coli and Enterococcus faecalis, respectively. The data presented here indicate that it is possible to inhibit prokaryotic dihydroorotate dehydrogenases selectively while sparing the mammalian enzyme. Thus, this enzyme may represent a valuable target for the development of novel antibiotic compounds.

Confirmation of primary active substances from high throughput screening of chemical and biological populations: a statistical approach and practical considerations.

Many biologically important substances are discovered through screening of relevant chemical or biological libraries. The ability to find the active substances ("hits") from any random collection is largely determined by the quality of the assay and screening conditions. When a large population is screened for a specific characteristic, each member of that population is usually tested only once. Errors in the measurements require additional follow-up tests to confirm that each hit from the primary screen is truly active. In this report, we present a statistical model system that predicts the reliability of hits from a primary test as affected by the error in the assay and the choice of the hit threshold (hit limit). The hit confirmation rate, as well as false positive (representing substances that initially fall above the hit limit but whose true activity are below the hit limit) and false negative (representing substances that initially fall below the hit limit but whose true activity are in fact greater than the hit limit) rates have been analyzed with this model by computational simulation. This model can also be used in screen validation and post-screening data analysis. The statistical analysis presented here has broad implications and is applicable to screening of any large population for any specific characteristic. Obvious applications include drug discovery, gene chip analysis, population biology, directed molecular evolution, biological panning, and combinatorial material sciences.

STAT3 mediates IL-6-induced neuroendocrine differentiation in prostate cancer cells .

BACKGROUND: In the human prostate cancer cell line LNCaP, interleukin (IL)-6 has been shown to regulate both growth and neuroendocrine (NE) differentiation. We recently observed that IL-6 mediated growth arrest in LNCaP by activating STAT 3. Since differentiation and growth arrest are often associated processes, we investigated whether STAT3 also mediated NE differentiation in this prostate cancer cell line. METHODS: We treated previously characterized clones LNCaP-neo (neomycin-resistant LNCaP) and LNCaP-SF (LNCaP-STAT3 dominant negative mutant) with IL-6 and screened for NE differentiation by observing morphological changes and immunoblotting for two NE markers, neuron-specific enolase (NSE) and chromogranin A (ChA). To characterize further the role of STAT3 in growth arrest and differentiation, we transfected a wild-type STAT3 vector into PC-3 cells and generated a subclone PC-3-S3. In this clone, we assessed differentiation by observing morphological changes and determined growth responses by cell counting and clonogenic assays. RESULTS: We observed that IL-6 induced formation of neurite extensions, morphologic features associated with NE differentiation, and enhanced expression of neuronal markers ChA and NSE in LNCaP-neo cells. In contrast, LNCaP-SF, possessing a dominant negative mutant form of STAT3, exhibited no characteristics of IL-6 induced NE differentiation. Furthermore, expression of a constitutively phosphorylated wild-type STAT3 in PC-3 cells inhibited growth and induced the formation of neurite extensions and NSE expression. CONCLUSIONS: These results indicate that STAT3 is a mediator of both NE differentiation and growth inhibition in LNCaP and PC-3, suggesting a connection between growth inhibition and NE differentiation in prostate cancer.

STAT3 mediates IL-6-induced growth inhibition in the human prostate cancer cell line LNCaP.

BACKGROUND: In prostate cancer, we and others have observed distinct phenotypic responses to interleukin-6 (IL-6), which acts either as a paracrine growth inhibitor in the LNCaP cell line or as an autocrine growth stimulator in PC-3, DU145, and TSU cell lines. To understand the underlying mechanism responsible for this phenotypic difference, we investigated differences in the IL-6-induced Janus kinase-signal transducers and activators of transcription (JAK-STAT) signal transduction pathway between these two phenotypes. METHODS: Prostate cancer cell lines were assayed for STAT3 activity by immunoblotting, electrophoretic gel shift assays (EMSA), and a luciferase reporter assay to test for STAT3 protein expression, phosphorylation, DNA binding, and transcriptional activity. To address the physiological role of STAT3, we introduced a dominant-negative mutant of STAT3 into LNCaP cells and assayed the effects of IL-6 on cell growth of this stable transfectant by cell counting, clonogenic assays, and c-myc expression. RESULTS: IL-6 induced transcriptional activity of STAT3 only in LNCaP. STAT3 was transcriptionally inactive in PC-3, TSU, and DU145 at the level of protein expression, tyrosine phosphorylation, and DNA binding/transcriptional activity, respectively. An isolated LNCaP subclone containing a dominant-negative mutant of STAT3, LNCaP-SF, did not show STAT3-DNA binding or transcriptional activity. LNCaP-SF exhibited a proliferative response to IL-6 as compared to the control LNCaP-neo clone, which underwent growth arrest. Unlike LNCaP-neo, LNCaP-SF was able form colonies and to maintain c-myc expression in the presence of IL-6. CONCLUSIONS: STAT3 transcriptional activation correlates with the growth-inhibitory signal of IL-6 in LNCaP, suggesting that STAT3 transcriptional activity is an important determinant in the different phenotypic responses to IL-6 in prostate cancer.

