A high-throughput screening procedure for identifying mice with aberrant taste and oromotor function

Little is known about how specific genes influence taste function in mammals. One of the most promising ways to fill this void is to screen the progeny of chemically mutagenized (or genetically altered) mice for aberrant taste phenotypes and then identify the mutated gene(s) that is associated with each taste anomaly. To exploit this approach, a high-throughput and robust screening procedure is needed. We have attempted to meet this demand by developing an automated procedure that assesses taste responsiveness of individual mice to palatable and unpalatable taste stimuli. We focused on three taste stimuli (quinine hydrochloride, QHCl; sodium chloride, NaCl; and sucrose) and one mouse strain (C57BL/6). We used a commercially available gustometer system that both monitors the licking responses of mice and controls the presentation of each taste stimulus during successive 5 s trials. We describe a screening procedure that (after 2 days of simple training) can generate a concentration-response curve for NaCl or sucrose during a single 30 min test session, and for QHCl over three 30 min test sessions. A normative database based on the responses of 98 mice subjected to our screening procedure is also presented. We envision that investigators could use this normative database to assess taste function in the progeny of mutagenized (or genetically altered) mice. Any mouse that deviates significantly-e.g. three standard deviations (SD)-from the mean of the normative database would be flagged as having a potentially interesting mutation. We also developed an additional second screen for identifying mice with oromotor abnormalities. This latter screen is necessary because oromotor problems could lead to false positives or negatives in the screen for taste function, but is also useful for researchers interested in genes influencing oromotor circuitry. Throughout the development of the screening protocol, we sought to balance two conflicting demands: the need to maximize the screen's sensitivity and minimize its duration. This screen represents a significant improvement over the common two-bottle preference test because it assesses taste function more specifically and in a fraction of the time.     

A procedure for identifying homologous alternative splicing events

Background  

The study of the functional role of alternative splice isoforms of a gene is a very active area of research in biology. The difficulty of the experimental approach (in particular, in its high-throughput version) leaves ample room for the development of bioinformatics tools that can provide a useful first picture of the problem. Among the possible approaches, one of the simplest is to follow classical protein function annotation protocols and annotate target alternative splice events with the information available from conserved events in other species. However, the application of this protocol requires a procedure capable of recognising such events. Here we present a simple but accurate method developed for this purpose.     

A simple screening procedure for adenylate kinase, hexokinase and glucose-6-phosphate dehydrogenase deficiencies

A simple screening procedure for the detection of adenilate kinase (AK), hexokinase (Hx) or glucose-6-phosphate dehydrogenase (G6PD) deficiencies in blood, is described. It consists of two assays : in the first, the ATP formed by blood AK is coupled to Hx and G6PD, and in the second, the glucose-6-phosphate formed by blood Hx is coupled to G6PD. The enzyme activities are visually estimated by the reduction of NADP+ (non-fluorescent) to NADH (fluorescent). The appearance of fluorescence in the first assay indicates that the three enzyme activities are present. The absence of fluorescence could be due to the deficiency of any one of the three enzymes; in this case the second assay used in combination with the Beutler's screening test for G6PD permits the detection of the specific enzymatic deficiency.     

A rapid screening procedure for staphylococcal plasmids

A method has been developed for rapidly screening representatives of all currently recognized species of the genus Staphylococcus for the presence of plasmid DNA. The isolated plasmid DNA is substantially free from contaminating chromosomal and relaxed plasmid DNA. The method will detect plasmids in strains grown on various types of solid or liquid culture media and is convenient enough for routine epidemiological studies.     

Effector-dependent conformational changes in protein kinase C gamma through epitope mapping with inhibitory monoclonal antibodies.

Three monoclonal antibodies (mAb) directed against the regulatory domain of the protein kinase C gamma (PKC gamma); 15G4, 5A2 and 36G9, were shown to display distinct properties with respect to PKC gamma kinase activity [Cazaubon, S., Marais, R., Parker, P. & Strosberg, A.D. (1989) Eur. J. Biochem. 182, 401-406]. The mAb 5A2 and 36G9, which act as potent inhibitors of the cofactor-dependent kinase activity, can no longer bind PKC gamma in the presence of phosphatidylserine and phosphatidylserine/phorbol ester, respectively; 15G4 binding is not influenced by effectors. Due to this functional relationship between the inhibitory mAb- and cofactor-binding sites, we sought to localize the mAb epitopes with respect to the functional sites of PKC gamma. For this purpose, several deletions were introduced at the 5' end of the PKC gamma cDNA and the mutant proteins were expressed in Escherichia coli. The determination of the immunoreactivity of the deleted PKC gamma proteins shows that the amino acid residues essential to the binding of 5A2 and 36G9 are directly adjacent to the second cysteine-rich motif: these are contained in the sequences at positions 151-163 and 164-197, respectively. In addition, various deletions around the C1 region of the regulatory domain allowed the identification of the second cysteine-rich motif as a functional binding site for phorbol dibutyrate. These deletion studies thus demonstrate that the epitopes recognized by the inhibitory mAbs 5A2 and 36G9 are distinct from the cofactor-binding sites. This suggests that the binding of phosphatidylserine and phorbol ester induce conformational changes in the regulatory domain of PKC, which are thus responsible for the loss of the 5A2 and 36G9 immunoreactivity of the native protein. In this conformational state, PKC gamma conserves its ability to interact with the non-inhibitory mAb 15G4. By using synthetic peptides, the 15G4 epitope was localized to the sequence 297-310 in the V3 variable region. This indicates that the flexibility of the V3 region, which delimits the C-terminus of the regulatory domain, may not be necessary for the allosteric activation of PKC. In view of these results, we propose that PKC activation by its cofactors results in intramolecular changes which allow the enzyme to bind exogenous substrates.     

