Enzymes for microplastic-free agricultural soils.

Plastic mulch films and biofertilizers (processed sewage sludge, compost or manure) have helped to increase crop yields. However, there is increasing evidence that these practices significantly contribute to microplastic contamination in agricultural soils, affecting biodiversity and soil health. Here, we draw attention to the use of hydrolase enzymes that depolymerize polyester-based plastics as a bioremediation technique for agricultural soils (in situ), biofertilizers and irrigation water (ex situ), and discuss the need for fully biodegradable plastic mulches. We also highlight the need for ecotoxicological assessment of the proposed approach and its effects on different soil organisms. Enzymes should be optimized to work effectively and efficiently under the conditions found in natural soils (typically, moist solids at an ambient temperature with low salinity). Such optimization is also necessary to ensure that already distressed ecosystems are not disrupted any further.

A deeper understanding of the spontaneous derepression of the URA3 gene in MaV203 Saccharomyces cerevisiae and its implications for protein engineering and the reverse two-hybrid system.

Within the field of protein-based biomaterials, the need exists for both covalent and oriented bioconjugation strategies for improved performance. Such bioconjugation reactions can be facilitated by engineering proteins with chemically activated amino acids at strategically chosen sites. The incorporation of these unnatural amino acids (uAAs) can be achieved by using the nonsense suppression technique. This requires an aminoacyl-tRNA-synthetase (aaRS) that exclusively recognizes the uAA and loads it to the corresponding tRNA. Appropriate (aaRS) mutants can be found through reverse engineering using the Saccharomyces cerevisiae strain MaV203. This strain contains a counterselectable, Gal4p-inducible SPAL10::URA3 fusion and deletions in the endogenous GAL80 and GAL4 genes. Therefore, it has been used extensively for the screening of aaRS mutant libraries. It is generally assumed that the SPAL10 promoter actively represses the URA3 gene in the absence of Gal4p, resulting in MaV203 cells with a Ura- phenotype. The current contribution reveals that in a small fraction of MaV203 cells, a basal expression of the URA3 gene occurs. The unexpected URA3 expression is reported for the first time, and the nature of the mutation causing this expression was identified as a spontaneous recessive mutation in a single gene of a protein involved in the repression of the SPAL10 promoter. The basal URA3 expression causes aaRS mutants to be missed, which affects the outcome of the library screening. It is demonstrated that the use of diploid cells can circumvent the MaV203 Ura+ phenotype, allowing for an optimization of S. cerevisiae library screening.

A Novel Biomimetic Tool for Assessing Vitamin K Status Based on Molecularly Imprinted Polymers.

Vitamin K was originally discovered as a cofactor required to activate clotting factors and has recently been shown to play a key role in the regulation of soft tissue calcification. This property of vitamin K has led to an increased interest in novel methods for accurate vitamin K detection. Molecularly Imprinted Polymers (MIPs) could offer a solution, as they have been used as synthetic receptors in a large variety of biomimetic sensors for the detection of similar molecules over the past few decades, because of their robust nature and remarkable selectivity. In this article, the authors introduce a novel imprinting approach to create a MIP that is able to selectively rebind vitamin K1. As the native structure of the vitamin does not allow for imprinting, an alternative imprinting strategy was developed, using the synthetic compound menadione (vitamin K3) as a template. Target rebinding was analyzed by means of UV-visible (UV-VIS) spectroscopy and two custom-made thermal readout techniques. This analysis reveals that the MIP-based sensor reacts to an increasing concentration of both menadione and vitamin K1. The Limit of Detection (LoD) for both compounds was established at 700 nM for the Heat Transfer Method (HTM), while the optimized readout approach, Thermal Wave Transport Analysis (TWTA), displayed an increased sensitivity with a LoD of 200 nM. The sensor seems to react to a lesser extent to Vitamin E, the analogue under study. To further demonstrate its potential application in biochemical research, the sensor was used to measure the absorption of vitamin K in blood serum after taking vitamin K supplements. By employing a gradual enrichment strategy, the sensor was able to detect the difference between baseline and peak absorption samples and was able to quantify the vitamin K concentration in good agreement with a validation experiment using High-Performance Liquid Chromatography (HPLC). In this way, the authors provide a first proof of principle for a low-cost, straightforward, and label-free vitamin K sensor.