Interleukin-6 activates phosphatidylinositol-3 kinase, which inhibits apoptosis in human prostate cancer cell lines.

BACKGROUND: A number of recent studies have identified interleukin (IL)-6 as an important regulator of prostate cancer growth. Here, we investigate the potential interaction of IL-6 with phosphatidylinositol (PI)-3 kinase, a key growth regulatory enzyme, in prostate cancer cell lines. METHODS: Tyrosine phosphorylation of p85, the regulatory subunit of PI-3 kinase, in the human prostate cancer cell lines LNCaP and PC-3 was assessed by sequential immunoprecipitation with anti-p85 antibody and immunoblotting with anti-phosphotyrosine. The effects of wortmannin, an inhibitor of PI-3 kinase, and/or IL-6 on cell growth were assessed by MTT assays. DNA laddering experiments were performed to assay for programmed cell death. RESULTS: Tyrosine phosphorylation of p85 is upregulated by IL-6 in both LNCaP and PC-3. IL-6 promotes coprecipitation of p85 with gp130, the signal-transducing component of the IL-6 receptor. Inhibition of PI-3 kinase with wortmannin induces programmed cell death in PC-3 cells. In contrast, wortmannin has no effect on LNCaP growth when used alone; however, combined with IL-6, wortmannin promotes apoptosis in these cells. CONCLUSIONS: PI-3 kinase is involved in IL-6 signal transduction and delivers an antiapoptotic signal in human prostate cancer cell lines.

Development of a carbon dioxide-capture assay in microtiter plate for aspartyl-beta-hydroxylase.

CO2-capture methods have been used for assaying many decarboxylating enzymes including hydroxylation-coupled decarboxylation reactions. The traditional CO2-capture method involves performing the reaction in capped tubes and radiometric measurement of trapped 14CO2 by scintillation counting. In this report, a 14CO2-capture method in a 96-well microtiter plate format has been developed and a phosphor imaging system has been employed for sample measurement. The new assay method has been used successfully to assay aspartyl-beta-hydroxylase activity in microtiter plate format. The results obtained here compare favorably with those obtained from the traditional tube method. The method is sensitive, suitable for high throughput, and generally applicable to many CO2-releasing enzyme assays.

Characterization of the role of IL-6 in the progression of prostate cancer.

BACKGROUND: We recently identified IL-6, a pleiotropic cytokine implicated in the neoplastic process of a variety of neoplasms, as a mediator of prostate cancer morbidity. In the present study, we investigated the expression of members of the IL-6 supergene family and related cytokines and the potential role of IL-6 in prostate cancer growth regulation. METHODS: Five established human prostate cancer cell lines were screened by ELISA for production of granulocyte colony-stimulating factor (G-CSF), leukemia inhibitory factor (LIF), ciliary neurotrophic factor (CNTF), oncostatin M (OSM), tumor necrosis factor (TNF), interleukin-1 (IL-1), and granulocyte macrophage colony-stimulating factor (GM-CSF). Expression of the ligand-binding component of the IL-6 receptor, IL-6Rp80, was evaluated by ELISA and RT-PCR. Sequential immunoprecipitation and immunoblotting were performed to assay for expression of the signal-transducing component of the IL-6 receptor, gp130. The effects of IL-6 on cell growth were assessed by MTT assays. RESULTS: The three hormone-refractory cell lines, DU-145, TSU, and PC-3, secreted distinct combinations of cytokines (DU-145: IL-6, GM-CSF; TSU: IL-6, LIF; PC-3: IL-6, G-CSF, LIF, IL-1, GM-CSF), each uniformly expressing IL-6. In contrast, neither of the two hormone-dependent cell lines, LNCaP-ATCC and LNCaP-GW, secreted significant quantities of any of the cytokines analyzed. None of the cell lines secreted detectable quantities of OSM, CNTF, or TNF. All cell lines, irrespective of hormone status, expressed both Il-6Rp80 and gp130. Addition of IL-6 in vitro inhibited growth of hormone-dependent cells, but had no effect on hormone-refractory lines. Anti-IL-6 neutralizing antibody inhibited growth of hormone-refractory cells. CONCLUSIONS: IL-6 appears to undergo a functional transition from paracrine growth inhibitor to autocrine growth stimulator during progression of prostate cancer to the hormone-refractory phenotype.