High-throughput screening in the diagnostics industry

Studying the characteristics of nanobody CDR regions based on sequence analysis in combination with 3D structures

Background

Single-domain antibodies or nanobodies have recently attracted much attention in research and applications because of their great potential and advantage over conventional antibodies. However, isolation of candidate nanobodies in the lab has been costly and time-consuming. Screening of leading nanobody candidates through synthetic libraries is a promising alternative, but it requires prior knowledge to control the diversity of the complementarity-determining regions (CDRs) while still maintaining functionality. In this work, we identified sequence characteristics that could contribute to nanobody functionality by analyzing three datasets, CDR1, CDR2, and CDR3.

Results

By classification of amino acids based on physicochemical properties, we found that two different amino acid groups were sufficient for CDRs. The nonpolar group accounted for half of the total amino acid composition in these sequences. Observation of the highest occurrence of each amino acid revealed that the usage of some important amino acids such as tyrosine and serine was highly correlated with the length of the CDR3. Amino acid repeat motifs were also under-represented and highly restricted as 3-mers. Inspecting the crystallographic data also demonstrated conservation in structural coordinates of dominant amino acids such as methionine, isoleucine, valine, threonine, and tyrosine and certain positions in the CDR1, CDR2, and CDR3 sequences.

Conclusions

We identified sequence characteristics that contributed to functional nanobodies including amino acid groups, the occurrence of each kind of amino acids, and repeat patterns. These results provide a simple set of rules to make it easier to generate desired candidates by computational means; also, they can be used as a reference to evaluate synthetic nanobodies.

Choosing a suitable method for the identification of replication origins in microbial genomes

As the replication of genomic DNA is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. Making sense of DNA replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. Thus, clearly comprehending the positions and sequences of replication origins which are fundamental to chromosome organization and duplication is the first priority of all. In view of such important roles of replication origins, tremendous work has been aimed at identifying and testing the specificity of replication origins. A number of computational tools based on various skew types have been developed to predict replication origins. Using various in silico approaches such as Ori-Finder, and databases such as DoriC, researchers have predicted the locations of replication origins sites for thousands of bacterial chromosomes and archaeal genomes. Based on the predicted results, we should choose an effective method for identifying and confirming the interactions at origins of replication. Here we describe the main existing experimental methods that aimed to determine the replication origin regions and list some of the many the practical applications of these methods.

Signal amplification systems in immunoassays: implications for clinical diagnostics

Biomarkers in physiological specimens serve as useful sensors for clinical diagnosis. Accurate detection of specific markers is crucial for the diagnosis of disease, monitoring drug therapy and patient screening. In vitro immunoassays are probably the most common, simple and relatively inexpensive serological tools used in clinical laboratories for the diagnosis and management of disease. Despite continued efforts to improve the performance of immunoassays in the past three decades, there is a need for highly sensitive assays that can detect the lowest levels of disease markers with greater accuracy. This review summarizes recent advances made towards increasing the sensitivity of immunoassays by amplifying detection signals, with implications for the development of highly sensitive diagnostic systems; it also discusses the principles of related methodologies.

Effects of simulated space radiation on immunoassay components for life-detection experiments in planetary exploration missions

The Life Marker Chip (LMC) instrument is part of the proposed payload on the ESA ExoMars rover that is scheduled for launch in 2018. The LMC will use antibody-based assays to detect molecular signatures of life in samples obtained from the shallow subsurface of Mars. For the LMC antibodies, the ability to resist inactivation due to space particle radiation (both in transit and on the surface of Mars) will therefore be a prerequisite. The proton and neutron components of the mission radiation environment are those that are expected to have the dominant effect on the operation of the LMC. Modeling of the radiation environment for a mission to Mars led to the calculation of nominal mission fluences for proton and neutron radiation. Various combinations and multiples of these values were used to demonstrate the effects of radiation on antibody activity, primarily at the radiation levels envisaged for the ExoMars mission as well as at much higher levels. Five antibodies were freeze-dried in a variety of protective molecular matrices and were exposed to various radiation conditions generated at a cyclotron facility. After exposure, the antibodies' ability to bind to their respective antigens was assessed and found to be unaffected by ExoMars mission level radiation doses. These experiments indicated that the expected radiation environment of a Mars mission does not pose a significant risk to antibodies packaged in the form anticipated for the LMC instrument.

Advances in the study of protein-DNA interaction

Protein-DNA interaction plays an important role in many biological processes. The classical methods and the novel technologies advanced have been developed for the interaction of protein-DNA. Recent developments of these methods and research achievements have been reviewed in this paper.

Determination of complementary antibody pairs using protein A capture with the AlphaScreen assay format

The utility of antibody reagents for the detection of specific cellular targets for both research and diagnostic applications is widespread and continually expanding. Often it is useful to develop specific antibodies as reagent pairs that distinguish different epitopes of the target such that sandwich enzyme-linked immunosorbent assay can be used for selective and specific detection. However, the identification of pairing antibodies is often cumbersome and labor-intensive even with the use of designed peptide-specific epitopes as antigens. We have developed a robust and high-throughput method for identifying pairing complementary antibodies derived either from commercial sources or during a rabbit hybridoma monoclonal screening and selection process using protein A capture with the AlphaScreen bead-based assay format. We demonstrate the value and effectiveness of this assay with three protein targets: Akt2, ATF3, and NAEβ (the β-subunit of the neddylation activation enzyme).

