A new evaluation method for quantifying PI3K activity by HTRF assay

PIK3CA, coding a catalytic subunit of PI3K p110α, is frequently mutated in cancer. In previous studies, p110α with hotspot mutations such as E545K and H1047R were shown to be gain-of-function mutations. However, quantitative evaluation of these mutants was not well established. Recently, a new method for measuring PI3K activity using homogeneous time-resolved fluorescence (HTRF) has been developed. Using this method, we constructed a quantitative evaluation system for PI3K activity. Serial dilutions of standard PIP3 were subjected to the PI3K-HTRF assay in order to establish a regression line for calibration. The recombinant FLAG-tagged p110α proteins were engineered together with a regulatory subunit p85α in human embryonic kidney 293T cells. Anti-FLAG-Ig immunoprecipitates were then subjected to the assay, which enabled us to quantitatively evaluate the activities of hotspot mutants of p110α. We believe this method will also be applicable to the evaluation of p110α having uncharacterized mutations found in cancer.     

Solid-liquid interface method (SLIM): A new crystallization method for proteins

Despite impressive advances in theories, methods and technologies, crystallization still remains a serious bottleneck in structural determination of macromolecules. Here we present a novel solid-liquid interface method (SLIM) for protein crystallization, based on the pre-adding and drying of a crystallization reagent, and thereafter the dispensing of a protein solution to the dried media to initiate crystallization from the solid-liquid interface. Not only quick and easy to perform, the method also allows for a less concentrated protein solution for setting up crystallization trials.     

A universal method for automated gene mapping

Small insertions or deletions (InDels) constitute a ubiquituous class of sequence polymorphisms found in eukaryotic genomes. Here, we present an automated high-throughput genotyping method that relies on the detection of fragment-length polymorphisms (FLPs) caused by InDels. The protocol utilizes standard sequencers and genotyping software. We have established genome-wide FLP maps for both Caenorhabditis elegans and Drosophila melanogaster that facilitate genetic mapping with a minimum of manual input and at comparatively low cost.     

A universal method for automated gene mapping

Small insertions or deletions (InDels) constitute a ubiquituous class of sequence polymorphisms found in eukaryotic genomes. Here, we present an automated high-throughput genotyping method that relies on the detection of fragment-length polymorphisms (FLPs) caused by InDels. The protocol utilizes standard sequencers and genotyping software. We have established genome-wide FLP maps for both Caenorhabditis elegans and Drosophila melanogaster that facilitate genetic mapping with a minimum of manual input and at comparatively low cost.     

Universal fluorescent labeling (UFL) method for automated microsatellite analysis.

We have devised a novel method for automated microsatellite analysis using "universal" fluorescent labeling. This system is based on polymerase chain reactions driven by sequence-specific primers and a reporter primer labeled with a fluorescent dye at its 5' end. The forward sequence-specific primer is designed with a tag region bearing no homology to any human genomic sequence. Complementary tag sequences act as templates for the 6-carboxyfluorescein-labeled reporter primer, and those products can be analyzed with an autosequencer. The results we achieved with this assay system were consistent with the results of conventional assays using radioisotope-labeled primers, and diagnosis required less time. Furthermore, the fluorescent-labeled reporter primer is "universal" in that it can be used with different sequence-specific primers designed to carry the appropriate tag sequence at their 5'-ends. Our observations suggest that the "universal" fluorescent labeling method is an efficient tool for analyzing sequence variations in human DNA.     

Rapid automated multichannel microspectrofluorometry : A new method for studies on the cell-to-cell transfer of molecules

A new microchemical method is described to study the transfer of molecules between neighboring cells: rapid multichannel microfluorometry. The cell-to-cell transfer rates of metabolites or fluorescent tracers (microinjected by a microelectrophoretic or piezoelectric technique) are followed at pace with the in situ velocities of such processes via multisite topographic monitoring of fluorescence in injected cell and neighbors (continuously before, during and after microinjection). Furthermore, the sensitivity of the method allows the kinetic study of cell-to-cell transfer using metabolites (e.g., glucose-6-P) which are not fluorescent themselves, but which elicit associated changes in the redox state of endogenous fluorochromes, i.e. NAD(P) NAD(P)H transients.Since the cell-to-cell transfer of chemicals is known to proceed in various cells and tissues via intercellular junctions, the above technique was applied to a known coupled system (e.g. Chironomus salivary gland) and an uncoupled system (e.g. L cells). The cell-to-cell transfer of fluorescein was observable kinetically in Chironomus salivary glands, liver, Chang liver and Chang conjunctiva cultures. Equilibration of the dye between injected cell and neighbor was completed within a few hundred msec to a few sec, corresponding to an intercellular half total flux per unit concentration difference (g_f) of ˜2–10 × 10⁴ μm³/min. Such transfer was practically basent or a rare occurrence in L cells. In NCTC 8739 and L cells, the cell-to-cell transfer of glucose-6-P seemed to occur more frequently than that of fluorescein, suggesting the possibility that glucose-6-P (or a catabolite) may move through non-junctional regions of the cell membrane. Thus multichannel microfluorometry makes possible the study of tracer or metabolite transfer, without the need for multiple implantation of electrodes and with more kinetic detail than obtainable by other tracer techniques.     

