High-throughput Screening Devices Research Articles

Screening the maize rhizobiome for consortia that improve Azospirillum brasilense root colonization and plant growth outcomes

Plant growth-promoting bacteria (PGPB) are valuable for supporting sustainable food production and may alleviate the negative impacts of chemical fertilizers on human health and the environment. While single-strain inoculations have proven unreliable due to poor survival and colonization in the rhizosphere, application of PGPB in multispecies consortia has the potential to improve these outcomes. Here, we describe a new approach for screening and identifying bacterial consortia that improve the growth of corn relative to plants inoculated with a single strain. The method uses the microwell recovery array (MRA), a microfabricated high-throughput screening device, to rapidly explore the maize (Zea mays L.) rhizobiome for higher-order combinations of bacteria that promote the growth and colonization of the nitrogen-fixing PGPB, Azospirillum brasilense. The device simultaneously generates thousands of random, unique combinations of bacteria that include A. brasilense and members of the maize rhizobiome, then tracks A. brasilense growth in each combination during co-culture. Bacteria that show the highest levels of A. brasilense growth promotion are then recovered from the device using a patterned light extraction technique and are identified. With this approach, the screen uncovered growth-promoting consortia consisting primarily of bacteria from the Acinetobacter-Enterobacter-Serratia genera, which were then co-inoculated with A. brasilense on axenic maize seedlings that were monitored inside a plant growth chamber. Compared to maize plants inoculated with A. brasilense alone, plants that were co-inoculated with these consortia showed accelerated growth after 15 days. Follow-up root colonization assays revealed that A. brasilense colonized at higher levels on roots from the co-inoculated seedlings. These findings demonstrate a new method for rapid bioprospecting of root and soil communities for complementary PGPB and for developing multispecies consortia with potential use as next-generation biofertilizers.

Autonomous high-throughput screening technology for accelerating drug molecule discovery and synthesis

<p indent="0mm">The discovery and synthesis of pharmaceutical small molecules is one of the important decisive steps in the process of new drug research and development. The traditional small molecule design and synthesis methods, however, is becoming increasingly difficult to meet the iteration and development speed of new drug molecules in modern human society. The recent emergence of chemical artificial intelligence and high-throughput screening (HTS) technology is a new direction to break through the bottleneck of traditional research and development efficiency. This review will focus on the development status of automatic HTS device driven by artificial intelligence decision algorithm, mainly including: (1) High-throughput screening device technology. Batch and flow HTS modes, reaction process intensification for HTS screening, and the analytical characterization technology for HTS are discussed. (2) Intelligent decision-making algorithm for driving HTS, discussing the autonomous decision algorithms for driving the automation device to realize intelligent autonomous exploration, target property optimization and high-quality experimental data generation. Finally, this review will discuss how to further develop intelligent HTS technology to accelerate the synthesis of pharmaceutical molecules in the future.

Silica/Proteoliposomal Nanocomposite as a Potential Platform for Ion Channel Studies.

The nanostructuration of solid matrices with lipid nanoparticles containing membrane proteins is a promising tool for the development of high-throughput screening devices. Here, sol-gel silica-derived nanocomposites loaded with liposome-reconstituted KcsA, a prokaryotic potassium channel, have been synthesized. The conformational and functional stability of these lipid nanoparticles before and after sol-gel immobilization have been characterized by using dynamic light scattering, and steady-state and time-resolved fluorescence spectroscopy methods. The lipid-reconstituted KcsA channel entrapped in the sol-gel matrix retained the conformational and stability changes induced by the presence of blocking or permeant cations in the buffer (associated with the conformation of the selectivity filter) or by a drop in the pH (associated with the opening of the activation gate of the protein). Hence, these results indicate that this novel device has the potential to be used as a screening platform to test new modulating drugs of potassium channels.