A rapid screening test for HIV-1 antibodies: application to biological studies on human tissue

Human umbilical cord vessels are commonly used as a source of human vascular tissue for physiological studies and as a source of endothelial and smooth muscle cells. Blood samples from 236 umbilical cords were tested for the presence of HIV-1 antibodies to access the prevalence of HIV-1 infection and to evaluate possible methods for screening umbilical cords. Ten of the 236 samples were HIV-1 antibody positive by ELISA whereas 3 were positive by Western blot and a new method, the Quick-Western blot. Two of the 3 positive samples contained antibody bands against gp160, gp120, gp41, and p24 HIV-1 proteins, and one sample had antibodies against only gp160, gp120 and gp41. The Quick-Western blot required only 45 minutes for the analysis while the ELISA and Western blot took 3 hours and 18 hours, respectively. These data indicate that HIV-1 infection in mothers may present a hazard to researchers using human umbilical cords as a source of vascular tissue. The Quick-Western blot method is a simple, portable, rapid and accurate method that may be used to screen blood. The short analysis time of the Quick-Western blot allows the identification of infected blood before the tissue deteriorates as a source of cells or vascular tissue for experimental studies.     

A cell based screening approach for identifying protein degradation regulators

Cellular transitions are achieved by the concerted actions of regulated degradation pathways. In the case of the cell cycle, ubiquitin mediated degradation ensures unidirectional transition from one phase to another. For instance, turnover of the cell cycle regulator cyclin B1 occurs after metaphase to induce mitotic exit. To better understand pathways controlling cyclin B1 turnover, the N-terminal domain of cyclin B1 was fused to luciferase to generate an N-cyclin B1-luciferase protein that can be used as a reporter for protein turnover. Prior studies demonstrated that cell-based screens using this reporter identified small molecules inhibiting the ubiquitin ligase controlling cyclin B1-turnover. Our group adapted this approach for the G2-M regulator Wee1 where a Wee1-luciferase construct was used to identify selective small molecules inhibiting an upstream kinase that controls Wee1 turnover. In the present study we present a screening approach where cell cycle regulators are fused to luciferase and overexpressed with cDNAs to identify specific regulators of protein turnover. We overexpressed approximately 14,000 cDNAs with the N-cyclin B1-luciferase fusion protein and determined its steady-state level relative to other luciferase fusion proteins. We identified the known APC/C regulator Cdh1 and the F-box protein Fbxl15 as specific modulators of N-cyclin B1-luciferase steady-state levels and turnover. Collectively, our studies suggest that analyzing the steady-state levels of luciferase fusion proteins in parallel facilitates identification of specific regulators of protein turnover.     

A protein kinase C inhibitory activity is present in rat brain homogenate

The partial purification and characterization of (a) factor(s) from rat brain which inhibit(s) the activity of calcium and phospholipid-dependent protein kinase from the same tissue is described. This factor, present in 100 000 X g rat brain homogenate supernatant, is inactivated upon treatment by trypsin and pepsin and is therefore assumed to be a protein. It was partially purified by ion-exchange chromatography on DEAE-cellulose, ammonium sulfate precipitation and gel filtration. This inhibitor is not stable to heating at 70 degrees C for 10 min, however partial renaturation of the inhibitory activity can be observed after incubation of the denatured inhibitor for 24 h at 4 degrees C. It is precipitable by 10% trichloroacetic acid and by 2 M ammonium sulfate. It exhibits a Stokes radius of 20 A by gel exclusion chromatography, corresponding to a molecular mass of 20 kDa assuming a globular shape. Kinetic analysis of the inhibition of calcium-phospholipid-dependent histone kinase activity indicates that the inhibitor is competitive with respect to the protein substrate. No change was observed in the kinetic values of the kinase for ATP, Ca2+ and phospholipids.     

A complete system for identifying inhibitors of creatine kinase B

We have developed a complete system for discovery of lead compounds as inhibitors of creatine kinase B. In this article, we describe production and purification of the recombinant protein, conditions and features of an optimized high-throughput screening assay, and results of our implementation of the system using a diverse compound library.     