Label-Free Detection of Small Organic Molecules by Molecularly Imprinted Polymer Functionalized Thermocouples: Toward In Vivo Applications.

Molecularly imprinted polymers (MIPs), synthetic polymeric receptors, have been combined successfully with thermal transducers for the detection of small molecules in recent years. However, up until now they have been combined with planar electrodes which limits their use for in vivo applications. In this work, a new biosensor platform is developed by roll-coating MIP particles onto thermocouples, functionalized with polylactic acid (PLLA). As a first proof-of-principle, MIPs for the neurotransmitter dopamine were incorporated into PLLA-coated thermocouples. The response of the synthetic receptor layer to an increasing concentration of dopamine in buffer was analyzed using a homemade heat-transfer setup. Binding of the template to the MIP layer blocks the heat transport through the thermocouple, leading to less heat loss to the environment and an overall higher temperature in the measuring chamber. The measured temperature increase is correlated to the neurotransmitter concentration, which enables measurement of dopamine levels in the micromolar regime. To demonstrate the general applicability of the proposed biosensor platform, thermocouples were functionalized with similar MIPs for cortisol and serotonin, indicating a similar response and limit-of-detection. As the platform does not require planar electrodes, it can easily be integrated in, e.g., a catheter. In this way, it is an excellent fit for the current niche in the market of therapeutics and diagnostics. Moreover, the use of a biocompatible and disposable PLLA-layer further illustrates its potential for in vivo diagnostics.

Biomimetic Bacterial Identification Platform Based on Thermal Wave Transport Analysis (TWTA) through Surface-Imprinted Polymers.

This paper introduces a novel bacterial identification assay based on thermal wave analysis through surface-imprinted polymers (SIPs). Aluminum chips are coated with SIPs, serving as synthetic cell receptors that have been combined previously with the heat-transfer method (HTM) for the selective detection of bacteria. In this work, the concept of bacterial identification is extended toward the detection of nine different bacterial species. In addition, a novel sensing approach, thermal wave transport analysis (TWTA), is introduced, which analyzes the propagation of a thermal wave through a functional interface. The results presented here demonstrate that bacterial rebinding to the SIP layer resulted in a measurable phase shift in the propagated wave, which is most pronounced at a frequency of 0.03 Hz. In this way, the sensor is able to selectively distinguish between the different bacterial species used in this study. Furthermore, a dose-response curve was constructed to determine a limit of detection of 1 × 104 CFU mL-1, indicating that TWTA is advantageous over HTM in terms of sensitivity and response time. Additionally, the limit of selectivity of the sensor was tested in a mixed bacterial solution, containing the target species in the presence of a 99-fold excess of competitor species. Finally, a first application for the sensor in terms of infection diagnosis is presented, revealing that the platform is able to detect bacteria in clinically relevant concentrations as low as 3 × 104 CFU mL-1 in spiked urine samples.

Studying the Drug Delivery Kinetics of a Nanoporous Matrix Using a MIP-Based Thermal Sensing Platform.

The implementation of Molecularly Imprinted Polymers (MIPs) into sensing systems has been demonstrated abundantly over the past few decades. In this article, a novel application for an MIP-based thermal sensing platform is introduced by using the sensor to characterize the drug release kinetics of a nanoporous silver-organic framework. This Ag nanoporous matrix was loaded with acetylsalicylic acid (aspirin) which was used as a model drug compound in this study. The drug elution properties were studied by placing the nanoporous matrix in phosphate buffered saline solution for two days and measuring the drug concentration at regular time intervals. To this extent, an acrylamide-based MIP was synthesized that was able to detect aspirin in a specific and selective manner. Rebinding of the template to the MIP was analyzed using a thermal sensor platform. The results illustrate that the addition of aspirin into the sensing chamber leads to a concentration-dependent increase in the phase shift of a thermal wave that propagates through the MIP-coated sensor chip. After constructing a dose-response curve, this system was used to study the drug release kinetics of the nanoporous matrix, clearly demonstrating that the metalorganic framework releases the drug steadily over the course of the first hour, after which the concentration reaches a plateau. These findings were further confirmed by UV⁻Visible spectroscopy, illustrating a similar time-dependent release in the same concentration range, which demonstrates that the MIP-based platform can indeed be used as a low-cost straightforward tool to assess the efficacy of drug delivery systems in a lab environment.