Microfluidics as a high-throughput solution for chromatographic process development – The complexity of multimodal chromatography used as a proof of concept

High-throughput technologies are fundamental to expedite the implementation of novel purification platforms. The possibility of performing process development within short periods of time while saving consumables and biological material are prime features for any high-throughput screening device. In this work, a microfluidic device is evaluated as high-throughput solution for a complete study of chromatographic operation conditions on ten different multimodal resins. The potential of this class of purification solutions is generally hindered by its complexity. Taking this into consideration, the microfluidic platform was herein applied and assessed as a tool for high-throughput applications. The commercially available multimodal ligands were studied for the binding of three antibody-based biomolecules (polyclonal mixture of whole antibodies, Fab and Fc fragments) at different pH and salt conditions, in a total of 450 experiments. The results obtained with the microfluidic device were comparable to a standard 96-well filtering microplate high-throughput tool. Additionally, five of the ten multimodal ligands tested were packed into a bench-scale column to perform a final validation of the microfluidic results obtained. All the data acquired in this work using different screening protocols corroborate each other, showing that microfluidic chromatography is a valuable tool for the fast implementation of a new purification step, particularly, if the goal is to narrow the downstream possibilities by being a first point of decision.

Improvements of ER-Ca2+ Based High-Throughput Screening Method for Searching Novel RyR2 Inhibitors

Type 2 ryanodine receptor (RyR2) is a Ca2+ release channel on the endoplasmic reticulum (ER) and plays a central role in excitation-contraction coupling in the heart. When the RyR2 activity is abnormally enhanced by miss-sense mutations and/or excessive phosphorylation, spontaneous Ca2+ release occurs from the ER, which often results in fatal ventricular arrhythmias. Therefore, specific inhibitors of RyR2 are expected to have an antiarrhythmic effect on the RyR2-related arrhythmias, but currently such specific drugs have not been reported. We have recently established a screening method for isoform specific ryanodine receptor (RyR) inhibitors using ER Ca2+ indicator, R-CEPIA1er, in HEK293 cells (Murayama et al., Mol Pharmacol, 2018). Although this method is very useful, it requires 3 consecutive experimental days, i.e., culture of HEK293 cells expressing inducible RyR and R-CEPIA1er in 96-well plates on the first day, induction of protein expression by doxycycline on the next day, and assay using FlexStation3 on the third day. In order to screen a larger number of compounds more efficiently using a high-throughput screening device equipped with EM-CCD camera such as FDSS7000 (Hamamatsu), we made several improvements to this method. First, a novel bright green fluorescent indicator, G-CEPIA2er was used instead of R-CEPIA1er, which greatly improved signal-to-noise ratio. Second, measurements were done in 384 well plate with FDSS7000 just after seeding of cryopreserved cells which had been treated with doxycycline to induce RyR2 expression. These improvements resulted in a 48-fold increase in assay efficiency. This method, having allowed us to screen more than 20,000 compounds so far for both RyR1 and RyR2, proved to be a versatile and powerful tool for the development of specific RyR2-modifying reagents. This research was supported by JSPS Kakenhi grant (19K07105), AMED grant (19ek0109202s0203) and BINDS from AMED (0033).

Spheroid Culture of Mammalian Olfactory Receptor Neurons: Potential Applications for a Bioelectronic Nose.

