Nanoparticles for Use in Enzyme Assays

Molecular Aspects of the Functioning of Pathogenic Bacteria Biofilm Based on Quorum Sensing (QS) Signal-Response System and Innovative Non-Antibiotic Strategies for Their Elimination

One of the key mechanisms enabling bacterial cells to create biofilms and regulate crucial life functions in a global and highly synchronized way is a bacterial communication system called quorum sensing (QS). QS is a bacterial cell-to-cell communication process that depends on the bacterial population density and is mediated by small signalling molecules called autoinducers (AIs). In bacteria, QS controls the biofilm formation through the global regulation of gene expression involved in the extracellular polymeric matrix (EPS) synthesis, virulence factor production, stress tolerance and metabolic adaptation. Forming biofilm is one of the crucial mechanisms of bacterial antimicrobial resistance (AMR). A common feature of human pathogens is the ability to form biofilm, which poses a serious medical issue due to their high susceptibility to traditional antibiotics. Because QS is associated with virulence and biofilm formation, there is a belief that inhibition of QS activity called quorum quenching (QQ) may provide alternative therapeutic methods for treating microbial infections. This review summarises recent progress in biofilm research, focusing on the mechanisms by which biofilms, especially those formed by pathogenic bacteria, become resistant to antibiotic treatment. Subsequently, a potential alternative approach to QS inhibition highlighting innovative non-antibiotic strategies to control AMR and biofilm formation of pathogenic bacteria has been discussed.

Biomonitoring and risk assessment of naturally and chemically synthesized iron-oxide nanoparticles: A comparative approach

Nanostructured oxides and oxyhydroxides of iron are imperative constituents of the Earth's geological and biological processes i.e. biogeochemical cycles. So, the characteristic applications of iron oxide nanoparticles (FeONps) are closely linked to their surroundings and biological sinks. This work reports a low-cost green approach to promote 'waste-to-wealth' ideology by the direct and self-catalysis of iron rust into its nanoparticles (N-FeONps). A comparison is drawn based on the properties, morphologies, and applications after synthesizing FeONps by chemical precipitation method (C-FeONps). Spherical nanoparticles with vibrational properties are obtained in the size domain of 32 nm (N-FeONps) and 23 nm (C-FeONps). The application of Uniform deformation model, Uniform stress deformation model, Uniform deformation energy density model, and Size-strain plot models reveal comparatively greater defects in the crystal structures of C-FeONps. The biosafety profiling of natural and chemically designed nano-units performed on the species of bacteria, fungus, algae, and plants have shown enhanced safety terms associated with N-FeONps. The performance of N-FeONps has surpassed its chemical counterpart in medical applications such as antioxidant activity and anti-inflammatory activity with approximate percentages of 26 % and 51 % respectively. The findings of this piece of work favors the naturally obtained FeONps (N-FeONps), as they are economically viable, non-toxic, and have a greater antioxidant and anti-inflammatory arena. Hence, this waste-to-wealth ideology should be promoted for maintaining waste and designing solutions for the medical industries in one go.

Enzyme Sensing Using 2-Mercaptopyridine-Carbonitrile Reporters and Surface-Enhanced Raman Scattering

The high sensitivity and functional group selectivity of surface-enhanced Raman scattering (SERS) make it an attractive method for enzyme sensing, but there is currently a severe lack of enzyme substrates that release SERS reporter molecules with favorable detection properties. We find that 2-mercaptopyridine-3-carbonitrile ( o-MPN) and 2-mercaptopyridine-5-carbonitrile ( p-MPN) are highly effective as SERS reporter molecules that can be captured by silver or gold nanoparticles to give intense SERS spectra, each with a distinctive nitrile peak at 2230 cm^-1. p-MPN is a more sensitive reporter and can be detected at low nanomolar concentrations. An assay validation study synthesized two novel substrate molecules, Glc-o-MPN and Glc-p-MPN, and showed that they can be cleaved efficiently by β-glucosidase (K _m = 228 and 162 μM, respectively), an enzyme with broad industrial and biomedical utility. Moreover, SERS detection of the released reporters ( o-MPN or p-MPN) enabled sensing of β-glucosidase activity and β-glucosidase inhibition. Comparative experiments using a crude almond flour extract showed that the presence of β-glucosidase activity could be confirmed by SERS detection in a much shorter time period (>10 time shorter) than by UV-vis absorption detection. It is likely that a wide range of enzyme assays and diagnostic tests can be developed using 2-mercaptopyridine-carbonitriles as SERS reporter molecules.

