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A unifying review of bioassay-guided fractionation, effect-directed analysis and related techniques
(2012)
The success of modern methods in analytical chemistry sometimes obscures the problem that the ever increasing amount of analytical data does not necessarily give more insight of practical relevance. As alternative approaches, toxicity- and bioactivity-based assays can deliver valuable information about biological effects of complex materials in humans, other species or even ecosystems. However, the observed effects often cannot be clearly assigned to specific chemical compounds. In these cases, the establishment of an unambiguous cause-effect relationship is not possible. Effect-directed analysis tries to interconnect instrumental analytical techniques with a biological/biochemical entity, which identifies or isolates substances of biological relevance. Successful application has been demonstrated in many fields, either as proof-of-principle studies or even for complex samples. This review discusses the different approaches, advantages and limitations and finally shows some practical examples. The broad emergence of effect-directed analytical concepts might lead to a true paradigm shift in analytical chemistry, away from ever growing lists of chemical compounds. The connection of biological effects with the identification and quantification of molecular entities leads to relevant answers to many real life questions.
A new class of boron-dipyrromethene (BDP or BODIPY) dyes was obtained by phenanthrene fusion to the β-pyrrole positions, absorbing in the wavelength range of important laser sources. Despite a 'propeller-like' distorted structure in the crystalline state, the chromophore absorbs (log ε ≥ 5) and fluoresces (Φf ≥ 0.8) strongly and can be easily turned into a fluorescence light-up probe. Incorporation into latex beads produces bright and photostable single-dye and Förster Resonance Energy Transfer (FRET) particles for microscopy applications.
Aflatoxins, a group of structurally related mycotoxins, are well known for their
toxic and carcinogenic effects in humans and animals. Aflatoxin derivatives and protein
conjugates are needed for diverse analytical applications. This work describes a reliable
and fast synthesis of novel aflatoxin derivatives, purification by preparative HPLC and
characterisation by ESI-MS and one- and two-dimensional NMR. Novel aflatoxin bovine
serum albumin conjugates were prepared and characterised by UV absorption and
MALDI-MS. These aflatoxin protein conjugates are potentially interesting as immunogens
for the generation of aflatoxin selective antibodies with novel specificities.
A new type of biodetector was designed based on a bioluminescence test with the bacterium Vibrio fischeri performed in a liquid continuous flow-through system. Here we describe the modification of a commercial tube luminescence detector to work in the flow mode by building a new flow cell holder and a new case including top cover to connect the flow cell with the waste and the incubation capillary in a light-proof manner. As different samples were injected successively it was necessary to keep the individual peaks separated. This was done using an air-segmented flow in the reaction coil. To afford fast screening, the incubation time of the sample and the Vibrio fischeri, which equaled the dead time of the detection system, was set at 5.6 min. Rapid monitoring of toxic substances is achieved by using 20 µL of sample and flow-rates of 110150 µL min-1. As a proof-of-principle, we show results for the detection of five selected di-, tri- and tetrachlorophenols at different concentrations varying from 1 to 200 mg L-1. Calculation of inhibition rates and EC50 values were performed and compared with corresponding values from the DIN EN ISO 11348-2 microplate format. Compared with the latter, the inhibition rates obtained with our flow-through biodetector for the compounds tested were generally about twofold lower, but importantly, a much faster detection is possible.
Set them free: Brightly fluorescent indicators that are loaded into mesoporous silica nanoparticle carriers, capped with bulky antibodies, are released into the lateral flow of a test strip upon analyte arrival. Integration of the system into a rapid, simple flow test with fluorescence readout is applied for the selective and sensitive determination of the presence of triacetone triperoxide (TATP) as a prototype small-molecule analyte (see figure).