The olfactory system can detect many odorants with high sensitivity and selectivity based on the expression of nearly a thousand types of olfactory receptors (ORs) in olfactory receptor neurons (ORNs). These ORs have a dynamic odorant detection range and contribute to signal encoding processes in the olfactory bulb (OB). To harness the capabilities of the olfactory system and develop a biomimetic sensor, stable culture and maintenance of ORNs are required. However, in vitro monolayer culture models have several key limitations: i) short available period of cultured neurons, ii) low cultural efficiency, and iii) long-term storage challenges. This study aims to develop a technique: i) to support the spheroid culture of primary ORN precursors facilitating stable maintenance and long-term storage, and ii) to demonstrate the viability of ORN spheroid culture in developing an olfactory system mimetic bioelectronic nose. Recombinant protein (REP; TGPG[VGRGD(VGVPG)6]20WPC) was used to form the ORN spheroids. Spheroid formation enabled preservation of primary cultured ORNs without a significant decrease in viability or the expression of stemness markers for ten days. Physiological characteristics of the ORNs were verified by monitoring intracellular calcium concentration upon odorant mixture stimulation; response upon odorant stimulation were observed at least for ten days in these cultivated ORNs differentiated from spheroids. Coupling ORNs with multi electrode array (MEA) enabled the detection and discrimination of odorants by analyzing the electrical signal patterns generated following odorant stimulation. Taken together, the ORN spheroid culture process is a promising technique for the development of a bioelectronic nose and high-throughput odorant screening device.

A Mass-Producible and Versatile Sensing System: Localized Surface Plasmon Resonance Excited by Individual Waveguide Modes.

A plasmonic sensing system that allows the excitation of localized surface plasmon resonance (LSPR) by individual waveguide modes is presented conceptually and experimentally. Any change in the local environment of the gold nanoparticles (AuNPs) alters the degree of coupling between LSPR and a polymer slab waveguide, which then modulates the transmission-output signal. In comparison to conventional LSPR sensors, this system is less susceptible to optical noise and positional variation of signals. Moreover, it enables more freedom in the exploitation of plasmonic hot spots with both transverse electric (TE) and transverse magnetic (TM) modes. Through real-time measurement, it is demonstrated that the current sensing system is more sensitive than comparable optical fiber plasmonic sensors. The highest normalized bulk sensitivity (7.744 RIU-1) is found in the TM1 mode. Biosensing with the biotin-streptavidin system shows that the detection limit is on the order of 10-14 M of streptavidin. With further optimization, this sensing system can easily be mass-produced and incorporated into high throughput screening devices, detecting a variety of chemical and biological analytes via immobilization of the appropriate recognition sites.

Prediction of Escherichia coli expression performance in microtiter plates by analyzing only the temporal development of scattered light during culture

BackgroundEscherichia coli is often used for recombinant protein production. The expression of recombinant proteins negatively affects the microbial growth, thus, a balance between protein expression and biomass formation is preferable to reach high product- and space-time-yield. Already in screening experiments, suboptimal conditions causing too weak or too strong induction must be avoided. High-throughput screening devices such as the BioLector are often applied for screening experiments. The BioLector allows optical online monitoring of each well in a continuously orbitally shaken microtiter plate via scattered light and fluorescence measurements. This technique enables a fast identification of promising clones. However, to determine the expression performance of non-fluorescent products elaborated offline analysis is often required.MethodsA mathematical method is developed to distinguish between cultures, which are insufficiently, optimally or too strongly induced. Therefore, just the temporal development of the scattered light intensity signal is investigated. It is found that discrimination between the different intensities of induction is possible via principal component analysis. By fitting an extended sigmoidal function to the trajectory of the scattered light over time, two characteristic parameters are found. These are used in an empirical model to predict the expression performance.ResultsThe method was established for a wide range of culture conditions based on 625 E. coli cultures. Three E. coli host strains (Tuner(DE3), BL21(DE3), and BL21-Gold(DE3)) expressing either flavin-mononucleotide-based fluorescent protein (FbFP) or Cellulase celA2 were investigated. Cultures were conducted in two different types of microtiter plates (48- and 96-wells), in two online measurement devices at four temperatures (28 °C, 30 °C, 34 °C, and 37 °C). More than 95% of the predicted values are in agreement with the offline measured expression performances with a satisfying accuracy of ±30%.ConclusionsThe properties of cultures studied can be represented by only two characteristic parameters (slope at and time of the inflection point) received from fitting an extended sigmoidal function to the respective scattered light trajectory. Based on these two characteristic parameters, predictions of the standardized expression performance are possible and for a first screen elaborated offline analysis can be avoided. To the best of our knowledge, this is the first work presenting a method for the general prediction of expression performance of E. coli based solely on the temporal development of scattered light signals.

