Generation of biochemical response patterns of different substances using a whole cell assay with multiple signaling pathways

Distinctive generation of biochemical response patterns of eight different substances, using an assay based on pigment containing cells, was demonstrated. Xenopus laevis melanophores, transfected with human beta(2)-adrenergic receptor, were seeded in a 96 well microplate and used to generate individual biochemical images through a two transient measuring protocol that contributes to highlight the response signatures of the agents. Adequate signal processing creates distinctive patterns in a time-concentration response space suitable for substance classification. The concept of biochemical images is introduced here. The assays were evaluated both with a standard microplate reader and with a computer screen photo-assisted technique (CSPT) yielding similar results. Since CSPT platforms only demand standard computer sets and web cameras as measuring setup, applications for these kind of assays outside main-laboratories were discussed.     

Microplate based biosensing with a computer screen aided technique

Melanophores, dark pigment cells from the frog Xenopus laevis, have the ability to change light absorbance upon stimulation by different biological agents. Hormone exposure (e.g. melatonin or alpha-melanocyte stimulating hormone) has been used here as a reversible stimulus to test a new compact microplate reading platform. As an application, the detection of the asthma drug formoterol in blood plasma samples is demonstrated. The present system utilizes a computer screen as a (programmable) large area light source, and a standard web camera as recording media enabling even kinetic microplate reading with a versatile and broadly available platform, which suffices to evaluate numerous bioassays. Especially in the context of point of care testing or self testing applications these possibilities become advantageous compared with highly dedicated comparatively expensive commercial systems.     

Automatic data recording of circadian rhythms

This paper illustrates a method for automatic data recording using the printer port of personal computer and software designed ad hoc. The system was tested by measuring circadian rhythms of activity in the subterranean rodent Ctenomys talarum. Data is recorded in a text-only comma-delimited file, and displayed on screen.     

High-throughput mass spectrometry screening for inhibitors of phosphatidylserine decarboxylase

A high-throughput mass spectrometry assay to measure the catalytic activity of phosphatidylserine decarboxylase (PISD) is described. PISD converts phosphatidylserine to phosphatidylethanolamine during lipid synthesis. Traditional methods of measuring PISD activity are low throughput and unsuitable for the high-throughput screening of large compound libraries. The high-throughput mass spectrometry assay directly measures phosphatidylserine and phosphatidylethanolamine using the RapidFiretrade mark platform at a rate of 1 sample every 7.5 s. The assay is robust, with an average Z' value of 0.79 from a screen of 9920 compounds. Of 60 compounds selected for confirmation, 54 are active in dose-response studies. The application of high-throughput mass spectrometry permitted a high-quality screen to be performed for an otherwise intractable target.     

A dual fluorescent/MALDI chip platform for analyzing enzymatic activity and for protein profiling

Being able to rapidly and sensitively detect specific enzymatic products is important when screening biological samples for enzymatic activity. We present a simple method for assaying protease activity in the presence of protease inhibitors (PIs) by measuring tryptic peptide accumulation on copolymer pMALDI target chips using a dual fluorescence/MALDI‐TOF‐MS read‐out. The small platform of the chip accommodates microliter amounts of sample and allows for rapid protein digestion. Fluorescamine labeling of tryptic peptides is used to indicate the proteolytic activity and is shown to be an affordable, simple process, yielding a strong fluorescence signal with a low background. Subsequent MALDI‐TOF‐MS analysis, performed in the same sample well, or in a parallel well without adding fluorescamine, detects the specific tryptic peptides and provides confidence in the assay. The dual read‐out method was applied to screen the inhibition activity of plant PIs, components of plant defense against herbivores and pathogens. Extracts of PIs from Solanum nigrum and trypsin were applied together to a pMALDI chip on which a suitable substrate was adsorbed. The fluorescence and MALDI‐TOF‐MS signal decrease were associated with the inhibitory effect of the PIs on trypsin. The developed platform can be modified to screen novel protease inhibitors, namely, those potentially useful for treating or preventing infection by viruses, including HIV and hepatitis C.     

A new method in computer-assisted imaging in neuroanatomy

A procedure is described yielding computed images of postmortem brains with high topographic accuracy. Structures of the brain are traced and registered by means of a digitizer capable of measuring coordinates three-dimensionally. The information corresponding to one brain model is stored on a flexible disk with a capacity of 256 Kbytes. According to the output desired, the resulting brain images are either completely or partially displayed on the computer screen as stereo pairs. The brain models possess a local fidelity of about 1 mm. The images are useful in simultaneously studying superficial and central parts of the brain, spatial relationships of the various structures and the projection of deep structures onto the surface of the brain. A RAM of about 100 Kbytes is necessary for a program enabling the user to perform stereo projections, three-dimensional transformations and other image manipulations. The special features of anatomical computer imaging as compared to computed tomography (CT) and nuclear magnetic resonance imaging (NMR) are outlined. A combination of these different techniques seems to improve clinical diagnosis.     