Antibodies are a promising tool for the fast and selective trace detection of explosives. Unfortunately, the production of high-quality antibodies is not trivial and often expensive. Therefore, excellent antibodies are a rare and limiting resource in fields such as biosensing, environmental analysis, diagnostics, cancer therapy, and proteomics. Here, we report the synthesis, bioconjugation, and application of the structurally optimized hapten 6-(2,4,6-trinitro)-phenylhexanoic acid to improve the selectivity and sensitivity of antibodies for the detection of one of the most important explosives, trinitrotoluene. With a conjugate of bovine serum albumin and a highly purified N-hydroxy-succinimide (NHS)activated hapten, two rabbits were immunized to obtain polyclonal antibodies. The immunization process was monitored by enzyme-linked immunosorbent assay to gain information about the progress of antibody titer and affinity. Finally, the polyclonal antibodies reached an affinity constant of (5.1 ± 0.6) × 109l/mol (rabbit R1) and (2.3 ± 0.2) × 109l/mol (rabbit R2). The respective assays show a minimum test midpoint (IC50 value) of 0.1 ± 0.01 µg/l (R1) and 0.2 ± 0.02 µg/l (R2) and a working range of 0.005 to 150 µg/l (R1) and 0.007 to 200 µg/l (R2), which corresponds to more than four orders of magnitude for both. This is quite remarkable for a competitive immunoassay, which is often believed to have a narrow dynamic range. The limit of detection was calculated to 0.6 ng/l (R1) and 1.5 ng/l (R2), which is up to 100 times improvement in relation to the assay of Zeck et al. (1999) on the basis of a monoclonal antibody. The excellent selectivity of the polyclonal antibodies was comprehensively examined by determining the cross-reactivity to common explosives and other nitroaromatics including nitro musk components. The widely held belief that polyclonal antibodies generally display higher cross-reactivities than monoclonals could be disproved.
A series of new epoxide-based monoliths is synthesized by self-polymerization of polyglycerol polyglycidyl ether as porous support for affinity chromatography. Porosity and mean pore sizes are investigated as a function of the porogen ratio and analyzed by mercury porosimetry. The morphologies are visualized by environmental scanning electron microscope. With a particularly rigid monolith prepared with 75 vol% porogen (66% porosity and 12 µm mean pore size), a capillary column (0.5 mm ID) is prepared and directly functionalized with recombinant protein A to extract immunoglobulin G from rabbit serum.
Algal blooms are a frequent phenomenon in nearly all kinds of fresh water. Global warming and eutrophication by waste water, air pollution and fertilizers seem to lead to an increased frequency of occurrence. Many cyanobacteria produce hazardous and quite persistent toxins, which can contaminate the respective water bodies. This may limit the use of the raw water for many purposes. The purification of the contaminated water might be quite costly, which makes a continuous and large scale treatment economically unfeasible in many cases. Due to the obvious risks of algal toxins, an online or mobile detection method would be highly desirable. Several biosensor systems have been presented in the literature for this purpose. In this review, their mode of operation, performance and general suitability for the intended purpose will be described and critically discussed. Finally, an outlook on current developments and future prospects will be given.
Silicon photonic micro-ring resonators (MRR) developed on the silicon-on-insulator (SOI) platform, owing to their high sensitivity and small footprint, show great potential for many chemical and biological sensing applications such as label-free detection in environmental monitoring, biomedical engineering, and food analysis. In this tutorial,we provide the theoretical background and give design guidelines for SOI-based MRR as well as examples of surface functionalization procedures for label-free detection of molecules. After introducing the advantages and perspectives of MRR, fundamentals of MRR are described in detail, followed by an introduction to the fabrication methods, which are based on a complementary metal-oxide semiconductor (CMOS) technology. Optimization of MRR for chemical and biological sensing is provided, with special emphasis on the optimization of waveguide geometry. At this point, the difference between chemical bulk sensing and label-free surface sensing is explained, and definitions like waveguide sensitivity, ring sensitivity, overall sensitivity as well as the limit of detection (LoD) of MRR are introduced. Further, we show and explain chemical bulk sensing of sodium chloride (NaCl) in water and provide a recipe for label-free surface sensing.