Clarifying intact 3D tissues on a microfluidic chip for high-throughput structural analysis

On-chip imaging of intact three-dimensional tissues within microfluidic devices is fundamentally hindered by intratissue optical scattering, which impedes their use as tissue models for high-throughput screening assays. Here, we engineered a microfluidic system that preserves and converts tissues into optically transparent structures in less than 1 d, which is 20× faster than current passive clearing approaches. Accelerated clearing was achieved because the microfluidic system enhanced the exchange of interstitial fluids by 567-fold, which increased the rate of removal of optically scattering lipid molecules from the cross-linked tissue. Our enhanced clearing process allowed us to fluorescently image and map the segregation and compartmentalization of different cells during the formation of tumor spheroids, and to track the degradation of vasculature over time within extracted murine pancreatic islets in static culture, which may have implications on the efficacy of beta-cell transplantation treatments for type 1 diabetes. We further developed an image analysis algorithm that automates the analysis of the vasculature connectivity, volume, and cellular spatial distribution of the intact tissue. Our technique allows whole tissue analysis in microfluidic systems, and has implications in the development of organ-on-a-chip systems, high-throughput drug screening devices, and in regenerative medicine.

A Simple Method for Ion Channel Recordings Using Fine Gold Electrode.

The artificial bilayer single-channel recording technique is commonly used to observe detailed pharmacological properties of various ion channel proteins. It permits easy control of the solution and membrane lipid composition, and is also compatible with pharmacological screening devices. However, its use is limited due to low measurement efficiency. Here, we develop a novel artificial bilayer single-channel recording technique in which bilayers are made and channels are reconstituted into the membranes by contacting a gold electrode to the lipid-solution interface. Using this technique, we measured the single-channel currents of two channel-forming peptides, gramicidin and alamethicin, and a channel-forming protein, α-hemolysin. This technique requires only one action, allowing the technique to potentially be combined with high-throughput screening devices.

Parallel online multi-wavelength (2D) fluorescence spectroscopy in each well of a continuously shaken microtiter plate.

Small-scale high-throughput screening devices are becoming increasingly important in bioprocess development. Conventional dipping probes for process monitoring are often too large to be used in these devices. Thus, optical measurements are often the method of choice. Even some parameters that cannot directly be measured by fluorescence become accessible via sensitive fluorescence dyes. However, not all compounds of interest are measurable by this technique. Recent studies applying multi-wavelength (2D) fluorescence spectroscopy in combination with chemometrics have shown that information on numerous analytes is obscured by the fluorescence data. Hitherto, this measurement technique has only been available on the scale of stirred tank fermenters. This work introduces a new device for multi-wavelength (2D) fluorescence spectroscopy in each well of a continuously shaken microtiter plate. Using a combination of spectrograph and CCD detector, the required time per measurement cycle in a 48-well microtiter plate was 0.5 h. Cultures of Hansenula polymorpha and Escherichia coli are monitored. The concentrations of glycerol, glucose and acetate as well as pH are determined using partial least square (PLS) models. Because a pH-sensitive fluorescence dye was not required, no dependency of the pKa of a fluorescence dye exists, and measurements in the low pH range can be obtained.

Fourier-transform infrared spectroscopic analyses of cellulose from different bacterial cultivations using microspectroscopy and a high-throughput screening device

Broad application of bacterial cellulose (BC) has led to search for new commercially interesting producers and consequently also for low-cost screening methods to select BC with particular properties. BC produced by four symbiotic Kombucha associations and fourteen acetic acid bacteria isolated from these Kombucha associations were purified by frequent washing with distilled water and pre-treatment with alkali. The obtained native and mercerized BC pellicles were analysed by two common time-saving FT-IR spectroscopy methods—high-throughput screening (HTS) and microspectroscopy. The FT-IR spectra showed traces of microbial cells and acids entrapped between the microfibrils of BC even after purification with alkali. This study showed that spectra of BC collected with HTS are more informative for the evaluation of the purity of BC than those obtained by microspectroscopy, which will be preferable for studies of crystallinity. Hierarchical cluster analysis of IR-spectra was helpful for fast screening of BC samples by their producer, fermentation medium, purity, and crystallinity. This study demonstrated HTS and IR-microspectroscopy as quick and cost-efficient methods for screening of BC and search of BC with particular properties.