A new method for isolation of S-adenosylmethionine (SAM)-accumulating yeast

S-Adenosylmethionine (SAM) is an important metabolite that participates in many reactions as a methyl group donor in all organisms, and has attracted much interest in clinical research because of its potential to improve many diseases, such as depression, liver disease, and osteoarthritis. Because of these potential applications, a more efficient means is needed to produce SAM. Accordingly, we developed a positive selection method to isolate SAM-accumulating yeast in this study. In Saccharomyces cerevisiae, one of the main reactions consuming SAM is thought to be the methylation reaction in the biosynthesis of ergosterol that is catalyzed by Erg6p. Mutants with deficiencies in ergosterol biosynthesis may accumulate SAM as a result of the reduction of SAM consumption in ergosterol biosynthesis. We have applied this method to isolate SAM-accumulating yeasts with nystatin, which has been used to select mutants with deficiencies in ergosterol biosynthesis. SAM-accumulating mutants from S. cerevisiae K-9 and X2180-1A were efficiently isolated through this method. These mutants accumulated 1.7–5.5 times more SAM than their parental strains. NMR and GC-MS analyses suggested that two mutants from K-9 have a mutation in the erg4 gene, and erg4 disruptants from laboratory strains also accumulated more SAM than their parental strains. These results indicate that mutants having mutations in the genes for enzymes that act downstream of Erg6p in ergosterol biosynthesis are effective in accumulating SAM.     

A new evaluation method for +Gz tolerance with loratadine by using a near-infrared spectroscopy

Background

Loratadine (Claritin^®), an over the counter antihistamine in U.S. and UK, is acceptable for use without adverse side effects by aircrew with mild or moderate allergic or other situations requiring an antihistamine. Although +Gz (head to foot direction) tolerance testing for aircrew with loratadine has not been documented in the published literature, it is commonly accepted that loratadine dose not effect +Gz tolerance. The purpose of this study was to offer and validate a new evaluation method for +Gz tolerance testing with loratadine by using a near-infrared spectroscopy (NIRS).

Methods

A double-blind, placebo-controlled, randomized, crossover protocol was used to administer 10 mg of loratadine or placebo in nine healthy subjects. The subjects didn't wear anti-G suit. The +Gz exposure profiles consisted of, in series, a gradual onset ran (0.1 G·sec^-1) to the subject's visual end-point (peripheral light loss) or loss of consciousness (GLOC), and rapid onset run (1.0 G·sec^-1) to the subject's same end-point. In this study, G-level tolerance was defined as the +Gz level at visual end-point and/or at GLOC. As a subject's G-duration tolerance, we measured the total time (seconds) during rapid onset run. Otherwise, to confirm the effect of loratadine on +Gz tolerance, we measured the cerebral NIRS variables (hemoglobin concentration changes and tissue oxygenation index) as a new quantitative method for +Gz tolerance during a centrifuge experiments.

Results

No significant differences were observed in +Gz tolerance (+Gz level, duration time and NIRS variables) between subjects taking loratadine and placebo.

Conclusion

Our results demonstrate that loratadine has no detectable effect on +Gz tolerance by using a new method with cerebral NIRS variables and the traditional method with +Gz level and duration time. This study represents the first use of a quantitative parameter such as cerebral NIRS variables to assess the effects of a drug on acceleration tolerance.

     

A method for the rapid automated assessment of olfactory function

We have developed a strategy for the rapid high-throughput screening of odor responsivity in genetically altered mice (in fact, any experimentally altered animal). Specifically, the report presents the development and validation of a fully automated procedure based on the evaluation of an animal's stimulus-induced reflexive breathing response (i.e. sniffing behavior) to both air and odorant stimuli. The method requires no training of the animal to be screened and the outcome of the evaluation yields an operationally defined measure. Briefly, using whole-body plethysmography, the procedure determines the numerical values for a set of 14 respiratory measures in response to the presentation of air and a well-above-threshold concentration of the odorant propanol. These measures of stimulus-induced sniffing are incorporated into a model that defines a single univariate measure of response behavior, or 'Sniffing Index', for each screened animal. The approach significantly discriminated between the reflexive sniffing response of a control group of mice and that of an experimentally defined manipulated group for which, a priori, we expected to observe a robust altered breathing response to odorant stimulation (i.e. non-odor-aversion-conditioned versus odor-aversion-conditioned C57BL/6J mice). Further, the procedure was able to significantly discriminate between a mutant phenotype with documented alterations in physiologic and behavioral function (namely, the OMP-null mutant), and their background strain. In addition, applying epidemiologic screening principles to the observed data, we established an operational procedure for the evaluation of unknown animals.     