Current trends in materials and life sciences are flanked by the need to push detection limits to single molecules or single cells, enable the characterization of increasingly complex matrices or sophisticated nanostructures, speed up the time of analysis, reduce instrument complexity and costs, and improve the reliability of data. This requires suitable analytical tools such as spectroscopic, separation and imaging techniques, mass spectrometry, and hyphenated techniques as well as sensors and their adaptation to application-specific challenges in the environmental, food, consumer product, health sector, nanotechnology, and bioanalysis. Increasing concerns about health threatening known or emerging pollutants in drinking water, consumer products, and food and about the safety of nanomaterials led to a new awareness of the importance of analytical sciences. Another important driver in this direction is the increasing demand by legislation, particularly in view of the 17 sustainable development goals by the United Nations addressing clean energy, industry, and innovation, sustainable cities, clean water, and responsible consumption and production. In this respect, also the development of analytical methods that enable the characterization of material flows in production processes and support recycling concepts of precious raw materials becomes more and more relevant. In the future, this will provide the basis for greener production in the chemical industry utilizing recycled or sustainable starting materials.
This makes analytical chemistry an essential player in terms of the circular economy helping to increase the sustainability of production processes. In the life sciences sector, products based on proteins, such as therapeutic and diagnostic antibodies, increase in importance. These increasingly biotechnologically produced functional biomolecules pose a high level of complexity of matrix and structural features that can be met only by highly advanced methods for separation, characterization, and detection. In addition, metrological traceability and target definition are still significant challenges for the future, particularly in the life sciences.
However, innovative reference materials as required for the health and food sector and the characterization of advanced materials can only be developed when suitable analytical protocols are available. The so-called reproducibility crisis in sciences underlines the importance of improved measures of quality control for all kinds of measurements and material characterization. This calls for thorough method validation concepts, suitable reference materials, and regular interlaboratory comparisons of measurements as well as better training of scientists in analytical sciences.
The important contribution of analytical sciences to these developments is highlighted by a broad collection of research papers, trend articles, and critical reviews from these different application fields. Special emphasis is dedicated to often-overlooked quality assurance and reference materials.
ADAMTS4-specific MR-probe to assess aortic aneurysms in vivo using synthetic peptide libraries
(2022)
The incidence of abdominal aortic aneurysms (AAAs) has substantially increased during the last 20 years and their rupture remains the third most common cause of sudden death in the cardiovascular field after myocardial infarction and stroke. The only established clinical parameter to assess AAAs is based on the aneurysm size. Novel biomarkers are needed to improve the assessment of the risk of rupture. ADAMTS4 (A Disintegrin And Metalloproteinase with ThromboSpondin motifs 4) is a strongly upregulated proteoglycan cleaving enzyme in the unstable course of AAAs. In the screening of a one-bead-one-compound library against ADAMTS4, a low-molecular-weight cyclic peptide is discovered with favorable properties for in vivo molecular magnetic resonance imaging applications. After identification and characterization, it’s potential is evaluated in an AAA mouse model. The ADAMTS4-specific probe enables the in vivo imaging-based prediction of aneurysm expansion and rupture.
MALDI-TOF-MS-Based Identification of Monoclonal Murine Anti-SARS-CoV-2 Antibodies within One Hour
(2022)
During the SARS-CoV-2 pandemic, many virus-binding monoclonal antibodies have been developed for clinical and diagnostic purposes. This underlines the importance of antibodies as universal bioanalytical reagents. However, little attention is given to the reproducibility crisis that scientific studies are still facing to date. In a recent study, not even half of all research antibodies mentioned in publications could be identified at all. This should spark more efforts in the search for practical solutions for the traceability of antibodies. For this purpose, we used 35 monoclonal antibodies against SARS-CoV-2 to demonstrate how sequence-independent antibody identification can be achieved by simple means applied to the protein. First, we examined the intact and light chain masses of the antibodies relative to the reference material NIST-mAb 8671. Already half of the antibodies could be identified based solely on these two parameters. In addition, we developed two complementary peptide mass fingerprinting methods with MALDI-TOF-MS that can be performed in 60 min and had a combined sequence coverage of over 80%. One method is based on the partial acidic hydrolysis of the protein by 5 mM of sulfuric acid at 99 degrees C. Furthermore, we established a fast way for a tryptic digest without an alkylation step. We were able to show that the distinction of clones is possible simply by a brief visual comparison of the mass spectra. In this work, two clones originating from the same immunization gave the same fingerprints. Later, a hybridoma sequencing confirmed the sequence identity of these sister clones. In order to automate the spectral comparison for larger libraries of antibodies, we developed the online software ABID 2.0. This open-source software determines the number of matching peptides in the fingerprint spectra. We propose that publications and other documents critically relying on monoclonal antibodies with unknown amino acid sequences should include at least one antibody fingerprint. By fingerprinting an antibody in question, its identity can be confirmed by comparison with a library spectrum at any time and context.