Photonic crystal protein hydrogel sensor materials enabled by conformationally induced volume phase transition.

Hydrogels that change volume in response to specific molecular stimuli can serve as platforms for sensors, actuators and drug delivery devices. There is great interest in designing intelligent hydrogels for tissue engineering, drug delivery, and microfluidics that utilize protein binding specificities and conformational changes. Protein conformational change induced by ligand binding can cause volume phase transitions (VPTs). Here, we develop a highly selective glucose sensing protein photonic crystal (PC) hydrogel that is fabricated from genetically engineered E. coli glucose/galactose binding protein (GGBP). The resulting 2-D PC-GGBP hydrogel undergoes a VPT in response to glucose. The volume change causes the 2-D PC array particle spacing to decrease, leading to a blue-shifted diffraction which enables our sensors to report on glucose concentrations. This 2-D PC-GGBP responsive hydrogel functions as a selective and sensitive sensor that easily monitors glucose concentrations from ∼0.2 μM to ∼10 mM. This work demonstrates a proof-of-concept for developing responsive, "smart" protein hydrogel materials with VPTs that utilize ligand binding induced protein conformational changes. This innovation may enable the development of other novel chemical sensors and high-throughput screening devices that can monitor protein-drug binding interactions.

Analysis of high-throughput screening reveals the effect of surface topographies on cellular morphology

Surface topographies of materials considerably impact cellular behavior as they have been shown to affect cell growth, provide cell guidance, and even induce cell differentiation. Consequently, for successful application in tissue engineering, the contact interface of biomaterials needs to be optimized to induce the required cell behavior. However, a rational design of biomaterial surfaces is severely hampered because knowledge is lacking on the underlying biological mechanisms. Therefore, we previously developed a high-throughput screening device (TopoChip) that measures cell responses to large libraries of parameterized topographical material surfaces. Here, we introduce a computational analysis of high-throughput materiome data to capture the relationship between the surface topographies of materials and cellular morphology. We apply robust statistical techniques to find surface topographies that best promote a certain specified cellular response. By augmenting surface screening with data-driven modeling, we determine which properties of the surface topographies influence the morphological properties of the cells. With this information, we build models that predict the cellular response to surface topographies that have not yet been measured. We analyze cellular morphology on 2176 surfaces, and find that the surface topography significantly affects various cellular properties, including the roundness and size of the nucleus, as well as the perimeter and orientation of the cells. Our learned models capture and accurately predict these relationships and reveal a spectrum of topographies that induce various levels of cellular morphologies. Taken together, this novel approach of high-throughput screening of materials and subsequent analysis opens up possibilities for a rational design of biomaterial surfaces.

One-step-purification of penicillin G amidase from cell lysate using ion-exchange membrane adsorbers

