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Eingeladener Vortrag
- nein (4)
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.
Triacetone triperoxide (TATP), an improvised explosive, is a potential security threat because of its cost-efficient synthesis and the difficulty in detecting it. A highly selective antibody could provide the necessary specificity to the detection process. To obtain antibodies, a hapten made from acetone, hydrogen peroxide, and 7-oxooctanoic acid has been designed, synthesized, and confirmed by NMR that displays the utmost similarity to the analyte. The single-crystal X-ray structures of the solvated species TATP·methanol (1:1) and the TATP derivate were determined. In both compounds, the molecules exhibit D3 symmetry and adopt a twisted boat-chair conformation. The hapten was coupled to bovine serum albumin, and mice were immunized. An immune response against TATP was elicited, and selective antibodies were detected in the mouse serum, which should be very useful for the development of a TATP biosensor system. An ELISA with a limit of detection for TATP of 65 µg L-1 is shown.
Zusammenfassung Selektivität
1. Widersprüchliche Definitionen in unterschiedlichen Bereichen
2. Analytische Definition (pragmatisch): Selektivität ist die Fähigkeit einer Methode zur Unterscheidung aller interessierender Stoffe in der Probe.
3. Tests: Blindwerte, Leerwerte, Blank Values; Peakform
4. Wichtige Einflussgrößen: Trennleistung, Auflösung, Peakkapazität, Trennkapazität
5. Verbesserung durch: Kopplungsverfahren, Änderung der chromatographischen „Selektivität“, Orthogonalität
6. Wichtig ist auch die Komplexität der Probe(n)
7. Selektivität in der Immunchemie/Biochemie wird oft als Kreuzreaktion gemessen.
Zusammenfassung Robustheit
1. Sehr individuelle Kriterien – sinnvolle Auswahl notwendig!
2. Wichtige Testphasen:
a)Änderung von Methodenparametern
b)Stabilität über die Zeit
c)Überführung in die Routine
3. Ringversuche bzw. Laborvergleichsmessungen
4. Wichtigstes Vergleichskriterium: Relative Verfahrensstandardabweichung
5. Extratipp: Maximale Diversität der Testproben sicherstellen (besonders bezüglich der Matrix)
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.
Homochirality is an obvious feature of life on Earth. On the other hand, extraterrestrial samples contain largely racemic compounds. The same is true for any common organic synthesis. Therefore, it has been a perplexing puzzle for decades how these racemates could have formed enantiomerically enriched fractions as a basis for the origin of homochiral life forms. Numerous hypotheses have been put forward as to how preferentially homochiral molecules could have formed and accumulated on Earth. In this article, it is shown that homochirality of the abiotic organic pool at the time of formation of the first self-replicating molecules is not necessary and not even probable. It is proposed to abandon the notion of a molecular ensemble and to focus on the level of individual molecules. Although the formation of the first self-replicating, most likely homochiral molecule, is a seemingly improbable event, on a closer look, it is almost inevitable that some homochiral molecules have formed simply on a statistical basis. In this case, the non-selective leap to homochirality would be one of the first steps in chemical evolution directly out of a racemic “ocean”. Moreover, most studies focus on the chirality of the primordial monomers with respect to an asymmetric carbon atom. However, any polymer with a minimal size that allows folding to a secondary structure would spontaneously lead to asymmetric higher structures (conformations). Most of the functions of these polymers would be influenced by this inherently asymmetric folding. Furthermore, a concept of physical compartmentalization based on rock nanopores in analogy to nanocavities of digital immunoassays is introduced to suggest that complex cell walls or membranes were also not required for the first steps of chemical evolution. To summarize, simple and universal mechanisms may have led to homochiral self-replicating systems in the context of chemical evolution. A homochiral monomer pool is deemed unnecessary and probably never existed on primordial Earth.