Superior Peroxidase-Like activity of Gold Nanorattles in Ultrasensitive H2O2 Sensing and Antioxidant Screening

Nanozymes are artificial enzyme systems which are easy to produce, highly stable and cost-effective in comparison to natural enzymes. Herein, we evaluated the peroxidase like activity of gold nanorattles (AuNRTs) having a solid gold octahedron core and thin, porous cubic gold shell. We also prepared solid gold nanocube and nanosphere of similar sizes and surface charge as that of AuNRTs and compared its activity with standard horse radish peroxidase (HRP) enzyme. All the prepared nanostructures followed Michaelis-Menten kinetics as observed from their substrate vs initial reaction velocity plot using 3',5,5'-tetramethylbenzidine (TMB) as a substrate. The kinetic parameters demonstrated that AuNRTs possess the best nanozymatic activity with lowest K M and highest catalytic efficiency (K cat /K M ). The better activity of AuNRTs compared with other nanostructures and HRP could be attributed to the hollow porous structure with a solid core where different surfaces are available for the nanozymatic reaction. AuNRTs, being the best amongst the tested nanozymes were further used for the sensing of hydrogen peroxide (H 2 O 2 ) and it was able to sense H 2 O 2 down to 0.5 μM concentration. Further, two naturally occurring antioxidants, tannic acid and ascorbic acid showed inhibitory effect on the peroxidase like activity of AuNRTs in a concentration dependent manner which can be further be used for screening of antioxidants or for determining the antioxidant potential.

Covalent Attachment of Active Enzymes to Upconversion Phosphors Allows Ratiometric Detection of Substrates

Upconverting phosphors (UCPs) convert multiple low energy photons into higher energy emission via the process of photon upconversion and offer an attractive alternative to organic fluorophores for use as luminescent probes. Here, UCPs were capped with functionalized silica in order to provide a surface to covalently conjugate proteins with surface-accessible cysteines. Variants of green fluorescent protein (GFP) and the flavoenzyme pentaerythritol tetranitrate reductase (PETNR) were then attached via maleimide-thiol coupling in order to allow energy transfer from the UCP to the GFP or flavin cofactor of PETNR, respectively. PETNR retains its activity when coupled to the UCPs, which allows reversible detection of enzyme substrates via ratiometric sensing of the enzyme redox state.

Collagen-Immobilized Extracellular FRET Reporter for Visualizing Protease Activity Secreted by Living Cells

Despite the diverse roles of cell-secreted proteases in the extracellular matrix (ECM), classical methods to analyze protease activity have not been explored at the cell culture site. Here, we report a stable, matrix-sticky, and protease-sensitive extracellular reporter that comprises a collagen-binding protein and a Förster resonance energy transfer (FRET) coupler of an enhanced green fluorescent protein and a small dye molecule. The extracellular FRET reporter via split intein-mediated protein trans-splicing is able to adhere to collagen matrices, leading to fluorescence changes by matrix metalloproteinase-2 (MMP2) activity during living cell culture without impeding cell viability. When a proMMP2 mutant (Y581A) with altered protease secretion and activity was transfected into cancer cells, the reporter revealed a dramatic reduction in MMP2 activity in both two- and three-dimensional culture systems, compared with cells transfected with wild-type proMMP2. Our reporter is immediately amenable to monitor protease activity in diverse ECM-resident cells as well as to study protease-related extracellular signaling and tissue remodeling.