A convenient automated method for the determination of proteolytic enzymes

An automated method for the assay of proteolytic enzymes is described. The insoluble dye-protein complex, Remazolbrilliant Blue-hide powder, is used as the substrate and is readily digested by trypsin, elastase, subtilisin, thermolysin, chymotrypsin, and to a lesser extent pronase, pepsin, and bacterial collagenase. The proteolytic activity of crude microbial culture preparations is expressed in terms of an equivalent concentration of crystalline trypsin, which itself can be readily determined within the concentration range 0.25–5.0 μg/ml.     

A new method for evaluation of cavitation near mechanical heart valves

Evaluation of cavitation in vivo is often based on recordings of high-pass filtered random high-frequency pressure fluctuations. We hypothesized that cavitation signal components are more appropriately assessed by a new method for extraction of random signal components of the pressure signals. We investigated three different valve types and found a high correlation between the two methods (r2: 0.8806-0.9887). The new method showed that the cavitation signal could be extracted without a priori knowledge needed for setting the high-pass filter cut off frequency, nor did it introduce bandwidth limitation of the cavitation signal.     

A new method for oligo(ADP-ribose) fractionation according to chain length

A new method was developed to separate mono- and oligo-(ADP-ribose) with chain lengths below 11 ADP-ribose units by size difference of one ADP-ribose residue. The separation was performed on a DEAE-cellulose column by elution with a NaCl gradient (0–0.3 $\text{M}$) in the presence of 7 $\text{M}$ urea at pH 7.6. Using this method, the chain length distribution of oligo(ADP-ribose) molecules attached to histones by incubation of isolated nuclei with radioactive NAD was determined. The average chain length estimated from this distribution coincided exactly with the value obtained by the phosphodiesterase digestion method, suggesting that the oligomers were synthesized directly on histones and not elongated from pre-existing ADP-ribose.     

A new method for the rapid evaluation of gas vacuoles regeneration and viability of cyanobacteria by flow cytometry

Flow cytometric analysis for measuring gas vacuole regeneration and viability of cyanobacteria was developed. This novel approach distinguished between cyanobacteria with intact and collapsed gas vacuoles. By this method, sonicated cyanobacteria under illuminated conditions were shown to regenerate their gas vacuoles to the level of the untreated cells within 1–3 days. Ultrasonically treated cyanobacteria cultured under non-aerated and non-illuminated conditions did not regenerate their gas vacuoles. Combined with dual staining, viable and non-viable cyanobacteria are easily and rapidly quantified or enumerated by measuring the intensity of red fluorescence and green fluorescence. A high correlation was found between the numbers of viable and non-viable cyanobacteria with flow cytometric measurement.     

A new statistical method for evaluation of L5178Ytk(+/-) mammalian cell mutation data using microwell method

A statistical method to evaluate data from the mouse lymphoma L5178Y/tk assay (MLA) using microwell method is proposed. This proposed method is designed for data obtained from a single culture protocol instead of the duplicate culture recommended by United Kingdom Environmental Mutagen Society (UKEMS). The proposed method consists of the following three steps: (1) to apply Dunnett type test for identifying clear negative; (2) to apply a Simpson-Margolin procedure for detecting downturn data; and (3) to apply a trend test to evaluate the dose-dependent increase in mutant frequency (MF). The performance of the proposed method was evaluated through a Monte Carlo study and a case study. False positive rates realized in the Monte Carlo study were comparable with the UKEMS method modified for a single culture protocol with the heterogeneity factors being kept at 1.0. False negative rates were less than those of the modified UKEMS method for dose response patterns with a sharp uprise in higher dose groups, whereas, they were comparable for other patterns. The results of evaluating the data from an International Collaborative Study by the proposed method seem comparable with the UKEMS method. The proposed method enables us to evaluate data from the microwell MLA with a single culture protocol.     

A sensitive automated method for adenosine triphosphatase kinetics.