Fast and accurate determination of the protein content of a sample is an important and non-trivial task of many biochemical, biomedical, food chemical, pharmaceutical, and environmental research activities. Different methods of total protein determination are used for a wide range of proteins with highly variable properties in complex matrices. These methods usually work reasonably well for proteins under controlled conditions, but the results for non-standard and complex samples are often questionable. Here, we compare new and well-established methods, including traditional amino acid analysis (AAA), aromatic amino acid analysis (AAAA) based on the amino acids phenylalanine and tyrosine, reversed-phase liquid chromatography of intact proteins with UV absorbance measurements at 220 and 280 nm (LC-220, LC-280), and colorimetric assays like Coomassie Blue G-250 dye-binding assay (Bradford) and bicinchoninic acid (BCA) assay. We investigated different samples, including proteins with challenging properties, chemical modifications, mixtures, and complex matrices like air particulate matter and pollen extracts. All methods yielded accurate and precise results for the protein and matrix used for calibration. AAA, AAAA with fluorescence detection, and the LC-220 method yielded robust results even under more challenging conditions (variable analytes and matrices). These methods turned out to be well-suited for reliable determination of the protein content in a wide range of samples, such as air particulate matter and pollen.
In this work, the optimization of the immunochemical response of antibody-gated indicator delivery (gAID) systems prepared with mesoporous silica nanoparticles has been studied along various lines of system tailoring, targeting the peroxide-type explosive TATP as an exemplary analyte. The mechanism of detection of these gAID systems relies on a displacement of an antibody “cap” bound to hapten derivatives anchored to the surface of a porous hybrid material, allowing the indicator cargo stored in the mesopores to escape and massively amplify the analyte-related signal. Since our aim was to obtain gAID systems with the best possible response in terms of sensitivity, selectivity, and assay time, sera obtained from different immunization boosts were screened, the influence of auxiliary reagents was assessed, structural hapten modification (hapten heterology) was investigated, and various indicator dyes and host materials were tested. Considering that highly selective and sensitive immunological responses are best obtained with high-affinity antibodies which, however, could possess rather slow dissociation constants, leading to slow responses, the main challenge was to optimize the immunochemical recognition system for a rapid response while maintaining a high sensitivity and selectivity. The best performance was observed by grafting a slightly mismatching (heterologous) hapten to the surface of the nanoparticles in combination with high-affinity antibodies as “caps”, yielding for the first time gAID nanomaterials for which the response time could be improved from hours to <5 min. The materials showed favorable detection limits in the lower ppb range and discriminated TATP well against H2O2 and other explosives. Further optimization led to straightforward integration of the materials into a lateral flow assay without further treatment or conditioning of the test strips while still guaranteeing remarkably fast overall assay times.
The allergenic and inflammatory potential of proteins can be enhanced by chemical modification upon exposure to atmospheric or physiological oxidants. The molecular mechanisms and kinetics of such modifications, however, have not yet been fully resolved. We investigated the oligomerization and nitration of the grass pollen allergen Phl p 5 by ozone (O3), nitrogen dioxide (NO2), and peroxynitrite (ONOO–). Within several hours of exposure to atmospherically relevant concentration levels of O3 and NO2, up to 50% of Phl p 5 were converted into protein oligomers, likely by formation of dityrosine cross-links. Assuming that tyrosine residues are the preferential site of nitration, up to 10% of the 12 tyrosine residues per protein monomer were nitrated. For the reaction with peroxynitrite, the largest oligomer mass fractions (up to 50%) were found for equimolar concentrations of peroxynitrite over tyrosine residues. With excess peroxynitrite, the nitration degrees increased up to 40% whereas the oligomer mass fractions decreased to 20%. Our results suggest that protein oligomerization and nitration are competing processes, which is consistent with a two-step mechanism involving a reactive oxygen intermediate (ROI), as observed for other proteins. The modified proteins can promote pro-inflammatory cellular signaling that may contribute to chronic inflammation and allergies in response to air pollution.