PC-based system for an objective quantification of manual movement disability for clinical and scientific purposes

In clinical management and research of movement disorders exact knowledge about the extent of motor impairment is essential. This paper presents a computer program which allows for an objective measurement of manual movement disability. The program was developed for standard hardware and can easily be used in a variety of clinical and research environments. The program runs on MS-DOS computers and uses a Microsoft computer mouse as the only input device. The temporal resolution is 100 Hz, the spatial resolution 400 dots per inch. The user may choose between standard test sets or he may design sets according to his individual needs from a pool of available protocols which includes tracking tasks, ballistic tasks, complex sequential tasks, and finger tapping. All tasks are implemented in a similar way in order to keep the test environment as consistent as possible for the patient. The patient must usually carry out movements which correspond to the movements of a target symbol on the computer screen. This entails the manipulation of a follower symbol, also visible on the computer screen, via the computer mouse. The program itself and the theoretical background of the protocols are described in the paper. Additionally, preliminary results from pilot experiments are presented.     

High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration

The high cost of lignocellulolytic enzymes is one of the main barriers towards the development of economically competitive biorefineries. Enzyme engineering can be used to significantly increase the production rate as well as specific activity of enzymes. However, the success of enzyme optimization efforts is currently limited by a lack of robust high-throughput (HTP) cellulase screening platforms for insoluble pretreated lignocellulosic substrates. We have developed a cost-effective microplate based HTP enzyme-screening platform for ionic liquid (IL) pretreated lignocellulose. By performing in-situ biomass regeneration in micro-volumes, we can volumetrically meter biomass (sub-mg loading) and also precisely control the amount of residual IL for engineering novel IL-tolerant cellulases. Our platform only requires straightforward liquid-handling steps and allows the integration of biomass regeneration, washing, saccharification, and imaging steps in a single microtiter plate. The proposed method can be used to screen individual cellulases as well as to develop novel cellulase cocktails.     

Mouse emulation based on facial electromyogram

This work introduces a novel human–computer interface based on electromyography (EMG). This tool allows the user to control the cursor on a computer screen through EMG activity resulting from specific facial movements. This type of human–computer interface may be useful for individuals who want to interact with computers and suffer from movement limitations of arms and hands. Although there are a number of EMG-based human–computer interfaces described in literature, most of them are not assessed with regard to the learning curve resulting from the interaction with such interfaces, being this factor one of the main contributions of the presented study. Another contribution of the investigation is the proposal and evaluation of a complete and practical solution that implements a two-channel EMG interface for generating seven distinct states which can be used as output commands. In the study, a Finite State Machine, which is the core of the system, is responsible for the conversion of features extracted from EMG signals into commands (i.e., SINGLE_CLICK, UP, DOWN, LEFT, RIGHT, ROTATE, and ON_STANDBY) used for the control of the cursor on a computer screen. The tool uses only two channels of information that combines the muscle activity of three facial muscles, i.e., the Left and Right Temporalis and the Frontalis. In order to evaluate learning when using the tool a customized graphical user interface was devised. This interface allowed subjects to execute pre-defined timed actions with distinct levels of difficulty. In total, 10 healthy subjects and a single subject suffering from muscular dystrophy were involved in the experiments. Approximately 60 h of practical experiments were carried out. The results suggest that just after one training session subjects could control the cursor on a computer screen, and also that incremental learning is verified over training sessions. Therefore, the devised tool may be integrated with specific programs and used by individuals whose facial muscles are not severely damaged.     

An eye movement study for identification of suitable font characters for presentation on a computer screen

We are experiencing a shifting of media: from the printed paper to the computer screen. This transition is modifying the process of how we read and understand a text. It is very difficult to conclude on suitability of font characters based upon subjective evaluation method only. Present study evaluates the effect of font type on human cognitive workload during perception of individual alphabets on a computer screen. Twenty six young subjects volunteered for this study. Here, subjects have been shown individual characters of different font types and their eye movements have been recorded. A binocular eye movement recorder was used for eye movement recording. The results showed that different eye movement parameters such as pupil diameter, number of fixations, fixation duration were less for font type Verdana. The present study recommends the use of font type Verdana for presentation of individual alphabets on various electronic displays in order to reduce cognitive workload.     