An automated method for measuring adenosine triphosphatase (ATPase) activity is described. A modified version of a Technicon Autoanalyzer utilizing a sensitive colourimetric technique for determining inorganic phosphate concentrations (1 nmol/ml) allows investigations on enzymes of low specific activities. Dialysis may be used for measuring tissue homogenate activities or bypassed by examining purified enzyme preparations. When combined with a gradient apparatus, the proposed technique is particularly well suited for the study of enzyme kinetics in relation to cation or anion concentrations.     

A method for the rapid,automated filtration of protein hydrolyzates

A method for the automated filtration of protein hydrolyzates prior to amino acid analysis is described. Minor modification of a Technicon Sampler II enables it to function simultaneously as a sampler and a filtrate collector. Samples are drawn from cups in the sampler tray and are forced through a Teflon filter (pore size, 0.2 μm) in a Millipore Swinnex filter holder by a variable-speed Technicon proportioning pump. The filtrates are collected in cups in the sampler tray opposite those containing unfiltered hydrolyzates. Using this technique, 12 hydrolyzates can be filtered in 25 min compared to the approximately 2 h of technician time required for their manual filtration. Aliquots from each of 48 samples representing different proteins and hydrolysis conditions are filtered manually and by the automated technique. Analysis of variance of the resulting recoveries of each amino acid indicate little likelihood of effects due to filtration method.     

Microbleed detection using automated segmentation (MIDAS): a new method applicable to standard clinical MR images

Background

Cerebral microbleeds, visible on gradient-recalled echo (GRE) T2* MRI, have generated increasing interest as an imaging marker of small vessel diseases, with relevance for intracerebral bleeding risk or brain dysfunction.

Methodology/Principal Findings

Manual rating methods have limited reliability and are time-consuming. We developed a new method for microbleed detection using automated segmentation (MIDAS) and compared it with a validated visual rating system. In thirty consecutive stroke service patients, standard GRE T2* images were acquired and manually rated for microbleeds by a trained observer. After spatially normalizing each patient''s GRE T2* images into a standard stereotaxic space, the automated microbleed detection algorithm (MIDAS) identified cerebral microbleeds by explicitly incorporating an “extra” tissue class for abnormal voxels within a unified segmentation-normalization model. The agreement between manual and automated methods was assessed using the intraclass correlation coefficient (ICC) and Kappa statistic. We found that MIDAS had generally moderate to good agreement with the manual reference method for the presence of lobar microbleeds (Kappa = 0.43, improved to 0.65 after manual exclusion of obvious artefacts). Agreement for the number of microbleeds was very good for lobar regions: (ICC = 0.71, improved to ICC = 0.87). MIDAS successfully detected all patients with multiple (≥2) lobar microbleeds.

Conclusions/Significance

MIDAS can identify microbleeds on standard MR datasets, and with an additional rapid editing step shows good agreement with a validated visual rating system. MIDAS may be useful in screening for multiple lobar microbleeds.     

A new method of evaluation of the masticatory function in humans

A method is proposed to estimate mastication by three indices: chewing effect, chewing performance, chewing efficiency. Definitions are given for these terms. A new chewing test is described, permits studying the influence of the number of chewing strokes, chewing force and volume of test portion on the mastication using a group of 25 dentate persons aged 17-25 years with class I occlusion. A new approach to the estimation of chewing efficiency changes traditional views. A strong positive correlation is first found between chewing effect (A) and integrated bioelectrical activity (J) of chewing muscles with the constant number of chewing strokes. A relation between A and J is established when the number of chewing strokes increases.     

A new method for the assay of poly(adenosine diphosphate ribose) glycohydrolase activity.

Poly(adenosine diphosphate ribulose) [poly(ADP-Rib)] glycohydrolase activity was determined by measuring the amount of ADP-Rib hydrolyzed from polymers of ADP-Rib as substrate. In principle, the method consists of incubating oligomers or polymers of [¹⁴C]ADP-Rib with testis glycohydrolase. The reaction was stopped by the addition of a suspension of Dowex 1X-2 formate in H₂O (1:3, $\text{v}\text{v}$) which adsorbed monomers and oligomers of ADP-Rib. The adsorbed [¹⁴C]ADP-Rib was selectively extracted from the resin with 6 m formic acid. The amount of [¹⁴C]ADP-Rib was estimated by measuring the radioactivity in aliquots of formic acid extract. Oligomers or polymers of ADP-Rib can be utilized as substrates since the reaction rates were the same with either compound.A method to determine phosphodiesterase and glycohydrolase activities was established. These two enzymic activities were distinguished by treating the products of the reactions with alkaline phosphatase and by differential extraction of the adsorbed reaction products on Dowex with 0.5 m and 6 m formic acid.