Homochirality is an obvious feature of life on Earth. On the other hand, extraterrestrial samples contain largely racemic compounds. The same is true for any common organic synthesis. Therefore, it has been a perplexing puzzle for decades how these racemates could have formed enantiomerically enriched fractions as a basis for the origin of homochiral life forms. Numerous hypotheses have been put forward as to how preferentially homochiral molecules could have formed and accumulated on Earth. In this article, it is shown that homochirality of the abiotic organic pool at the time of formation of the first self-replicating molecules is not necessary and not even probable. It is proposed to abandon the notion of a molecular ensemble and to focus on the level of individual molecules. Although the formation of the first self-replicating, most likely homochiral molecule is a seemingly improbable event, on a closer look, it is almost inevitable that homochiral molecules have formed simply on a statistical basis. In this case, the non-selective leap to homochirality would be one of the first steps in chemical evolution directly out of a racemic “ocean”. Moreover, most studies focus on the chirality of the primordial monomers with respect to an asymmetric carbon atom. However, any polymer with a minimal size that allows folding to a secondary structure, would spontaneously lead to asymmetric higher structures (conformations). Most of the functions of these polymers would be influenced by this inherently asymmetric folding. To summarize, simple and universal mechanisms may have led to homochiral self-replicating systems in the context of chemical evolution. A homochiral monomer pool is deemed unnecessary and probably never existed on primordial Earth.
The quality of research antibodies is an issue for decades. Although several papers have been published to improve the situation, their impact seems to be limited. This publication makes the effort to simplify the description of validation criteria in a way that the occasional antibody user is able to assess the validation level of an immunochemical reagent. A simple, 1-page checklist is supplied for the practical application of these criteria.
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.
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 minute. 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 nanofiltration step. The purity of the IgG was > 95% in one step and nearly 99% with a second polishing run.
Chemical modifications such as nitration and cross-linking may enhance the allergenic potential of proteins. The kinetics and mechanisms of the underlying chemical processes, however, are not yet well understood. Here, we present a size-exclusion chromatography/spectrophotometry method (SEC-HPLC-DAD) that allows a simultaneous detection of mono-, di-, tri-, and higher protein oligomers, as well as their individual nitration degrees (NDs). The ND results of proteins from this new method agree well with the results from an alternative well-established method, for the analysis of tetranitromethane (TNM)- and nitrogen dioxide and ozone (NO2/O3)-nitrated protein samples. Importantly, the NDs for individual oligomer fractions can be obtained from the new method, and also, we provide a proof of principle for the calculation of the concentrations for individual protein oligomer fractions by their determined NDs, which will facilitate the investigation of the kinetics and mechanism for protein tyrosine nitration and cross-linking.
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.
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.
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).
Hydroxyl radical-induced oxidation of proteins and peptides can lead to the cleavage of the peptide, leading to a release of fragments. Here, we used high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) and pre-column online ortho-phthalaldehyde (OPA) derivatization-based amino acid analysis by HPLC with diode array detection and fluorescence detection to identify and quantify free amino acids released upon oxidation of proteins and peptides by hydroxyl radicals. Bovine serum albumin (BSA), ovalbumin (OVA) as model proteins, and synthetic tripeptides (comprised of varying compositions of the amino acids Gly, Ala, Ser, and Met) were used for reactions with hydroxyl radicals, which were generated by the Fenton reaction of iron ions and hydrogen peroxide. The molar yields of free glycine, aspartic acid, asparagine, and alanine per peptide or protein varied between 4 and 55%. For protein oxidation reactions, the molar yields of Gly (∼32-55% for BSA, ∼10-21% for OVA) were substantially higher than those for the other identified amino acids (∼5-12% for BSA, ∼4-6% for OVA). Upon oxidation of tripeptides with Gly in C-terminal, mid-chain, or N-terminal positions, Gly was preferentially released when it was located at the C-terminal site. Overall, we observe evidence for a site-selective formation of free amino acids in the OH radical-induced oxidation of peptides and proteins, which may be due to a reaction pathway involving nitrogen-centered radicals.