Direct Immobilization of Biomolecules through Magnetic Forces on Ni Electrodes via Ni Nanoparticles: Applications in Electrochemical Biosensors

The present work describes a new simple procedure for the direct immobilization of biomolecules on Ni electrodes using magnetic Ni nanoparticles (NiNPs) as biomolecule carriers. Ni electrodes were fabricated by electroplating, and NiNPs were chemically synthesized. The chemical composition, crystallinity, and granular size of Ni electrodes, NiNP, and NiNP-modified Ni electrodes (NiNP/Ni) were determined by X-ray diffraction, scanning electron microscopy, and X-ray photoelectron spectroscopy (XPS). The electrochemical characterization of Ni electrodes by cyclic voltammetry and electrochemical impedance spectroscopy confirmed the existence of nickel oxides, hydroxides, and oxohydroxide films at the surface of Ni. Magnetic characterization and micromagnetic simulations were performed in order to prove that the magnetic force is responsible for the immobilization process. Further, Ni electrodes were employed as amperometric sensors for the detection of hydrogen peroxide because it is an important performance indicator for a material to be applied in biosensing. The working principle for magnetic immobilization of the enzyme-functionalized NiNP, without the use of external magnetic sources, was demonstrated for glucose oxidase (GOx) as a model enzyme. XPS results enabled to identify the presence of GOx attached to the NiNP (GOx-NiNP) on Ni electrodes. Finally, glucose detection and quantification were evaluated with the newly developed GOx-NiNP/Ni biosensor by amperometry at different potentials, and control experiments at different electrode materials in the presence and absence of NiNP demonstrated their importance in the biosensor architecture.

Small Surface, Big Effects, and Big Challenges: Toward Understanding Enzymatic Activity at the Inorganic Nanoparticle-Substrate Interface

Enzymes are important biomarkers for molecular diagnostics and targets for the action of drugs. In turn, inorganic nanoparticles (NPs) are of interest as materials for biological assays, biosensors, cellular and in vivo imaging probes, and vectors for drug delivery and theranostics. So how does an enzyme interact with a NP, and what are the outcomes of multivalent conjugation of its substrate to a NP? This invited feature article addresses the current state of the art in answering this question. Using gold nanoparticles (Au NPs) and semiconductor quantum dots (QDs) as illustrative materials, we discuss aspects of enzyme structure-function and the properties of NP interfaces and surface chemistry that determine enzyme-NP interactions. These aspects render the substrate-on-NP configurations far more complex and heterogeneous than the conventional turnover of discrete substrate molecules in bulk solution. Special attention is also given to the limitations of a standard kinetic analysis of the enzymatic turnover of these configurations, the need for a well-defined model of turnover, and whether a "hopping" model can account for behaviors such as the apparent acceleration of enzyme activity. A detailed and predictive understanding of how enzymes turn over multivalent NP-substrate conjugates will require a convergence of many concepts and tools from biochemistry, materials, and interface science. In turn, this understanding will help to enable rational, optimized, and value-added designs of NP bioconjugates for biomedical and clinical applications.

Exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens

Emerging infectious diseases remain among the leading causes of global mortality. Traditional laboratory diagnostic approaches designed to detect and track infectious disease agents provide a framework for surveillance of bio threats. However, surveillance and outbreak investigations using such time-consuming approaches for early detection of pathogens remain the major pitfall. Hence, reasonable real-time surveillance systems to anticipate threats to public health and environment are critical for identifying specific aetiologies and preventing the global spread of infectious disease. The current review discusses the growing need for monitoring and surveillance of pathogens with the same zeal and approach as adopted by microbial forensics laboratories, and further strengthening it by integrating with the innovative nanotechnology for rapid detection of microbial pathogens. Such innovative diagnostics platforms will help to track pathogens from high risk areas and environment by pre-emptive approach that will minimize damages. The various scenarios with the examples are discussed where the high risk associated human pathogens in particular were successfully detected using various nanotechnology approaches with potential future prospects in the field of microbial forensics.

Gold nanodome SERS platform for label-free detection of protease activity

Surface-enhanced Raman scattering provides a promising technology for sensitive and selective detection of protease activity by monitoring peptide cleavage. Not only are peptides and plasmonic hotspots similarly sized, Raman fingerprints also hold large potential for spectral multiplexing. Here, we use a gold-nanodome platform for real-time detection of trypsin activity on a CALNNYGGGGVRGNF substrate peptide. First, we investigate the spectral changes upon cleavage through the SERS signal of liquid-chromatography separated products. Next, we show that similar patterns are detected upon digesting surface-bound peptides. We demonstrate that the relative intensity of the fingerprints from aromatic amino acids before and after the cleavage site provides a robust figure of merit for the turnover rate. The presented method offers a generic approach for measuring protease activity, which is illustrated by developing an analogous substrate for endoproteinase Glu-C.