High-throughput automated platform for nuclear magnetic resonance-based structural proteomics

The development of new systems and strategies capable of synthesizing any desired soluble, labeled protein or protein fragment on a preparative scale is one of the most important tasks in biotechnology today. The Center for Eukaryotic Structural Genomics (WI, USA), in co-operation with Ehime University (Matsuyama, Japan) and CellFree Sciences Co., Ltd, has developed an automated platform for nuclear magnetic resonance-based structural proteomics that employs wheat germ extracts for cell-free production of labeled protein. The platform utilizes a single construct for all targets without any redesign of the DNA or RNA. Therefore, it offers advantages over commercial cell-free methods utilizing Escherichia coli extracts that require multiple constructs or redesign of the open reading frame. The protein production and labeling protocol is no more costly than E. coli cell-based approaches, is robust and scalable for high-throughput applications. This protocol has been used in the authors center to screen eukaryotic open reading frames from the Arabidopsis thaliana and human genomes and for the determination of nuclear magnetic resonance structures. With the recent addition of the GeneDecoder 1000 (CellFree Sciences Co., Ltd) robotic system, the Center for Eukaryotic Structural Genomics is able to carry out as many as 384 small-scale (50 microl) screening reactions per week. Furthermore, the Protemist (CellFree Sciences Co., Ltd) robotic system enables the Center for Eukaryotic Structural Genomics to carry out 16 production-scale (4 ml) reactions per week. Utilization of this automated platform technology to screen targets for expression and solubility and to produce stable isotope-labeled samples for nuclear magnetic resonance structure determinations is discussed.     

Ultra-high throughput screen of two-million-member combinatorial compound collection in a miniaturized, 1536-well assay format

Results of a complete survey of the more than 2-million-member Pharmacopeia compound collection in a 1536-well microvolume screening assay format are reported. A complete technology platform, enabling the performance of ultra-high throughput screening in a miniaturized 1536-well assay format, has been assembled and utilized. The platform consists of tools for performing microvolume assays, including assay plates, liquid handlers, optical imagers, and data management software. A fluorogenic screening assay for inhibition of a protease enzyme target was designed and developed using this platform. The assay was used to perform a survey screen of the Pharmacopeia compound collection for active inhibitors of the target enzyme. The results from the survey demonstrate the successful implementation of the ultra-high throughout platform for routine screening purposes. Performance of the assay in the miniaturized format is equivalent to that of a standard 96-well assay, showing the same dependence on kinetic parameters and ability to measure enzyme inhibition. The survey screen identified an active class of compounds within the Pharmacopeia compound collection. These results were confirmed using a standard 96-well assay.     

A homogeneous high throughput nonradioactive method for measurement of functional activity of Gs-coupled receptors in membranes

A method is described for measuring the activity of G(s)-coupled receptors in a nonradioactive homogeneous membrane-based assay. This method has several major advantages over currently used methods for measuring functional activity of G(s)-coupled receptors. The assay is high throughput (>150,000 data points/day using a single reader). Dimethyl sulfoxide tolerance is high ( approximately 10%). Compared to complex cell-based assays, there is limited potential for nonspecific compound action. This resulted in low compound hit rates in robustness screening, where hit rates from a simulated screen were 1.0% (antagonist screen) and 0.1% (agonist screen). No continuous cell culture is required for the assay, reducing cell culture overheads and allowing the screen to run every day. Automation is simple and requires no temperature- or humidity-controlled incubation. No radioactivity is required. The method relies on measurement of cyclic AMP (cAMP) generation by fluorescence polarization assay using commercially available reagents. Membranes (1-2 microg protein per well, containing anti-cAMP antibody) are transferred to 384-well plates containing 1 microl test compound. For antagonist screens, agonist is added 15 min later. After 30 min incubation at room temperature, one further assay reagent (fluorescein-cAMP in a buffer containing detergent) is added. The signal may be read after 1 h and is stable for greater than 12 h. Typical Z' for the assay is approximately 0.5.     

Self-Reported Screen Time and Cardiometabolic Risk in Obese Dutch Adolescents

Background

It is not clear whether the association between sedentary time and cardiometabolic risk exists among obese adolescents. We examined the association between screen time (TV and computer time) and cardiometabolic risk in obese Dutch adolescents.

Methods and Findings

For the current cross-sectional study, baseline data of 125 Dutch overweight and obese adolescents (12–18 years) participating in the Go4it study were included. Self-reported screen time (Activity Questionnaire for Adolescents and Adults) and clustered and individual cardiometabolic risk (i.e. body composition, systolic and diastolic blood pressure, low-density (LDL-C), high-density (HDL-C) and total cholesterol (TC), triglycerides, glucose and insulin) were assessed in all participants. Multiple linear regression analyses were used to assess the association between screen time and cardiometabolic risk, adjusting for age, gender, pubertal stage, ethnicity and moderate-to-vigorous physical activity. We found no significant relationship between self-reported total screen time and clustered cardiometabolic risk or individual risk factors in overweight and obese adolescents. Unexpectedly, self-reported computer time, but not TV time, was slightly but significantly inversely associated with TC (B = −0.002; CI = [−0.003;−0.000]) and LDL-C (B = −0.002; CI = [−0.001;0.000]).