A general method for the induction and screening of antisera for cDNA-encoded polypeptides: antibodies specific for a coronavirus putative polymerase-encoding gene

A prokaryotic vector, pGE374, containing the recA and lacZ genes, out-of-frame, was used for the expression of cDNA derived from the putative polymerase-encoding gene of the coronavirus mouse hepatitis virus strain A59 (MHV-A59). The pGE374/viral recombinant vector generates a tripartite bacterial/viral protein composed of a segment of the RecA protein at the N terminus, the coronaviral sequences in the middle, and an enzymatically active beta-galactosidase at the C terminus. Rabbits immunized with such recombinant proteins generated antibodies to the MHV-A59 portion of the tripartite protein. Because the MHV-A59 polymerase proteins have been difficult to identify during infection, we used a novel method to demonstrate the viral specificity of the antiserum. The viral cDNA was excised from the expression vector, and transferred to a pGem vector, downstream from and in-frame with a portion of the cat gene. This construct contained a bacteriophage RNA polymerase promoter that enabled the cell-free synthesis of a fusion protein that was used to verify that antibodies were generated to the expressed viral DNA. This strategy was shown to successfully result in the specific generation of antibodies to the encoded information of the viral cDNA. Furthermore, this method has general applicability in the generation and characterization of antibodies directed against proteins encoded in cDNAs.     

A quantitative mass spectrometry-based approach for identifying protein kinase clients and quantifying kinase activity

The Homo sapiens and Arabidopsis thaliana genomes are believed to encode more than 500 and 1000 protein kinases, respectively. Despite this abundance, few bona fide kinase-client relationships have been described in detail. Here we describe a quantitative mass spectrometry (MS)-based approach for identifying kinase-client proteins. During method development, we used the dedicated kinase pyruvate dehydrogenase kinase (PDK) for the in vitro assays. As kinase substrate, we used synthetic peptide cocktails and, in the process, demonstrated that the assay is both sensitive and specific. The method is also useful for characterizing protein kinase-substrate kinetics once the peptide substrate is detected. Applying a label-free spectral counting method, the activity of PDK was determined using the peptide substrate YHGH²⁹²SMSDPGSTYR derived from the pyruvate dehydrogenase E1α subunit sequence. The utility of spectral counting was further validated by studying the negative effect of Met oxidation on peptide phosphorylation. We also measured the activity of the unrelated calcium-dependent protein kinase 3 (CPK3), demonstrating the utility of the method in protein kinase screening applications.     

A rapid procedure for the humanization of monoclonal antibodies

An efficient and rapid procedure for the humanization of murine monoclonal antibodies (MumAb) is described. It consists of site-directed mutagenesis (SDM) to transfer the murine complementarity-determining regions (MuCDR) onto human framework regions (HuFR), followed by polymerase chain reaction (PCR) of the SDM product. Using SDM/PCR, rapid and correct humanization of MumAb heavy chains is clearly demonstrated. Compared to current protocols this method considerably reduces the time and labour required to generate humanized mAb.     

A cell-based ultra-high-throughput screening assay for identifying inhibitors of D-amino acid oxidase

Enzymes are often considered less "druggable" targets than ligand-regulated proteins such as G-protein-coupled receptors, ion channels, or other hormone receptors. Reasons for this include cellular location (intracellular vs. cell surface), typically lower affinities for the binding of small molecules compared to ligand-specific receptors, and binding (catalytic) sites that are often charged or highly polar. A practical drawback to the discovery of compounds targeting enzymes is that screening of compound libraries is typically carried out in cell-free activity assays using purified protein in an inherently artificial environment. Cell-based assays, although often arduous to design for enzyme targets, are the preferred discovery tool for the screening of large compound libraries. The authors have recently described a novel cell-based approach to screening for inhibitors of a phosphatase enzyme and now report on the development and implementation of a homogeneous 3456-well plate assay for D-amino acid oxidase (DAO). Human DAO was stably expressed in Chinese hamster ovary (CHO) cells, and its activity was measured as the amount of hydrogen peroxide detected in the growth medium following feeding the cells with D-serine. In less than 12 weeks, the authors proved the concept in 96-and then 384-well formats, miniaturized the assay to the 3456-well (nanoplate) scale, and screened a library containing more than 1 million compounds. They have identified several cell-permeable inhibitors of DAO from this cell-based high-throughput screening, which provided the discovery program with a few novel and attractive lead structures.     

Substrate activity screening (SAS): a general procedure for the preparation and screening of a fragment-based non-peptidic protease substrate library for inhibitor discovery

Substrate activity screening (SAS) is a fragment-based method for the rapid development of novel substrates and their conversion into non-peptidic inhibitors of Cys and Ser proteases. The method consists of three steps: (i) a library of N-acyl aminocoumarins with diverse, low-molecular-weight N-acyl groups is screened to identify protease substrates using a simple fluorescence-based assay; (ii) the identified N-acyl aminocoumarin substrates are optimized by rapid analog synthesis and evaluation; and (iii) the optimized substrates are converted into inhibitors by direct replacement of the aminocoumarin with known mechanism-based pharmacophores. This protocol describes a general procedure for the solid-phase synthesis of a library of N-acyl aminocoumarin substrates and the screening procedure to identify weak binding substrates.