This study describes the purification of penicillin G amidase (PGA) by ion exchange membrane adsorbers in a one-step-process. Preliminary experiments with high-throughput screening devices in microliter scale (8-strip modules) were performed to find suitable purification strategy and appropriate ion exchange ligands as well as basic process conditions for binding and elution. Best purification results were achieved by strong cation-exchange (S-) membrane adsorbers loaded with 2ml/min enzyme solution at pH 6.0 and eluted at pH 6.0 with 0.05M NaCl, which led to a high yield of bound PGA (98%) without any visible remains of host cell proteins and with a residual enzyme activity of 80–85%. The binding of PGA to the S-membrane was further investigated in an upscaling to milliliter scale with LP15 modules and breakthrough curves were determined by varying the flow rates: the PGA-binding to S-membrane adsorbers is independent of the flow rate. Dynamic binding capacities were estimated to be 0.69mg PGA/cm2 (25.5mg/ml) for 10% breakthrough respectively 0.95mg/cm2 (35.2mg/ml) for 100% breakthrough. Finally, real cell lysate samples from Escherichia coli culture containing PGA were processed under the found optimal conditions. Despite exceeded loading PGA was isolated from this complex mixture successfully fourfold concentrated and with a purification factor of 101.3 and a resulting specific activity of 4.97U/mg.

High Throughput Screening of CO2 Solubility in Aqueous Monoamine Solutions

Post-combustion Carbon Capture and Storage technology (CCS) is viewed as an efficient solution to reduce CO(2) emissions of coal-fired power stations. In CCS, an aqueous amine solution is commonly used as a solvent to selectively capture CO(2) from the flue gas. However, this process generates additional costs, mostly from the reboiler heat duty required to release the carbon dioxide from the loaded solvent solution. In this work, we present thermodynamic results of CO(2) solubility in aqueous amine solutions from a 6-reactor High Throughput Screening (HTS) experimental device. This device is fully automated and designed to perform sequential injections of CO(2) within stirred-cell reactors containing the solvent solutions. The gas pressure within each reactor is monitored as a function of time, and the resulting transient pressure curves are transformed into CO(2) absorption isotherms. Solubility measurements are first performed on monoethanolamine, diethanolamine, and methyldiethanolamine aqueous solutions at T = 313.15 K. Experimental results are compared with existing data in the literature to validate the HTS device. In addition, a comprehensive thermodynamic model is used to represent CO(2) solubility variations in different classes of amine structures upon a wide range of thermodynamic conditions. This model is used to fit the experimental data and to calculate the cyclic capacity, which is a key parameter for CO(2) process design. Solubility measurements are then performed on a set of 50 monoamines and cyclic capacities are extracted using the thermodynamic model, to asses the potential of these molecules for CO(2) capture.

Low-dose DNA damage and replication stress responses quantified by optimized automated single-cell image analysis

Maintenance of genome integrity is essential for homeostasis and survival as impaired DNA damage response (DDR) may predispose to grave pathologies such as neurodegenerative and immunodeficiency syndromes, cancer and premature aging. Therefore, accurate assessment of DNA damage caused by environmental or metabolic genotoxic insults is critical for contemporary biomedicine. The available physical, flow cytometry and sophisticated scanning approaches to DNA damage estimation each have some drawbacks such as insufficient sensitivity, limitation to analysis of cells in suspension, or high costs and demand for trained personnel. Here we present an option how to transform a regular fluorescence microscope and personal computer with common software into a functional alternative to high-throughput screening devices. In two detailed protocols we introduce a new semi-automatic procedure allowing for very sensitive, quantitative, rapid and simple fluorescence image analysis in thousands of adherent cells per day. Sensitive DNA breakage estimation through analysis of phosphorylated histone H2AX (g-H2AX), and homologous recombination (HR) assessed by a new RPA/Rad51 dual-marker approach illustrate the advantages and applicability of this technique. Our present data on assessment of low radiation doses, repair kinetics, spontaneous DNA damage in cancer cells, as well as constitutive and replication stress-induced HR events and their dependence on upstream factors within the DDR machinery document the versatility of the method. We believe this affordable approach may facilitate mechanistic insights into the role of low-dose DNA damage in human diseases, and generally promote both basic and translational research in many areas of biomedicine where suitable fluorescence markers are available.