In this work, a cost-effective optofluidic system is proposed and preliminary experimental results are presented. A microfluidic channel monolithically integrated into a photonic integrated circuit technology is used in conjunction with a cyclic olefin copolymer (COC) substrate to provide fluidic in- and output ports. We report on initial experimental results as well as on the simple and cost-effective fabrication of this optofluidic system by means of micro-milling.
The Protocol Gap
(2021)
Although peer review is considered one of the main pillars of modern science, experimental methods and protocols seem to be not a rigorous subject of this process in many papers. Commercial equipment, test kits, labeling kits, previously published concepts, and standard protocols are often considered to be not worth a detailed description or validation. Even more disturbing is the extremely biased citation behavior in this context, which sometimes leads to surrogate citations to avoid low-impact journals, preprints, or to indicate traditional practices. This article describes some of these surprising habits and suggests some measures to avoid the most unpleasant effects, which in the long term may undermine the credibility of science as a whole.
The trafficking of illegal drugs by criminal networks at borders, harbors, or airports is an increasing issue for public health as these routes ensure the main supply of illegal drugs. The prevention of drug smuggling, including the installation of scanners and other analytical devices to detect small traces of drugs within a reasonable time frame, remains a challenge. The presented immunosensor is based on a monolithic affinity column with a large excess of immobilized hapten, which traps fluorescently labeled antibodies as long as the analyte cocaine is absent. In the presence of the drug, some binding sites of the antibody will be blocked, which leads to an immediate breakthrough of the labeled protein, detectable by highly sensitive laser-induced fluorescence with the help of a Peltier-cooled complementary metal-oxide-semiconductor (CMOS) camera. Liquid handling is performed with high-precision syringe pumps and microfluidic chip-based mixing devices and flow cells. The biosensor achieved limits of detection of 7 ppt (23 pM) of cocaine with a response time of 90 s and a total assay time below 3 min. With surface wipe sampling, the biosensor was able to detect 300 pg of cocaine. This immunosensor belongs to the most sensitive and fastest detectors for cocaine and offers near-continuous analyte measurement.
A novel stationary phase for affinity separations is presented. This material is based on sintered borosilicate glass readily available as semi-finished filter plates with defined porosity and surface area. The material shows fast binding kinetics and excellent long-term stability under real application conditions due to lacking macropores and high mechanical rigidity. The glass surface can be easily modified with standard organosilane chemistry to immobilize selective binders or other molecules used for biointeraction. In this paper, the manufacturing of the columns and their respective column holders by 3D printing is shown in detail. The model system protein A/IgG was chosen as an example to examine the properties of such monolithic columns under realistic application conditions. Several specifications, such as (dynamic) IgG capacity, pressure stability, long-term performance, productivity, non-specific binding, and peak shape, are presented. It could be shown that due to the very high separation speed, 250 mg antibody per hour and column can be collected, which surpasses the productivity of most standard columns of the same size. The total IgG capacity of the shown columns is around 4 mg (5.5 mg/mL), which is sufficient for most tasks in research laboratories. The cycle time of an IgG separation can be less than 1 min. Due to the glass material’s excellent pressure resistance, these columns are compatible with standard HPLC systems. This is usually not the case with standard affinity columns, limited to manual use or application in low-pressure systems. The use of a standard HPLC system also improves the ability for automation, which enables the purification of hundreds of cell supernatants in one day. The sharp peak shape of the elution leads to an enrichment effect, which might increase the concentration of IgG by a factor of 3. The final concentration of IgG can be around 7.5 mg/mL without the need for an additional nano-filtration step. The purity of the IgG was > 95% in one step and nearly 99% with a second polishing run.