Highly sensitive detection of protein toxins by surface plasmon resonance with biotinylation-based inline atom transfer radical polymerization amplification

Ultrasensitive detection of proteins is of great importance to proteomics studies. We report here a method to enhance detection sensitivity in surface plasmon resonance (SPR) spectroscopy by coupling a polymerization initiator to a biospecific interaction and inducing inline atom transfer radical polymerization (ATRP) for amplifying SPR response. Bacterial cholera toxin (CT) is chosen as the model protein that has been covalently immobilized on the surface for demonstrating the principle. The specific recognition is achieved by use of biotinylated anti-CT, which allows initiators with a biotin tag to be fixed at the protein binding site through a neutravidin bridge and triggers the localized growth of polymer brushes of poly(hydroxyl-ethyl methacrylate) (PHEMA) via an ATRP mechanism. To further enhance the signal, a second ATRP reaction is conducted that takes advantage of the hydroxyl groups of PHEMA brushes from the first step to form hyperbranched polymers onto the sensing surface. The two consecutive ATRP steps significantly improve SPR detection, allowing low amounts of CT that yield no direct measurement to be quantified with large signals. The resulting polymer film has been characterized by optical and atomic force microscopy. Ascorbic acid (AA) is employed as deoxygen reagent in the catalyst mixture that effectively suppresses oxygen interference, shortening the reaction time and making it possible for applying this ATRP approach to flow injection based SPR detection. A calibration curve of PHEMA amplification for CT detection based on surface coverage has been obtained that displays a correlation in a range from 8.23 x 10(-15) to 3.61 x 10(-12) mol/cm(2) with a limit of detection of 6.27 x 10(-15) mol/cm(2). The versatile biotin-neutravidin interaction used here should allow adaptation of ATRP enhancement to many other systems that include DNA, RNA, peptides, and carbohydrates, opening new avenues for ultrasensitive analysis of biomolecules with flow-injection assay and SPR spectroscopy.

High throughput screening of protein formulation stability: practical considerations

The formulation of protein drugs is a difficult and time-consuming process, mainly due to the complexity of protein structure and the very specific physical and chemical properties involved. Understanding protein degradation pathways is essential for the success of a biopharmaceutical drug. The present review concerns the application of high throughput screening techniques in protein formulation development. A protein high throughput formulation (HTF) platform is based on the use of microplates. Basically, the HTF platform consists of two parts: (i) sample preparation and (ii) sample analysis. Sample preparation involves automated systems for dispensing the drug and the formulation ingredients in both liquid and powder form. The sample analysis involves specific methods developed for each protein to investigate physical and chemical properties of the formulations in microplates. Examples are presented of the use of protein intrinsic fluorescence for the analysis of protein aqueous properties (e.g., conformation and aggregation). Different techniques suitable for HTF analysis are discussed and some of the issues concerning implementation are presented with reference to the use of microplates.

Surface-directed capillary system; theory, experiments and applications

We present a capillary flow system for liquid transport in microsystems. Our simple microfluidic system consists of two planar parallel surfaces, separated by spacers. One of the surfaces is entirely hydrophobic, the other mainly hydrophobic, but with hydrophilic pathways defined on it by photolithographic means. By controlling the wetting properties of the surfaces in this manner, the liquid can be confined to certain areas defined by the hydrophilic pathways. This technique eliminates the need for alignment of the two surfaces. Patterned plasma-polymerized hexafluoropropene constitutes the hydrophobic areas, whereas the untreated glass surface constitutes the hydrophilic pathways. We developed a theoretical model of the capillary flow and obtained analytical solutions which are in good agreement with the experimental results. The capillarity-driven microflow system was also used to pattern and immobilize biological material on planar substrates: well-defined 200 microm wide strips of human cells (HeLa) and fluorescence labelled proteins (fluorescein isothiocyanate-labelled bovine serum albumin, i.e., FITC-BSA) were fabricated using the capillary flow system presented here.

Microplate-based screening methods for the efficient development of sandwich immunoassays

The selection of suitable antibodies is a critical step in immunoassay development, since the final assay performance is predetermined by this decision to a large extent. Particularly, the screening for matching pairs in sandwich immunoassays is difficult, if both antibodies are derived from one species or when monoclonal antibodies are only available as cell supernatants. Several microplate-based approaches for in situ labeling of detection antibodies were tested, in order to avoid time consuming purification of antibodies for enzyme conjugate synthesis. We investigated labeling with anti-species antibodies and Fab fragments thereof, labeling with protein G and biotinylation of cell supernatants without prior purification. Antibodies against peanut proteins were used as a model and signal-to-blank ratios were used in all cases as a measure of the antibody pair performance. Amongst the investigated approaches, preincubation of the detection antibody with labeled anti-species antibody turned out to be most suitable under our conditions. Diagrams, showing the performance of all possible antibody combinations, were generated with this method and were compared to results obtained with covalently labeled detection antibodies. Finally, a flowchart is presented, suggesting an efficient strategy for the development of highly sensitive sandwich immunoassays.

A survey of the year 2002 commercial optical biosensor literature

We have compiled 819 articles published in the year 2002 that involved commercial optical biosensor technology. The literature demonstrates that the technology's application continues to increase as biosensors are contributing to diverse scientific fields and are used to examine interactions ranging in size from small molecules to whole cells. Also, the variety of available commercial biosensor platforms is increasing and the expertise of users is improving. In this review, we use the literature to focus on the basic types of biosensor experiments, including kinetics, equilibrium analysis, solution competition, active concentration determination and screening. In addition, using examples of particularly well-performed analyses, we illustrate the high information content available in the primary response data and emphasize the impact of including figures in publications to support the results of biosensor analyses.