Conclusions

In obese adolescents we could not confirm the hypothesised positive association between screen time and cardiometabolic risk. Future studies should consider computer use as a separate class of screen behaviour, thereby also discriminating between active video gaming and other computer activities.     

Automated phenotyping of mosquito larvae enables high-throughput screening for novel larvicides and offers potential for smartphone-based detection of larval insecticide resistance

Pyrethroid-impregnated nets have contributed significantly to halving the burden of malaria but resistance threatens their future efficacy and the pipeline of new insecticides is short. Here we report that an invertebrate automated phenotyping platform (INVAPP), combined with the algorithm Paragon, provides a robust system for measuring larval motility in Anopheles gambiae (and An. coluzzi) as well as Aedes aegypti with the capacity for high-throughput screening for new larvicides. By this means, we reliably quantified both time- and concentration-dependent actions of chemical insecticides faster than using the WHO standard larval assay. We illustrate the effectiveness of the system using an established larvicide (temephos) and demonstrate its capacity for library-scale chemical screening using the Medicines for Malaria Venture (MMV) Pathogen Box library. As a proof-of-principle, this library screen identified a compound, subsequently confirmed to be tolfenpyrad, as an effective larvicide. We have also used the INVAPP / Paragon system to compare responses in larvae derived from WHO classified deltamethrin resistant and sensitive mosquitoes. We show how this approach to monitoring larval response to insecticides can be adapted for use with a smartphone camera application and therefore has potential for further development as a simple portable field-assay with associated real-time, geo-located information to identify hotspots.     

Forward Genetic Approach to Uncover Stress Resistance Genes in Mice — A High-throughput Screen in ES Cells

Phenotype-driven genetic screens in mice is a powerful technique to uncover gene functions, but are often hampered by extremely high costs, which severely limits its potential. We describe here the use of mouse embryonic stem (ES) cells as surrogate cells to screen for a phenotype of interest and subsequently introduce these cells into a host embryo to develop into a living mouse carrying the phenotype. This method provides (1) a cost effective, high-throughput platform for genetic screen in mammalian cells; (2) a rapid way to identify the mutated genes and verify causality; and (3) a short-cut to develop mouse mutants directly from these selected ES cells for whole animal studies. We demonstrated the use of paraquat (PQ) to select resistant mutants and identify mutations that confer oxidative stress resistance. Other stressors or cytotoxic compounds may also be used to screen for resistant mutants to uncover novel genetic determinants of a variety of cellular stress resistance.     

A chemically mediated amperometric biosensor for monitoring eubacterial respiration

The development of a novel biosensor system for measuring the respiratory activity of whole eubacterial cells is described. The biosensor incorporates a physically immobilized layer of cells held in intimate contact with an amperometric transducing electrode and uses a chemical mediator, potassium ferricyanide, to divert electrons from the respiratory system of the bacteria to the poised electrode. The current thus produced is proportional to the level of respiratory activity of the immobilized bacterial cells and can be monitored by a computer interface system. The paper outlines the principles of the biosensor and describes the results of a screen of potentially useful eubacteria. Also described are the effects of physical parameters on the sensor and a strategy for the long term preservation of the biosensor by freeze-drying.     

Identification of small molecules that modify the protein folding activity of heat shock protein 70

Molecular chaperones, such as heat shock protein 70 (Hsp70) and its bacterial ortholog DnaK, play numerous important roles in protein folding. In vitro, this activity can be observed by incubating purified chaperones with denatured substrates and measuring the recovery of properly folded protein. In an effort to rapidly identify small molecules that modify this folding activity, we modified an existing method for use in 96-well plates. In this assay, denatured firefly luciferase was treated with a mixture of DnaK and prospective chemical modulators. The luminescence of refolded luciferase was used to follow the reaction progress, and counterscreens excluded compounds that target luciferase; thus, hits from these screens modify protein folding via their effects on the function of the chaperone machine. Using this platform, we screened a pilot chemical library and found five new inhibitors of DnaK and one compound that promoted folding. These chemical probes may be useful in studies aimed at understanding the many varied roles of chaperones in cellular protein folding. Moreover, this assay provides the opportunity to rapidly screen for additional compounds that might regulate the folding activity of Hsp70.