Miniaturized Microfluidic Formats for Cell-Based High-Throughput Screening

Cell-based high-throughput screening (HTS) has become an important method used in pharmaceutical drug discovery, and is presently carried out using robots and micro-well plates. A microfluidic-based device for cell-based HTS using a traditional cell-culture protocol would be a key enabler in miniaturization and in increasing throughput without consequent detrimental effects on the physiological significance of the screen. In this paper, we illustrate the advances in miniaturization of cell-based HTS, especially using microfabrication and microfluidics. We also detail a novel microfluidic HTS device targeted for cell-based assays using traditional non-compartmentalized agar gel as a cell-culture medium and electric control over drug dose. The basic design of this device consists of a gel layer supported by a nanoporous membrane that is bonded to microchannels underneath it. The pores of the membrane are blocked everywhere except in selected regions that serve as fluidic interfaces between the microchannel below and the gel above. Upon application of an electric field, nanopores start to act as electrokinetic pumps. By selectively switching an array of such micropumps, a number of spots containing drug molecules are created simultaneously in the gel layer. By diffusion, drugs reach the top surface of the gel where cells are to be grown. Based on this principle, a number of different devices can be fabricated using microfabrication technology. The fabricated devices include a single drug spot-forming device, a multiple drug spot-forming device, and a microarray drug spot-forming device. By controlling the pumping potential and duration, spots sizes ranging from 200 mu;m to 6 mm in diameter and having inter-spot distances of 0.4 to 10 mm have been created. The absence of diffusional transport through the nanoporous interfaces without an electric field is demonstrated. A number of representative molecules, including surrogate drug molecules (trypan blue and methylene blue) and biomolecules (DNA and protein) were selected for demonstration purposes. A dosing range of 50 to 3000 mu;g and a spot density of 156 spots/cm2 were achieved. The drug spot density was found to be limited by molecular diffusion in gel, so a numerical study was carried to determine ways to increase density. Based on this simulation, a diffusion barrier was proposed, which uses a specially dimensioned (having shallow grooves) gel sheet to reduce diffusion.

R/parallel – speeding up bioinformatics analysis with R

BackgroundR is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly reused and adapted to each particular experiment. However, in experiments where large amounts of data are generated, for example using high-throughput screening devices, the processing time required to analyze data is often quite long. A solution to reduce the processing time is the use of parallel computing technologies. Because R does not support parallel computations, several tools have been developed to enable such technologies. However, these tools require multiple modications to the way R programs are usually written or run. Although these tools can finally speed up the calculations, the time, skills and additional resources required to use them are an obstacle for most bioinformaticians.ResultsWe have designed and implemented an R add-on package, R/parallel, that extends R by adding user-friendly parallel computing capabilities. With R/parallel any bioinformatician can now easily automate the parallel execution of loops and benefit from the multicore processor power of today's desktop computers. Using a single and simple function, R/parallel can be integrated directly with other existing R packages. With no need to change the implemented algorithms, the processing time can be approximately reduced N-fold, N being the number of available processor cores.ConclusionR/parallel saves bioinformaticians time in their daily tasks of analyzing experimental data. It achieves this objective on two fronts: first, by reducing development time of parallel programs by avoiding reimplementation of existing methods and second, by reducing processing time by speeding up computations on current desktop computers. Future work is focused on extending the envelope of R/parallel by interconnecting and aggregating the power of several computers, both existing office computers and computing clusters.

Lipid Bilayers at the Gel Interface for Single Ion Channel Recordings

Single-channel recording using artificial lipid bilayers is along with the patch-clamp technique a very powerful tool to physiologically and pharmacologically study ion channels. It is particularly advantageous in studying channels that are technically difficult to access with a patch pipet. However, the fragility of the bilayers and the difficulty to incorporate ion channels into them significantly compromises measurement efficiency. We have developed a novel method for forming artificial lipid bilayers on a hydrogel surface that significantly improves the measurement efficiency. Bilayers formed almost instantly (<1 s) and were able to incorporate various types of ion channel proteins within a short time (<30 s) enabling multichannel measurements. These results indicate that this method can potentially be applied to developing high-throughput screening devices for drug design.