Enhanced Biosensor Platforms for Detecting the Atherosclerotic Biomarker VCAM1 Based on Bioconjugation with Uniformly Oriented VCAM1-Targeting Nanobodies.

Surface bioconjugation of biomolecules has gained enormous attention for developing advanced biomaterials including biosensors. While conventional immobilization (by physisorption or covalent couplings using the functional groups of the endogenous amino acids) usually results in surfaces with low activity, reproducibility and reusability, the application of methods that allow for a covalent and uniformly oriented coupling can circumvent these limitations. In this study, the nanobody targeting Vascular Cell Adhesion Molecule-1 (NbVCAM1), an atherosclerotic biomarker, is engineered with a C-terminal alkyne function via Expressed Protein Ligation (EPL). Conjugation of this nanobody to azidified silicon wafers and Biacore™ C1 sensor chips is achieved via Copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) "click" chemistry to detect VCAM1 binding via ellipsometry and surface plasmon resonance (SPR), respectively. The resulting surfaces, covered with uniformly oriented nanobodies, clearly show an increased antigen binding affinity, sensitivity, detection limit, quantitation limit and reusability as compared to surfaces prepared by random conjugation. These findings demonstrate the added value of a combined EPL and CuAAC approach as it results in strong control over the surface orientation of the nanobodies and an improved detecting power of their targets-a must for the development of advanced miniaturized, multi-biomarker biosensor platforms.

Protein engineering for directed immobilization.

Much effort has been put into the optimization of the functional activity of proteins. For biosensors this protein functional optimization will increase the biosensor's sensitivity and/or selectivity. However, the strategy chosen for the immobilization of the proteins to the sensor surface might be equally important for the development of sensor surfaces that are optimally biologically active. Several studies published in recent years show that the oriented immobilization of the bioactive molecules improves the sensor's properties. In this review, we discuss the state of the art of the different protein immobilization strategies that are commonly used today with a special focus on biosensor applications. These strategies include nonspecific immobilization techniques either by physical adsorption, by covalent coupling, or by specific immobilization via site-specifically introduced tags or bio-orthogonal chemistry. The different tags and bio-orthogonal chemistry available and the techniques to site-specifically introduce these groups in proteins are also discussed.

Accumulation and toxicity of cadmium in the aquatic oligochaete Tubifex tubifex: a kinetic modeling approach.

Heavy metal pollution is a serious threat to ecosystem functioning. Different approaches have been developed to relate the exposure of heavy metals to their accumulation and toxicity. One approach is to relate metal toxicity to the concentrations of the metals in the whole body or a specific target tissue instead of the external exposure concentrations. To test the usefulness of this approach, the relationship between cadmium exposure, accumulation, and toxicity was investigated using an oligochaete worm and kinetic modeling. The uptake and elimination of cadmium by the aquatic oligochaete Tubifex tubifex from the aqueous phase was studied as function of time at different exposure concentrations using both radioactive and non-radioactive cadmium. A two-compartmental pharmacokinetic model was constructed and parametrized by fitting the model to the measured cadmium body concentrations during exposure to different cadmium concentrations. The uptake rate constants were dependent on the cadmium exposure concentration, and this relation could be well-described by incorporation of Michaelis-Menten type uptake kinetics. The toxicity of cadmium was analyzed by determining the lethal exposure concentration associated with a mortality of 50% (LC50) at different time points. LC50 values decreased with increasing exposure time reaching the incipient lethal level after 15 d. Critical body concentrations (CBC) associated with 50% mortality were calculated by combining the model-predicted pharmacokinetic parameters and the measured LC50 values. The predicted mean CBC (0.32 micromol/g wet weight +/- 0.02) was in good agreement with the experimentally obtained CBC for cadmium found in T. tubifex (0.37 micromol/g wet weight +/- 0.07) and appeared to be independent of exposure time and exposure concentration. Our results show that a pharmacokinetic modeling approach provides a tool to link metal exposure to availability, accumulation, and toxicity under variable exposure scenarios taking into account the kinetics of the processes.