Referee Report 06 March 2017
(2017)
Quantitative 1H Nuclear Magnetic Resonance (qNMR) of Aromatic Amino Acids for Protein Quantification
(2022)
qNMR is a valuable technique for metrological studies due to the uniformity of its signal response for all chemical species of an isotope of interest, which enables compound-independent calibration. However, protein quantification remained challenging as large molecules produce wide, low-intensity signals that reduce the already low sensitivity. Combining qNMR with the hydrolysis of protein samples into amino acids circumvents many of these issues and facilitates the use of NMR spectroscopy for absolute protein and peptide quantification.In this work, different conditions have been tested for quantifying aromatic amino acids and proteins. First, we examined the pH-based signal shifts in the aromatic region. The preferable pH depends on the selection of the amino acids for quantification and which internal standard substance should be used to avoid peak overlap. Several aromatic compounds, such as terephthalic acid, sulfoisophthalic acid, and benzene tricarboxylic acid, have been applied as internal standards. The quantification of amino acids from an amino acid standard, as well as from a certified reference material (bovine serum albumin), was performed. Using the first two suggested internal standards, recovery was ~ 97 % for histidine, phenylalanine, and tyrosine at a concentration of approximately 1 mM in solution. Acidic hydrolysis of a certified reference material (CRM) of bovine serum albumin (BSA) and subsequent quantification of Phe and Tyr yielded recoveries of 98 ± 2 and 88 ± 4 %, respectively, at a protein concentration of 16 g/L or 250 µM.
Quantitative 1H Nuclear Magnetic Resonance (qNMR) of Aromatic Amino Acids for Protein Quantification
(2023)
Hydrolysis of protein samples into amino acids facilitates the use of NMR spectroscopy for protein and peptide quantification. Different conditions have been tested for quantifying aromatic amino acids and proteins. The pH-dependent signal shifts in the aromatic region of amino acid samples were examined. A pH of 12 was found to minimize signal overlap of the four aromatic amino acids. Several aromatic compounds, such as terephthalic acid, sulfoisophthalic acid, and benzene tricarboxylic acid, were applied as internal standards. The quantification of amino acids from an amino acid standard was performed. Using the first two suggested internal standards, recovery was ~97% for histidine, phenylalanine, and tyrosine at a concentration of approximately 1 mM in solution. Acidic hydrolysis of a certified reference material (CRM) of bovine serum albumin (BSA) and subsequent quantification of Phe and Tyr yielded recoveries of 98% ± 2% and 88% ± 4%, respectively, at a protein concentration of 16 g/L or 250 µM.
N-Hydroxysuccinimide (NHS) esters are the most important activated esters used in many different bioconjugation techniques, such as protein labelling by fluorescent dyes and enzymes, surface activation of chromatographic supports, microbeads, nanoparticles, and microarray slides, and also in the chemical synthesis of peptides. Usually, reactions with NHS esters are very reliable and of high yield, however, the compounds are sensitive to air moisture and water traces in solvents. Therefore, the quantification of NHS would be a very helpful approach to identify reagent impurities or degradation of stored NHS esters. No robust and sensitive method for the detection of NHS (or the more hydrophilic sulfo-NHS) has been reported yet. Here, a chromatographic method based on HILIC conditions and UV detection is presented, reaching a detection limit of about 1 mg L-1, which should be sensitive enough for most of the applications mentioned above. Exemplarily, the hydrolytic degradation of a biotin-NHS ester and a purity check of a fluorescent dye NHS ester are shown. An important advantage of this approach is its universality, since not the structurally variable ester compound is monitored, but the constant degradation product NHS or sulfo-NHS, which avoids the necessity to optimize the separation conditions and facilitates calibration considerably.
According to several recent studies, an unexpectedly high number of landmark papers seem to be not reproducible by Independent laboratories. Nontherapeutic antibodies used for research, diagnostic, food analytical, environmental, and other purposes play a significant role in this matter. Although some papers have been published offering suggestions to improve the situation, they do not seem to be comprehensive enough to cover the full complexity of this issue. In addition, no obvious improvements could be noticed in the field as yet. This article tries to consolidate the remarkable variety of conclusions and suggested activities into a more coherent conception. It is concluded that funding agencies and journal publishers need to take first and immediate measures to resolve these problems and lead the way to a more sustainable way of bioanalytical research, on which all can rely with confidence.